From 7bc226b58110fa26d9dbd3f0c78095d06909ffc3 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 7 Feb 2007 15:11:09 +0000
Subject: [PATCH] Formatting

---
 src/com/stevesoft/pat/AmpersandRule.java           |   27 +-
 src/com/stevesoft/pat/Any.java                     |   57 +-
 src/com/stevesoft/pat/BackG.java                   |   50 +-
 src/com/stevesoft/pat/BackMatch.java               |   66 +-
 src/com/stevesoft/pat/BackRefRule.java             |   33 +-
 src/com/stevesoft/pat/Backup.java                  |   51 +-
 src/com/stevesoft/pat/BasicStringBufferLike.java   |   12 +-
 src/com/stevesoft/pat/Bits.java                    | 5871 ++++++++++----------
 src/com/stevesoft/pat/Boundary.java                |  121 +-
 src/com/stevesoft/pat/Bracket.java                 |  103 +-
 src/com/stevesoft/pat/CaseMgr.java                 | 5862 ++++++++++++++-----
 src/com/stevesoft/pat/ChangeRule.java              |   47 +-
 src/com/stevesoft/pat/CodeRule.java                |   31 +-
 src/com/stevesoft/pat/Ctrl.java                    |  522 +-
 src/com/stevesoft/pat/Custom.java                  |   70 +-
 src/com/stevesoft/pat/CustomEndpoint.java          |   46 +-
 src/com/stevesoft/pat/DirFileRegex.java            |   24 +-
 src/com/stevesoft/pat/DotMulti.java                |  286 +-
 src/com/stevesoft/pat/End.java                     |   78 +-
 src/com/stevesoft/pat/FastBracket.java             |  379 +-
 src/com/stevesoft/pat/FastMulti.java               |  238 +-
 src/com/stevesoft/pat/FileRegex.java               |  396 +-
 src/com/stevesoft/pat/Group.java                   |   87 +-
 src/com/stevesoft/pat/LeftRule.java                |   23 +-
 src/com/stevesoft/pat/Multi.java                   |  107 +-
 src/com/stevesoft/pat/MultiMin.java                |   14 +-
 src/com/stevesoft/pat/Multi_stage2.java            |  209 +-
 src/com/stevesoft/pat/NoPattern.java               |   32 +-
 src/com/stevesoft/pat/NonDirFileRegex.java         |   24 +-
 src/com/stevesoft/pat/NotImplementedError.java     |   11 +-
 src/com/stevesoft/pat/NullPattern.java             |   36 +-
 src/com/stevesoft/pat/NullRule.java                |   21 +-
 src/com/stevesoft/pat/Or.java                      |  166 +-
 src/com/stevesoft/pat/OrMark.java                  |   92 +-
 src/com/stevesoft/pat/PartialBuffer.java           |   55 +-
 src/com/stevesoft/pat/Pattern.java                 |  433 +-
 src/com/stevesoft/pat/PatternSub.java              |   10 +-
 src/com/stevesoft/pat/PopRule.java                 |   17 +-
 src/com/stevesoft/pat/Prop.java                    |   85 +-
 src/com/stevesoft/pat/Pthings.java                 |   44 +-
 src/com/stevesoft/pat/PushRule.java                |   41 +-
 src/com/stevesoft/pat/RBuffer.java                 |   39 +-
 src/com/stevesoft/pat/Range.java                   |  125 +-
 src/com/stevesoft/pat/RegOpt.java                  |  720 ++-
 src/com/stevesoft/pat/RegRes.java                  |  394 +-
 src/com/stevesoft/pat/RegSyntax.java               |   19 +-
 src/com/stevesoft/pat/RegSyntaxError.java          |   29 +-
 src/com/stevesoft/pat/Regex.java                   | 3260 ++++++-----
 src/com/stevesoft/pat/RegexReader.java             |  281 +-
 src/com/stevesoft/pat/RegexTokenizer.java          |  231 +-
 src/com/stevesoft/pat/RegexWriter.java             |  334 +-
 src/com/stevesoft/pat/ReplaceRule.java             |  571 +-
 src/com/stevesoft/pat/Replacer.java                |  522 +-
 src/com/stevesoft/pat/RightRule.java               |   25 +-
 src/com/stevesoft/pat/Rthings.java                 |   70 +-
 src/com/stevesoft/pat/RuleHolder.java              |   42 +-
 src/com/stevesoft/pat/Skip.java                    |  263 +-
 src/com/stevesoft/pat/Skip2.java                   |   61 +-
 src/com/stevesoft/pat/SkipBMH.java                 |  390 +-
 src/com/stevesoft/pat/Skipped.java                 |   53 +-
 src/com/stevesoft/pat/SpecialRule.java             |   11 +-
 src/com/stevesoft/pat/Start.java                   |   63 +-
 src/com/stevesoft/pat/StrPos.java                  |  245 +-
 src/com/stevesoft/pat/StringBufferLike.java        |  102 +-
 src/com/stevesoft/pat/StringLike.java              |   43 +-
 src/com/stevesoft/pat/StringRule.java              |   33 +-
 src/com/stevesoft/pat/SubMark.java                 |   29 +-
 src/com/stevesoft/pat/TransPat.java                |   54 +-
 src/com/stevesoft/pat/Transformer.java             |  293 +-
 src/com/stevesoft/pat/UniValidator.java            |   19 +-
 src/com/stevesoft/pat/Validator.java               |   98 +-
 src/com/stevesoft/pat/WantMoreTextReplaceRule.java |   21 +-
 src/com/stevesoft/pat/lookAhead.java               |  115 +-
 src/com/stevesoft/pat/oneChar.java                 |   95 +-
 src/com/stevesoft/pat/parsePerl.java               |  591 +-
 src/com/stevesoft/pat/patInf.java                  |    9 +-
 src/com/stevesoft/pat/patInt.java                  |  213 +-
 .../stevesoft/pat/wrap/CharArrayBufferWrap.java    |   39 +-
 src/com/stevesoft/pat/wrap/CharArrayWrap.java      |   81 +-
 .../stevesoft/pat/wrap/RandomAccessFileWrap.java   |  229 +-
 src/com/stevesoft/pat/wrap/StringBufferWrap.java   |   25 +-
 src/com/stevesoft/pat/wrap/StringWrap.java         |   62 +-
 src/com/stevesoft/pat/wrap/WriterWrap.java         |   40 +-
 src/ext/vamsas/IRegistry.java                      |    7 +-
 src/ext/vamsas/IRegistryService.java               |   12 +-
 src/ext/vamsas/IRegistryServiceLocator.java        |  265 +-
 src/ext/vamsas/Jpred.java                          |   19 +-
 src/ext/vamsas/JpredService.java                   |   12 +-
 src/ext/vamsas/JpredServiceLocator.java            |  264 +-
 src/ext/vamsas/JpredSoapBindingStub.java           |  604 +-
 src/ext/vamsas/MuscleWS.java                       |   56 +-
 src/ext/vamsas/MuscleWSService.java                |   48 +-
 src/ext/vamsas/MuscleWSServiceLocator.java         |  316 +-
 src/ext/vamsas/MuscleWSSoapBindingStub.java        |  788 +--
 src/ext/vamsas/RegistryServiceSoapBindingStub.java |  352 +-
 src/ext/vamsas/ServiceHandle.java                  |  445 +-
 src/ext/vamsas/ServiceHandles.java                 |  239 +-
 src/jalview/analysis/AAFrequency.java              |  220 +-
 src/jalview/analysis/AlignSeq.java                 | 1499 ++---
 src/jalview/analysis/AlignmentSorter.java          |  805 +--
 src/jalview/analysis/Conservation.java             |  884 +--
 src/jalview/analysis/Finder.java                   |  531 +-
 src/jalview/analysis/NJTree.java                   | 2081 +++----
 src/jalview/analysis/PCA.java                      |  402 +-
 src/jalview/analysis/SeqsetUtils.java              |  128 +-
 src/jalview/analysis/SequenceIdMatcher.java        |   86 +-
 src/jalview/appletgui/APopupMenu.java              |  318 +-
 src/jalview/appletgui/AlignFrame.java              | 1770 +++---
 src/jalview/appletgui/AlignViewport.java           |  420 +-
 src/jalview/appletgui/AlignmentPanel.java          |  194 +-
 src/jalview/appletgui/AnnotationColourChooser.java |   94 +-
 src/jalview/appletgui/AnnotationLabels.java        |  109 +-
 src/jalview/appletgui/AnnotationPanel.java         |  717 +--
 src/jalview/appletgui/CutAndPasteTransfer.java     |  158 +-
 src/jalview/appletgui/EditNameDialog.java          |   21 +-
 src/jalview/appletgui/FeatureRenderer.java         |  601 +-
 src/jalview/appletgui/FeatureSettings.java         |  435 +-
 src/jalview/appletgui/Finder.java                  |  144 +-
 src/jalview/appletgui/FontChooser.java             |  126 +-
 src/jalview/appletgui/IdCanvas.java                |  121 +-
 src/jalview/appletgui/IdPanel.java                 |   48 +-
 src/jalview/appletgui/IdwidthAdjuster.java         |    2 +-
 src/jalview/appletgui/OverviewPanel.java           |  145 +-
 src/jalview/appletgui/PCAPanel.java                |  141 +-
 src/jalview/appletgui/PaintRefresher.java          |  279 +-
 src/jalview/appletgui/PairwiseAlignPanel.java      |   43 +-
 src/jalview/appletgui/RedundancyPanel.java         |  268 +-
 src/jalview/appletgui/RotatableCanvas.java         |   85 +-
 src/jalview/appletgui/ScalePanel.java              |  126 +-
 src/jalview/appletgui/SeqCanvas.java               |  837 +--
 src/jalview/appletgui/SeqPanel.java                | 1634 +++---
 src/jalview/appletgui/SequenceRenderer.java        |   75 +-
 src/jalview/appletgui/SliderPanel.java             |  119 +-
 src/jalview/appletgui/Tooltip.java                 |  376 +-
 src/jalview/appletgui/TreeCanvas.java              |  143 +-
 src/jalview/appletgui/TreePanel.java               |  155 +-
 src/jalview/appletgui/UserDefinedColours.java      |  256 +-
 src/jalview/bin/Cache.java                         |  474 +-
 src/jalview/bin/Jalview.java                       |  608 +-
 src/jalview/bin/JalviewLite.java                   |  860 +--
 src/jalview/commands/ChangeCaseCommand.java        |   23 +-
 src/jalview/commands/CommandI.java                 |   10 +-
 src/jalview/commands/EditCommand.java              |  394 +-
 src/jalview/commands/OrderCommand.java             |   80 +-
 src/jalview/commands/RemoveGapColCommand.java      |   27 +-
 src/jalview/commands/RemoveGapsCommand.java        |   46 +-
 src/jalview/commands/TrimRegionCommand.java        |   67 +-
 src/jalview/datamodel/Alignment.java               |  997 ++--
 src/jalview/datamodel/AlignmentAnnotation.java     |  533 +-
 src/jalview/datamodel/AlignmentI.java              |  449 +-
 src/jalview/datamodel/AlignmentOrder.java          |  451 +-
 src/jalview/datamodel/AlignmentView.java           |  160 +-
 src/jalview/datamodel/Annotation.java              |  117 +-
 src/jalview/datamodel/BinaryNode.java              |  440 +-
 src/jalview/datamodel/BinarySequence.java          |  283 +-
 src/jalview/datamodel/CigarArray.java              |  168 +-
 src/jalview/datamodel/CigarBase.java               |  228 +-
 src/jalview/datamodel/CigarCigar.java              |   35 +-
 src/jalview/datamodel/CigarSimple.java             |   14 +-
 src/jalview/datamodel/ColumnSelection.java         |  413 +-
 src/jalview/datamodel/DBRefEntry.java              |   14 +-
 src/jalview/datamodel/DBRefSource.java             |   52 +-
 src/jalview/datamodel/GraphLine.java               |   58 +-
 src/jalview/datamodel/HiddenSequences.java         |  152 +-
 src/jalview/datamodel/PDBEntry.java                |   30 +-
 src/jalview/datamodel/Provenance.java              |   17 +-
 src/jalview/datamodel/ProvenanceEntry.java         |   41 +-
 src/jalview/datamodel/SearchResults.java           |  101 +-
 src/jalview/datamodel/SeqCigar.java                |  152 +-
 src/jalview/datamodel/Sequence.java                |  189 +-
 src/jalview/datamodel/SequenceFeature.java         |  460 +-
 src/jalview/datamodel/SequenceGroup.java           |  956 ++--
 src/jalview/datamodel/SequenceI.java               |  473 +-
 src/jalview/datamodel/SequenceNode.java            |  234 +-
 src/jalview/datamodel/SequencePoint.java           |   24 +-
 src/jalview/datamodel/UniprotEntry.java            |   42 +-
 src/jalview/datamodel/UniprotFile.java             |   19 +-
 src/jalview/datamodel/UniprotProteinName.java      |    4 +-
 src/jalview/datamodel/UniprotSequence.java         |   14 +-
 src/jalview/gui/AlignFrame.java                    | 1420 ++---
 src/jalview/gui/AlignViewport.java                 | 2888 +++++-----
 src/jalview/gui/AlignmentPanel.java                |  268 +-
 src/jalview/gui/AnnotationColourChooser.java       |   96 +-
 src/jalview/gui/AnnotationExporter.java            |  113 +-
 src/jalview/gui/AnnotationLabels.java              | 1065 ++--
 src/jalview/gui/AnnotationPanel.java               | 2080 +++----
 src/jalview/gui/CutAndPasteTransfer.java           |  342 +-
 src/jalview/gui/DasSourceBrowser.java              |  571 +-
 src/jalview/gui/Desktop.java                       | 1429 ++---
 src/jalview/gui/EPSOptions.java                    |   17 +-
 src/jalview/gui/EditNameDialog.java                |   20 +-
 src/jalview/gui/FeatureRenderer.java               | 1139 ++--
 src/jalview/gui/FeatureSettings.java               |  835 +--
 src/jalview/gui/Finder.java                        |  306 +-
 src/jalview/gui/FontChooser.java                   |  386 +-
 src/jalview/gui/IdCanvas.java                      |  712 +--
 src/jalview/gui/IdPanel.java                       |  629 +--
 src/jalview/gui/IdwidthAdjuster.java               |  243 +-
 src/jalview/gui/Jalview2XML.java                   | 2735 ++++-----
 src/jalview/gui/Jalview2XML_V1.java                |  757 +--
 src/jalview/gui/OverviewPanel.java                 |  673 +--
 src/jalview/gui/PCAPanel.java                      |  723 ++-
 src/jalview/gui/PaintRefresher.java                |  293 +-
 src/jalview/gui/PairwiseAlignPanel.java            |  218 +-
 src/jalview/gui/PopupMenu.java                     | 1897 +++----
 src/jalview/gui/Preferences.java                   |  769 +--
 src/jalview/gui/RedundancyPanel.java               |  483 +-
 src/jalview/gui/RotatableCanvas.java               | 1228 ++--
 src/jalview/gui/ScalePanel.java                    |  683 +--
 src/jalview/gui/SeqCanvas.java                     | 1472 ++---
 src/jalview/gui/SeqPanel.java                      | 2429 ++++----
 src/jalview/gui/SequenceFetcher.java               |  308 +-
 src/jalview/gui/SequenceRenderer.java              |  653 +--
 src/jalview/gui/SliderPanel.java                   |  545 +-
 src/jalview/gui/SplashScreen.java                  |  251 +-
 src/jalview/gui/TextColourChooser.java             |   55 +-
 src/jalview/gui/TreeCanvas.java                    |   34 +-
 src/jalview/gui/TreePanel.java                     | 1001 ++--
 src/jalview/gui/UserDefinedColours.java            | 1381 ++---
 src/jalview/gui/UserQuestionnaireCheck.java        |  223 +-
 src/jalview/gui/VamsasClient.java                  |  161 +-
 src/jalview/gui/WebserviceInfo.java                |  776 +--
 src/jalview/io/AMSAFile.java                       |  131 +-
 src/jalview/io/AlignFile.java                      |  290 +-
 src/jalview/io/AnnotationFile.java                 |  350 +-
 src/jalview/io/AppletFormatAdapter.java            |  456 +-
 src/jalview/io/BLCFile.java                        |  324 +-
 src/jalview/io/ClustalFile.java                    |   12 +-
 src/jalview/io/DBRefFetcher.java                   |  119 +-
 src/jalview/io/DasSequenceFeatureFetcher.java      |  352 +-
 src/jalview/io/EBIFetchClient.java                 |  415 +-
 src/jalview/io/FastaFile.java                      |  330 +-
 src/jalview/io/FeaturesFile.java                   |  878 +--
 src/jalview/io/FileLoader.java                     |  238 +-
 src/jalview/io/FileParse.java                      |    4 +-
 src/jalview/io/FormatAdapter.java                  |  201 +-
 src/jalview/io/HTMLOutput.java                     |  224 +-
 src/jalview/io/IdentifyFile.java                   |  284 +-
 src/jalview/io/JPredFile.java                      |  598 +-
 src/jalview/io/JalviewFileChooser.java             |   48 +-
 src/jalview/io/JalviewFileFilter.java              |    4 +-
 src/jalview/io/JalviewFileView.java                |    2 +-
 src/jalview/io/JnetAnnotationMaker.java            |   97 +-
 src/jalview/io/MSFfile.java                        |  639 +--
 src/jalview/io/ModellerDescription.java            |   34 +-
 src/jalview/io/NewickFile.java                     | 1411 ++---
 src/jalview/io/PIRFile.java                        |  138 +-
 src/jalview/io/PfamFile.java                       |   13 +-
 src/jalview/io/PileUpfile.java                     |   55 +-
 src/jalview/io/StockholmFile.java                  |  754 +--
 src/jalview/io/VamsasDatastore.java                |  998 ++--
 src/jalview/io/WSWUBlastClient.java                |  482 +-
 src/jalview/jbgui/GAlignFrame.java                 |  121 +-
 src/jalview/jbgui/GAlignmentPanel.java             |    2 +-
 src/jalview/jbgui/GCutAndPasteTransfer.java        |  289 +-
 src/jalview/jbgui/GDasSourceBrowser.java           |   23 +-
 src/jalview/jbgui/GDesktop.java                    |  470 +-
 src/jalview/jbgui/GFinder.java                     |   31 +-
 src/jalview/jbgui/GFontChooser.java                |  350 +-
 src/jalview/jbgui/GPCAPanel.java                   |    6 +-
 src/jalview/jbgui/GPairwiseAlignPanel.java         |  136 +-
 src/jalview/jbgui/GPreferences.java                |  430 +-
 src/jalview/jbgui/GSequenceLink.java               |   57 +-
 src/jalview/jbgui/GSliderPanel.java                |  296 +-
 src/jalview/jbgui/GTreePanel.java                  |    5 +-
 src/jalview/jbgui/GUserDefinedColours.java         |  286 +-
 src/jalview/jbgui/GWebserviceInfo.java             |  171 +-
 src/jalview/math/Matrix.java                       | 1473 +++--
 src/jalview/math/RotatableMatrix.java              |  469 +-
 src/jalview/schemabinding/version2/Annotation.java | 1214 ++--
 .../schemabinding/version2/AnnotationColours.java  |  732 +--
 .../version2/AnnotationColoursDescriptor.java      |  810 +--
 .../version2/AnnotationDescriptor.java             | 1133 ++--
 .../schemabinding/version2/AnnotationElement.java  |  680 +--
 .../version2/AnnotationElementDescriptor.java      |  821 +--
 src/jalview/schemabinding/version2/Colour.java     |  307 +-
 .../schemabinding/version2/ColourDescriptor.java   |  451 +-
 src/jalview/schemabinding/version2/DBRef.java      |  359 +-
 .../schemabinding/version2/DBRefDescriptor.java    |  529 +-
 src/jalview/schemabinding/version2/Feature.java    | 1049 ++--
 .../schemabinding/version2/FeatureDescriptor.java  |  959 ++--
 .../schemabinding/version2/FeatureSettings.java    |  466 +-
 .../version2/FeatureSettingsDescriptor.java        |  385 +-
 src/jalview/schemabinding/version2/Features.java   |  178 +-
 .../schemabinding/version2/FeaturesDescriptor.java |  295 +-
 .../schemabinding/version2/HiddenColumns.java      |  415 +-
 .../version2/HiddenColumnsDescriptor.java          |  476 +-
 src/jalview/schemabinding/version2/JGroup.java     | 1787 +++---
 .../schemabinding/version2/JGroupDescriptor.java   | 1563 +++---
 src/jalview/schemabinding/version2/JSeq.java       | 1674 +++---
 .../schemabinding/version2/JSeqDescriptor.java     |  994 ++--
 .../schemabinding/version2/JalviewModel.java       |  418 +-
 .../version2/JalviewModelDescriptor.java           |  630 ++-
 .../version2/JalviewModelSequence.java             | 1818 +++---
 .../version2/JalviewModelSequenceDescriptor.java   |  761 +--
 .../schemabinding/version2/JalviewUserColours.java |  542 +-
 .../version2/JalviewUserColoursDescriptor.java     |  457 +-
 src/jalview/schemabinding/version2/OtherData.java  |  307 +-
 .../version2/OtherDataDescriptor.java              |  458 +-
 src/jalview/schemabinding/version2/Pdbentry.java   |  670 +--
 .../schemabinding/version2/PdbentryDescriptor.java |  606 +-
 .../schemabinding/version2/PdbentryItem.java       |  358 +-
 .../version2/PdbentryItemDescriptor.java           |  385 +-
 src/jalview/schemabinding/version2/Pdbids.java     |  178 +-
 .../schemabinding/version2/PdbidsDescriptor.java   |  295 +-
 src/jalview/schemabinding/version2/Property.java   |  307 +-
 .../schemabinding/version2/PropertyDescriptor.java |  458 +-
 src/jalview/schemabinding/version2/Sequence.java   |  464 +-
 .../schemabinding/version2/SequenceDescriptor.java |  392 +-
 .../schemabinding/version2/SequenceSet.java        |  870 +--
 .../version2/SequenceSetDescriptor.java            |  538 +-
 .../schemabinding/version2/SequenceType.java       |  411 +-
 .../version2/SequenceTypeDescriptor.java           |  617 +-
 src/jalview/schemabinding/version2/Setting.java    |  467 +-
 .../schemabinding/version2/SettingDescriptor.java  |  563 +-
 .../schemabinding/version2/ThresholdLine.java      |  467 +-
 .../version2/ThresholdLineDescriptor.java          |  554 +-
 src/jalview/schemabinding/version2/Tree.java       | 1635 +++---
 .../schemabinding/version2/TreeDescriptor.java     | 1652 +++---
 .../schemabinding/version2/UserColourScheme.java   |  178 +-
 .../version2/UserColourSchemeDescriptor.java       |  295 +-
 .../schemabinding/version2/UserColours.java        |  308 +-
 .../version2/UserColoursDescriptor.java            |  459 +-
 src/jalview/schemabinding/version2/VAMSAS.java     |  812 +--
 .../schemabinding/version2/VAMSASDescriptor.java   |  464 +-
 .../schemabinding/version2/VamsasModel.java        |  178 +-
 .../version2/VamsasModelDescriptor.java            |  295 +-
 src/jalview/schemabinding/version2/Viewport.java   | 3497 ++++++------
 .../schemabinding/version2/ViewportDescriptor.java | 3180 ++++++-----
 src/jalview/schemes/AnnotationColourGradient.java  |  305 +-
 src/jalview/schemes/Blosum62ColourScheme.java      |   20 +-
 src/jalview/schemes/BuriedColourScheme.java        |   76 +-
 src/jalview/schemes/ClustalxColourScheme.java      |   23 +-
 src/jalview/schemes/ColourSchemeI.java             |    5 +-
 src/jalview/schemes/ColourSchemeProperty.java      |  704 +--
 src/jalview/schemes/Consensus.java                 |    2 +-
 src/jalview/schemes/HelixColourScheme.java         |    2 +-
 src/jalview/schemes/HydrophobicColourScheme.java   |   76 +-
 src/jalview/schemes/NucleotideColourScheme.java    |  132 +-
 src/jalview/schemes/PIDColourScheme.java           |   37 +-
 src/jalview/schemes/ResidueColourScheme.java       |  426 +-
 src/jalview/schemes/ResidueProperties.java         |   44 +-
 src/jalview/schemes/ScoreColourScheme.java         |  198 +-
 src/jalview/schemes/ScoreMatrix.java               |   41 +-
 src/jalview/schemes/StrandColourScheme.java        |   76 +-
 src/jalview/schemes/TaylorColourScheme.java        |    2 +-
 src/jalview/schemes/TurnColourScheme.java          |   76 +-
 src/jalview/schemes/UserColourScheme.java          |   97 +-
 src/jalview/schemes/ZappoColourScheme.java         |   52 +-
 src/jalview/util/BrowserLauncher.java              |    7 +-
 src/jalview/util/Comparison.java                   |   60 +-
 src/jalview/util/DBRefUtils.java                   |   85 +-
 src/jalview/util/Format.java                       | 1432 ++---
 src/jalview/util/ImageMaker.java                   |   55 +-
 src/jalview/util/MapList.java                      |  443 +-
 src/jalview/util/QuickSort.java                    |    2 +-
 src/jalview/util/ShiftList.java                    |   74 +-
 src/jalview/util/TableSorter.java                  |  928 ++--
 src/jalview/ws/Discoverer.java                     |  141 +-
 src/jalview/ws/JPredClient.java                    |  132 +-
 src/jalview/ws/JPredThread.java                    |  325 +-
 src/jalview/ws/MsaWSClient.java                    |   72 +-
 src/jalview/ws/MsaWSThread.java                    |   84 +-
 src/jalview/ws/WSClient.java                       |   12 +-
 src/jalview/ws/WSClientI.java                      |   22 +-
 src/jalview/ws/WSThread.java                       |  249 +-
 .../biojava/dasobert/das/DAS_FeatureRetrieve.java  |  369 +-
 .../biojava/dasobert/das/DAS_Feature_Handler.java  |  322 +-
 src/org/biojava/dasobert/das/FeatureThread.java    |  282 +-
 src/org/biojava/dasobert/das2/Das2Capability.java  |   47 +-
 .../biojava/dasobert/das2/Das2CapabilityImpl.java  |  165 +-
 src/org/biojava/dasobert/das2/Das2Source.java      |   28 +-
 src/org/biojava/dasobert/das2/Das2SourceImpl.java  |  211 +-
 .../biojava/dasobert/das2/DasSourceConverter.java  |   93 +-
 .../dasobert/das2/io/DAS2SourceHandler.java        |  309 +-
 .../biojava/dasobert/das2/io/DasSourceReader.java  |   11 +-
 .../dasobert/das2/io/DasSourceReaderImpl.java      |  260 +-
 .../biojava/dasobert/dasregistry/Das1Source.java   |  386 +-
 .../dasobert/dasregistry/Das2Validator.java        |   31 +-
 .../dasregistry/DasCoordSysComparator.java         |  156 +-
 .../dasobert/dasregistry/DasCoordinateSystem.java  |  293 +-
 .../biojava/dasobert/dasregistry/DasSource.java    |  104 +-
 .../dasobert/dasregistry/DasSourceComparator.java  |  220 +-
 .../biojava/dasobert/eventmodel/FeatureEvent.java  |   99 +-
 .../dasobert/eventmodel/FeatureListener.java       |   38 +-
 .../dasobert/eventmodel/ObjectListener.java        |   38 +-
 .../biojava/dasobert/eventmodel/SequenceEvent.java |   37 +-
 .../dasobert/eventmodel/SequenceListener.java      |   51 +-
 src/org/jibble/epsgraphics/EpsDocument.java        |  423 +-
 src/org/jibble/epsgraphics/EpsException.java       |   37 +-
 src/org/jibble/epsgraphics/EpsGraphics2D.java      | 2647 ++++-----
 src/uk/ac/ebi/www/Data.java                        |  215 +-
 src/uk/ac/ebi/www/InputParams.java                 |  805 +--
 src/uk/ac/ebi/www/WSFile.java                      |  215 +-
 src/uk/ac/ebi/www/WSWUBlast.java                   |   32 +-
 src/uk/ac/ebi/www/WSWUBlastService.java            |   12 +-
 src/uk/ac/ebi/www/WSWUBlastServiceLocator.java     |  169 +-
 src/uk/ac/ebi/www/WSWUBlastSoapBindingStub.java    |  773 ++-
 src/vamsas/IMsaWS.java                             |   57 +-
 src/vamsas/objects/simple/Alignment.java           |  297 +-
 src/vamsas/objects/simple/Alignment_Helper.java    |  141 +-
 src/vamsas/objects/simple/JpredResult.java         |  179 +-
 src/vamsas/objects/simple/JpredResult_Helper.java  |   95 +-
 src/vamsas/objects/simple/MsaResult.java           |  169 +-
 src/vamsas/objects/simple/MsaResult_Helper.java    |  117 +-
 src/vamsas/objects/simple/Msfalignment.java        |  179 +-
 src/vamsas/objects/simple/Msfalignment_Helper.java |   95 +-
 src/vamsas/objects/simple/Object.java              |  110 +-
 src/vamsas/objects/simple/Object_Helper.java       |  104 +-
 src/vamsas/objects/simple/Result.java              |  632 ++-
 src/vamsas/objects/simple/Result_Helper.java       |  194 +-
 src/vamsas/objects/simple/Secstructpred.java       |  126 +-
 .../objects/simple/Secstructpred_Helper.java       |   84 +-
 src/vamsas/objects/simple/Sequence.java            |  179 +-
 src/vamsas/objects/simple/SequenceSet.java         |  182 +-
 src/vamsas/objects/simple/SequenceSet_Helper.java  |  117 +-
 src/vamsas/objects/simple/Sequence_Helper.java     |   95 +-
 src/vamsas/objects/simple/WsJobId.java             |  212 +-
 src/vamsas/objects/simple/WsJobId_Helper.java      |  129 +-
 419 files changed, 90515 insertions(+), 77145 deletions(-)

diff --git a/src/com/stevesoft/pat/AmpersandRule.java b/src/com/stevesoft/pat/AmpersandRule.java
index 934d9c0..f838ab2 100755
--- a/src/com/stevesoft/pat/AmpersandRule.java
+++ b/src/com/stevesoft/pat/AmpersandRule.java
@@ -8,13 +8,22 @@
 package com.stevesoft.pat;
 
 /** This implements the $& element of the second argument to
-  * Regex.
-  * @see com.stevesoft.pat.ReplaceRule
-  */
-public final class AmpersandRule extends ReplaceRule {
-    public AmpersandRule() {}
-    public void apply(StringBufferLike sb,RegRes res) {
-        sb.append(res.stringMatched());
-    }
-    public String toString1() { return "$&"; }
+ * 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 234c343..e833662 100755
--- a/src/com/stevesoft/pat/Any.java
+++ b/src/com/stevesoft/pat/Any.java
@@ -6,23 +6,50 @@
 //    -- Happy Computing!
 //
 package com.stevesoft.pat;
-import java.util.Hashtable;
+
+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();
+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);
+      }
     }
-    public patInt minChars() { return new patInt(1); }
-    public patInt maxChars() { return new patInt(1); }
-    public Pattern clone1(Hashtable h) { return new Any(); }
+    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 78115f8..72c4c9a 100755
--- a/src/com/stevesoft/pat/BackG.java
+++ b/src/com/stevesoft/pat/BackG.java
@@ -6,21 +6,41 @@
 //    -- Happy Computing!
 //
 package com.stevesoft.pat;
-import java.util.Hashtable;
+
+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(); }
+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 168faec..2eed23b 100755
--- a/src/com/stevesoft/pat/BackMatch.java
+++ b/src/com/stevesoft/pat/BackMatch.java
@@ -6,28 +6,52 @@
 //    -- Happy Computing!
 //
 package com.stevesoft.pat;
-import java.util.Hashtable;
+
+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);
+ * 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;
     }
-    Pattern clone1(Hashtable h) { return new BackMatch(id); }
-}
+    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 64a5d6e..8488ba3 100755
--- a/src/com/stevesoft/pat/BackRefRule.java
+++ b/src/com/stevesoft/pat/BackRefRule.java
@@ -11,13 +11,28 @@ package com.stevesoft.pat;
     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 "$"+n; }
-    public Object clone1() { return new BackRefRule(n); }
+public class BackRefRule
+    extends ReplaceRule
+{
+  int n;
+  public BackRefRule(int n)
+  {
+    this.n = n;
+  }
+
+  public void apply(StringBufferLike sb, RegRes res)
+  {
+    String x = res.stringMatched(n);
+    sb.append(x == null ? "" : x);
+  }
+
+  public String toString1()
+  {
+    return "$" + 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 df480ea..31c41c4 100755
--- a/src/com/stevesoft/pat/Backup.java
+++ b/src/com/stevesoft/pat/Backup.java
@@ -6,22 +6,47 @@
 //    -- Happy Computing!
 //
 package com.stevesoft.pat;
-import java.util.Hashtable;
+
+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);
+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;
     }
-    public patInt minChars() { return new patInt(-bk); }
-    public patInt maxChars() { return new patInt(-bk); }
-    public Pattern clone1(Hashtable h) { return new Backup(bk); }
+    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 6e7b26c..7563703 100755
--- a/src/com/stevesoft/pat/BasicStringBufferLike.java
+++ b/src/com/stevesoft/pat/BasicStringBufferLike.java
@@ -1,18 +1,22 @@
-package//
+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;
+    com.stevesoft.pat;
 
 /** An abstraction of the StringBuffer which only
     implements a subset of StringBuffer's methods.
-    */
-public interface BasicStringBufferLike {
+ */
+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 0c67903..f26d1fb 100755
--- a/src/com/stevesoft/pat/Bits.java
+++ b/src/com/stevesoft/pat/Bits.java
@@ -1,40 +1,48 @@
-package//
+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;
+    com.stevesoft.pat;
 
-
-public class Bits {
+public class Bits
+{
   char[] carray;
-  Bits(char[] carray) {
+  Bits(char[] carray)
+  {
     this.carray = carray;
   }
-  public boolean get(int i) {
-    return ((carray[i>>4]) & (1<<(i&15))) != 0;
+
+  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 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) {
+     public static String n4(char c) {
     String s = Integer.toHexString(c);
     while(s.length()<4)
       s = "0"+s;
     return s;
-  }
-  static abstract class Tester {
+     }
+     static abstract class Tester {
     abstract boolean test(char c);
-  }
-  public static void main(String[] args) throws Exception {
+     }
+     public static void main(String[] args) throws Exception {
     //pw_s.println("  static {");
     FileWriter fw = new FileWriter("x.out");
     fw.close();
@@ -80,30 +88,30 @@ public class Bits {
     });
     test("punct",new Tester() {
       boolean test(char c) {
-	boolean r = false;
+    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;
+   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 {
+     }
+     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);
@@ -129,2943 +137,2960 @@ public class Bits {
     pw.println("  }");
 
     pw.close();
-  }
-  */
+     }
+   */
   public static Bits upper;
-  static void upper_f() {
+  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;
+    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() {
+  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;
+    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() {
+  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;
+    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() {
+  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;
+    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() {
+  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;
+    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() {
+  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;
+    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() {
+  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;
+    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() {
+  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;
+    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() {
+  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;
+    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 959bb04..d6481b4 100755
--- a/src/com/stevesoft/pat/Boundary.java
+++ b/src/com/stevesoft/pat/Boundary.java
@@ -6,46 +6,87 @@
 //    -- Happy Computing!
 //
 package com.stevesoft.pat;
-import java.util.Hashtable;
+
+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(); }
+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 9f60179..175731b 100755
--- a/src/com/stevesoft/pat/Bracket.java
+++ b/src/com/stevesoft/pat/Bracket.java
@@ -6,43 +6,82 @@
 //    -- Happy Computing!
 //
 package com.stevesoft.pat;
-import java.util.Vector;
-import java.util.Hashtable;
+
+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 "[";
+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;
+  }
+
+  String rightForm()
+  {
+    return "]";
+  }
+
+  String sepForm()
+  {
+    return "";
+  }
+
+  public int matchInternal(int pos, Pthings pt)
+  {
+    if (pos >= pt.src.length())
+    {
+      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;
+    int r = super.matchInternal(pos, pt);
+    if ( (neg && r < 0) || (!neg && r >= 0))
+    {
+      return nextMatch(pos + 1, pt);
     }
-    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;
+    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 2de70d4..ff93f25 100755
--- a/src/com/stevesoft/pat/CaseMgr.java
+++ b/src/com/stevesoft/pat/CaseMgr.java
@@ -19,1519 +19,4389 @@ package com.stevesoft.pat;
     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;
+ */
+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 Character.toUpperCase(c);
+      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;
     }
-    /** 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;
+    if (!ign)
+    {
+      for (int i = i2; i < itot; i++)
+      {
+        if (s2.charAt(i) != s1.charAt(i1++))
+        {
+          return false;
         }
-        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();
+    else
+    {
+      for (int i = i2; i < itot; i++)
+      {
+        if (toLowerCase(s2.charAt(i)) != toLowerCase(s1.charAt(i1++)))
+        {
+          return false;
+        }
+      }
     }
-    /** 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();
+    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;
     }
-    /** 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();
+    if (!ign)
+    {
+      for (int i = i2; i < itot; i++)
+      {
+        if (s2.charAt(i) != s1.charAt(i1++))
+        {
+          return false;
+        }
+      }
     }
-    /** 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;
+    else
+    {
+      for (int i = i2; i < itot; i++)
+      {
+        if (toLowerCase(s2.charAt(i)) != toLowerCase(s1.charAt(i1++)))
+        {
+          return false;
         }
-        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(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;
         }
-        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;
+    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;
         }
-        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;
+    else
+    {
+      for (int i = i2; i < itot; i++)
+      {
+        if (toLowerCase(s2.charAt(i)) != toLowerCase(s1.charAt(i1++)))
+        {
+          return false;
         }
-        return true;
+      }
     }
+    return true;
+  }
 }
diff --git a/src/com/stevesoft/pat/ChangeRule.java b/src/com/stevesoft/pat/ChangeRule.java
index d9ea870..31046ee 100755
--- a/src/com/stevesoft/pat/ChangeRule.java
+++ b/src/com/stevesoft/pat/ChangeRule.java
@@ -8,15 +8,40 @@
 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) {}
+ * 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 31c779f..763bf3e 100755
--- a/src/com/stevesoft/pat/CodeRule.java
+++ b/src/com/stevesoft/pat/CodeRule.java
@@ -8,14 +8,25 @@
 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; }
+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 ba7fc20..6fee70f 100755
--- a/src/com/stevesoft/pat/Ctrl.java
+++ b/src/com/stevesoft/pat/Ctrl.java
@@ -1,269 +1,271 @@
-package//
+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;
+    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
+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 e7621a1..72aebc7 100755
--- a/src/com/stevesoft/pat/Custom.java
+++ b/src/com/stevesoft/pat/Custom.java
@@ -6,7 +6,8 @@
 //    -- Happy Computing!
 //
 package com.stevesoft.pat;
-import java.util.Hashtable;
+
+import java.util.*;
 
 /** Simple custom patterns.  See
     <a href="http://javaregex.com/code/deriv2.java.html">deriv2.java</a>
@@ -14,29 +15,46 @@ import java.util.Hashtable;
     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;
-    }
+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 b8fc704..ac6c4ba 100755
--- a/src/com/stevesoft/pat/CustomEndpoint.java
+++ b/src/com/stevesoft/pat/CustomEndpoint.java
@@ -6,22 +6,38 @@
 //    -- Happy Computing!
 //
 package com.stevesoft.pat;
-import java.util.Hashtable;
+
+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));
+ * 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 c46762e..24c0cf6 100755
--- a/src/com/stevesoft/pat/DirFileRegex.java
+++ b/src/com/stevesoft/pat/DirFileRegex.java
@@ -9,10 +9,22 @@ 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);
-    }
+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 514c161..4691728 100755
--- a/src/com/stevesoft/pat/DotMulti.java
+++ b/src/com/stevesoft/pat/DotMulti.java
@@ -6,120 +6,200 @@
 //    -- Happy Computing!
 //
 package com.stevesoft.pat;
-import java.util.Hashtable;
+
+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;
+ * common subpattern ".*" is encountered.
+ */
+class DotMulti
+    extends PatternSub
+{
+  patInt fewestMatches, mostMatches;
+  public patInt minChars()
+  {
+    return fewestMatches;
+  }
 
-    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();
+  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;
+      }
     }
-    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;
-    }
-    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;
-                }
-            }
+      }
+      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;
+          }
         }
-        int nMatches = 0;
-        while(fewestMatches.intValue() > nMatches) {
-            i=submatchInternal(i,pt);
-            if(i >= 0)
-                nMatches++;
-            else
-                return -1;
+      }
+      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;
+          }
         }
-        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;
-            }
+      }
+      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++;
         }
-        while(m >= pos) {
-            int r=nextMatch(m,pt);
-            if(r >= 0) return r;
-            m -= step;
-            nMatches--;
-            if(nMatches < fewestMatches.intValue())
-                return -1;
+        else
+        {
+          break;
         }
-        return -1;
+      }
     }
-    Pattern clone1(Hashtable h) {
-        DotMulti dm = new DotMulti(fewestMatches,mostMatches);
-        dm.matchFewest = matchFewest;
-        return dm;
+    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 75e5acf..42894b3 100755
--- a/src/com/stevesoft/pat/End.java
+++ b/src/com/stevesoft/pat/End.java
@@ -6,37 +6,65 @@
 //    -- Happy Computing!
 //
 package com.stevesoft.pat;
-import java.util.Hashtable;
+
+import java.util.*;
 
 //class AddToEnd extends RegSyntax {};
 
 /** Compiles the '$' or the '\Z' Pattern.  It is
  an error to have further Pattern elements after
  '\Z'.  It is the end of the String. */
-class End extends Pattern {
-    boolean retIsEnd;
-    End(boolean b) { retIsEnd = b; }
-    public int matchInternal(int pos,Pthings pt) {
-        if(retIsEnd && pt.mFlag && pos < pt.src.length()) {
-            if(pt.src.charAt(pos)=='\n') {
-                return nextMatch(pos,pt);
-	    }
-	}
-        if(pt.src.length() == pos)
-            return nextMatch(pos,pt);
-	else if(pos<pt.src.length())
-	    // Access the next character...
-	    // this is crucial to making 
-	    // RegexReader work.
-	    pt.src.charAt(pos);
-        return -1;
+class End
+    extends Pattern
+{
+  boolean retIsEnd;
+  End(boolean b)
+  {
+    retIsEnd = b;
+  }
+
+  public int matchInternal(int pos, Pthings pt)
+  {
+    if (retIsEnd && pt.mFlag && pos < pt.src.length())
+    {
+      if (pt.src.charAt(pos) == '\n')
+      {
+        return nextMatch(pos, pt);
+      }
+    }
+    if (pt.src.length() == pos)
+    {
+      return nextMatch(pos, pt);
+    }
+    else if (pos < pt.src.length())
+    {
+      // Access the next character...
+      // this is crucial to making
+      // RegexReader work.
+      pt.src.charAt(pos);
     }
-    public String toString() {
-        if(retIsEnd)
-            return "$";
-        else
-            return "\\Z";
+    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); }
+  }
+
+  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 2720cc4..5f5fff0 100755
--- a/src/com/stevesoft/pat/FastBracket.java
+++ b/src/com/stevesoft/pat/FastBracket.java
@@ -12,180 +12,245 @@ 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();
+ */
+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;
 
-        // 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;
+      // 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);
+          }
         }
+      }
 
-        // 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;
+      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);
         }
+      }
 
-        // return the normal Bracket.
-        return b;
+      b.v = v = nv;
+    }
+    catch (RegSyntax e)
+    {
+      e.printStackTrace();
     }
 
-    // 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;
+    // 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;
     }
 
-    // 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;
-        }
+    // 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);
     }
-    // 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));
+    if (fb != null)
+    {
+      fb.parent = b.parent;
+      fb.next = b.next;
+      return fb;
     }
-    static final char min(char a,char b) {
-        return a<b ? a : b;
+
+    // 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;
     }
-    static final char max(char a,char b) {
-        return a>b ? a : b;
+    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;
     }
+  }
 
-    // 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;
+  // 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;
     }
-    // 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;
+    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 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 2a38281..53130fa 100755
--- a/src/com/stevesoft/pat/FastMulti.java
+++ b/src/com/stevesoft/pat/FastMulti.java
@@ -6,106 +6,166 @@
 //    -- Happy Computing!
 //
 package com.stevesoft.pat;
-import java.util.Hashtable;
+
+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;
+ * 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);
+  }
 
-    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();
+  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.");
     }
-    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;
-                }
+    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;
+          }
         }
-        int nMatches = 0;
-        while(fewestMatches.intValue() > nMatches) {
-            i=sub.matchInternal(i,pt);
-            if(i >= 0)
-                nMatches++;
-            else
-                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++;
         }
-        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;
-            }
+        else
+        {
+          break;
+        }
+      }
+    }
+    else
+    {
+      while (true)
+      {
+        i = sub.matchInternal(i, pt);
+        if (i >= 0)
+        {
+          m = i;
+          nMatches++;
         }
-        while(m >= pos) {
-            int r=nextMatch(m,pt);
-            if(r >= 0) return r;
-            m -= step;
-            nMatches--;
-            if(nMatches < fewestMatches.intValue())
-                return -1;
+        else
+        {
+          break;
         }
+      }
+    }
+    while (m >= pos)
+    {
+      int r = nextMatch(m, pt);
+      if (r >= 0)
+      {
+        return r;
+      }
+      m -= step;
+      nMatches--;
+      if (nMatches < fewestMatches.intValue())
+      {
         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;
-        }
+    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 f5ac448..37729eb 100755
--- a/src/com/stevesoft/pat/FileRegex.java
+++ b/src/com/stevesoft/pat/FileRegex.java
@@ -6,6 +6,7 @@
 //    -- Happy Computing!
 //
 package com.stevesoft.pat;
+
 import java.io.*;
 import java.util.*;
 
@@ -40,176 +41,253 @@ import java.util.*;
  </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;
+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;
     }
-    /** 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;
+      }
     }
-    /** 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);
+    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);
     }
-    int dirflag = 0;
-    final static int EITHER=0,DIR=1,NONDIR=2;
+    String[] sa = new String[v.size()];
+    v.copyInto(sa);
+    return sa;
+  }
 
-    /** 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);
+  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;
     }
-    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;
+    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);
+      }
     }
-    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);
+    else
+    {
+      File base = new File(path);
 
-            String dir_s = base.getParent();
-            if(dir_s==null) dir_s=".";
-            File dir = new File(dir_s);
+      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]);
-            }
-        }
+      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();
+  /** 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;
     }
-    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;
+    int ParenLvl = 0;
+    while (!sp.eos())
+    {
+      if (File.separatorChar == '\\')
+      {
+        if (sp.escaped())
+        {
+          sb.append("\\\\");
         }
-        return true;
+        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 4f73114..4f538b5 100755
--- a/src/com/stevesoft/pat/Group.java
+++ b/src/com/stevesoft/pat/Group.java
@@ -6,37 +6,70 @@
 //    -- Happy Computing!
 //
 package com.stevesoft.pat;
-import java.util.Hashtable;
+
+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++;
-            }
-        }
+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;
+      }
     }
-    public String toString() {
-        return "(?@"+op+cl+")"+nextString();
+    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++;
+        }
+      }
     }
-    public patInt minChars() { return new patInt(2); }
-    Pattern clone1(Hashtable h) { return new Group(op,cl); }
+    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 1737abd..0b9bae3 100755
--- a/src/com/stevesoft/pat/LeftRule.java
+++ b/src/com/stevesoft/pat/LeftRule.java
@@ -11,11 +11,20 @@ package com.stevesoft.pat;
     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 "$`"; }
+ */
+public class LeftRule
+    extends ReplaceRule
+{
+  public LeftRule()
+  {}
+
+  public void apply(StringBufferLike sb, RegRes res)
+  {
+    sb.append(res.left());
+  }
+
+  public String toString1()
+  {
+    return "$`";
+  }
 }
diff --git a/src/com/stevesoft/pat/Multi.java b/src/com/stevesoft/pat/Multi.java
index 2960b75..14b3a06 100755
--- a/src/com/stevesoft/pat/Multi.java
+++ b/src/com/stevesoft/pat/Multi.java
@@ -6,7 +6,8 @@
 //    -- Happy Computing!
 //
 package com.stevesoft.pat;
-import java.util.Hashtable;
+
+import java.util.*;
 
 /** Matches any number of instances of sub Pattern
  this was the hardest method to write.  It implements
@@ -14,47 +15,71 @@ import java.util.Hashtable;
  @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();
+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);
     }
-    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);
+    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;
     }
-    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;
-        }
+    catch (RegSyntax rs)
+    {
+      return null;
     }
+  }
 };
diff --git a/src/com/stevesoft/pat/MultiMin.java b/src/com/stevesoft/pat/MultiMin.java
index f6d2fd8..f741e99 100755
--- a/src/com/stevesoft/pat/MultiMin.java
+++ b/src/com/stevesoft/pat/MultiMin.java
@@ -10,9 +10,13 @@ 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;
-    }
+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 41afa39..990b0e6 100755
--- a/src/com/stevesoft/pat/Multi_stage2.java
+++ b/src/com/stevesoft/pat/Multi_stage2.java
@@ -6,98 +6,151 @@
 //    -- Happy Computing!
 //
 package com.stevesoft.pat;
-import java.util.Hashtable;
+
+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;
+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 += "?";
     }
-    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");
+    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.");
     }
-    public Pattern getNext() {
-        return nextRet;
+    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);
     }
-    int pos_old = -1;
-    public int matchInternal(int pos,Pthings pt) {
-        sub.setParent(this);
+    patInt i = new patInt( -1);
+    if (a.lessEq(i))
+    {
+      //throw new BadMultiArgs();
+      RegSyntaxError.endItAll("Bad Multi Args: " + a + "< 0");
+    }
+  }
 
-        int canUse = -1;
+  public Pattern getNext()
+  {
+    return nextRet;
+  }
 
-        // check for some forms of infinite recursion...
-        if(pos_old >= 0 && pos == pos_old) {
-            return -1;
-        }
-        pos_old = pos;
+  int pos_old = -1;
+  public int matchInternal(int pos, Pthings pt)
+  {
+    sub.setParent(this);
 
-        if(matchMin.lessEq(count))
-            canUse = pos;
-        if(!count.lessEq(matchMax) || pos > pt.src.length())
-            return -1;
+    int canUse = -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;
-        }
+    // check for some forms of infinite recursion...
+    if (pos_old >= 0 && pos == pos_old)
+    {
+      return -1;
+    }
+    pos_old = pos;
 
-        count.inc();
-        try {
-            if(count.lessEq(matchMax)) {
-                int r = testMatch(sub,pos,pt);
-                if(r >= 0)
-                    return r;
-            }
-        } finally { count.dec(); }
+    if (matchMin.lessEq(count))
+    {
+      canUse = pos;
+    }
+    if (!count.lessEq(matchMax) || pos > pt.src.length())
+    {
+      return -1;
+    }
 
-        if(!matchFewest && canUse >= 0) {
-            Pattern n = super.getNext();
-            if(n == null)
-                return canUse;
-            int ret = testMatch(n,pos,pt);
-            return ret;
-        } else return canUse;
+    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;
+      }
     }
-    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;
+
+    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 3bac329..c5eba3c 100755
--- a/src/com/stevesoft/pat/NoPattern.java
+++ b/src/com/stevesoft/pat/NoPattern.java
@@ -1,19 +1,33 @@
-package//
+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;
+    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(); }
+ * 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 7ef24a3..cb7b69d 100755
--- a/src/com/stevesoft/pat/NonDirFileRegex.java
+++ b/src/com/stevesoft/pat/NonDirFileRegex.java
@@ -9,10 +9,22 @@ 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);
-    }
+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 f8835f2..246ecad 100755
--- a/src/com/stevesoft/pat/NotImplementedError.java
+++ b/src/com/stevesoft/pat/NotImplementedError.java
@@ -1,14 +1,17 @@
-package//
+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;
+    com.stevesoft.pat;
 
-public class NotImplementedError extends Error {
-  public NotImplementedError(String s) {
+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 082b0f3..abdc5fa 100755
--- a/src/com/stevesoft/pat/NullPattern.java
+++ b/src/com/stevesoft/pat/NullPattern.java
@@ -6,16 +6,32 @@
 //    -- Happy Computing!
 //
 package com.stevesoft.pat;
-import java.util.Hashtable;
+
+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(); }
+ * 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 454c81e..fe4e837 100755
--- a/src/com/stevesoft/pat/NullRule.java
+++ b/src/com/stevesoft/pat/NullRule.java
@@ -10,10 +10,19 @@ 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 ""; }
+ */
+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 9791c74..05981aa 100755
--- a/src/com/stevesoft/pat/Or.java
+++ b/src/com/stevesoft/pat/Or.java
@@ -12,70 +12,116 @@ 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;
+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());
     }
-    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();
+    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);
     }
-    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;
+    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());
     }
-    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;
+    return m;
+  }
+
+  public patInt maxChars()
+  {
+    if (v.size() == 0)
+    {
+      return new patInt(0);
     }
-    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;
+    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());
     }
-    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;
+    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 c323a9d..77aac0f 100755
--- a/src/com/stevesoft/pat/OrMark.java
+++ b/src/com/stevesoft/pat/OrMark.java
@@ -6,45 +6,67 @@
 //    -- Happy Computing!
 //
 package com.stevesoft.pat;
-import java.util.Hashtable;
+
+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;
+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;
+      }
     }
-    String leftForm() { return "("; }
-    public Pattern getNext() {
-        return sm;
+    pt.marks[id] = pos;
+    int ret = super.matchInternal(pos, pt);
+    if (ret < 0)
+    {
+      pt.marks[id] = -1;
     }
-    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;
+    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;
     }
-    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;
+    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 fd57b27..121dd32 100755
--- a/src/com/stevesoft/pat/PartialBuffer.java
+++ b/src/com/stevesoft/pat/PartialBuffer.java
@@ -7,7 +7,6 @@
 //
 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
@@ -43,41 +42,65 @@ package com.stevesoft.pat;
       sb.append(more data);
     }
     </pre>
-    */
-class PartialBuffer implements StringLike {
+ */
+class PartialBuffer
+    implements StringLike
+{
   int off;
   public boolean allowOverRun = true;
   public boolean overRun = false;
   StringBuffer sb;
-  PartialBuffer(StringBuffer sb) {
+  PartialBuffer(StringBuffer sb)
+  {
     this.sb = sb;
   }
-  public char charAt(int n) {
+
+  public char charAt(int n)
+  {
     n += off;
-    if(n == sb.length()) {
+    if (n == sb.length())
+    {
       overRun = true;
       return 0;
     }
     return sb.charAt(n);
   }
-  public int length() {
-    return allowOverRun ? sb.length()+1 : sb.length();
+
+  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)
+
+  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++)
+
+  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() {
+  public BasicStringBufferLike newStringBufferLike()
+  {
     return null;
   }
 }
diff --git a/src/com/stevesoft/pat/Pattern.java b/src/com/stevesoft/pat/Pattern.java
index 404991c..a441b37 100755
--- a/src/com/stevesoft/pat/Pattern.java
+++ b/src/com/stevesoft/pat/Pattern.java
@@ -6,188 +6,275 @@
 //    -- 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 = "[]{}(),$,-\"^.";
-
-    /** The interal match function, it must be provided by any
-        class which wishes to extend Pattern. */
-    public abstract int matchInternal(int i,Pthings p);
-    public abstract String toString();
-
-    // Class Pattern is a singly linked list
-    // chained together by member next.  The member
-    // parent is used so that sub patterns can access
-    // the chain they are branching from.
-    Pattern next=null,parent=null;
-
-    /** This gets the next element of a Pattern that
-            we wish to match.  If we are at the end of a
-            subchain of patterns, it will return us to the
-            parent chain. */
-    public Pattern getNext() {
-        return next != null ? next :
+ */
+/**
+ Class Pattern is the base class on which all the other pattern
+ elements are built. */
+
+public abstract class Pattern
+{
+  /** The ESC character, the user can provide his own value
+          for the escape character through regex.esc */
+  public final static char ESC = '\\';
+  final static String PROTECT_THESE = "[]{}(),$,-\"^.";
+
+  /** 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);
     }
-    /** 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);
+    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;
     }
-    /** 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;
+    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];
         }
-        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;
+      }
+      catch (Throwable t)
+      {}
     }
-    public boolean equals(Object o) {
-        return o == this;
+    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 d88296b..57576e3 100755
--- a/src/com/stevesoft/pat/PatternSub.java
+++ b/src/com/stevesoft/pat/PatternSub.java
@@ -8,8 +8,10 @@
 package com.stevesoft.pat;
 
 /** This is simply a subclass of pattern that
-  * contains a sub pattern.
-  */
-abstract class PatternSub extends Pattern {
-    Pattern sub;
+ * 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 1428edb..c8622f3 100755
--- a/src/com/stevesoft/pat/PopRule.java
+++ b/src/com/stevesoft/pat/PopRule.java
@@ -8,9 +8,16 @@
 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}"; }
+ * 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 9319db5..b6490a6 100755
--- a/src/com/stevesoft/pat/Prop.java
+++ b/src/com/stevesoft/pat/Prop.java
@@ -8,45 +8,66 @@
 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);
+ <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();
     }
-    /** 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);
+    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();
     }
-    /** 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);
+    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 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 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);
+  /** 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 0a465ce..84e327b 100755
--- a/src/com/stevesoft/pat/Pthings.java
+++ b/src/com/stevesoft/pat/Pthings.java
@@ -6,28 +6,30 @@
 //    -- Happy Computing!
 //
 package com.stevesoft.pat;
+
 import java.util.*;
 
-/** 
-Things that need to be kept track of during a
+/**
+ 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;
+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 cdc33f9..3fbfe14 100755
--- a/src/com/stevesoft/pat/PushRule.java
+++ b/src/com/stevesoft/pat/PushRule.java
@@ -11,12 +11,37 @@ package com.stevesoft.pat;
     <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 "${+"+name+"}"; }
-    public void apply(StringBufferLike sbl,RegRes rr) {}
+public class PushRule
+    extends SpecialRule
+{
+  Regex NewRule;
+  public PushRule(PushRule p)
+  {
+    NewRule = p.NewRule;
+  }
+
+  public PushRule(String nm, Regex rr)
+  {
+    name = nm;
+    NewRule = rr;
+  }
+
+  public PushRule(String nm, Transformer tr)
+  {
+    name = nm;
+    NewRule = tr.rp;
+  }
+
+  public Object clone1()
+  {
+    return new PushRule(this);
+  }
+
+  public String String1()
+  {
+    return "${+" + 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 b9dda64..44657af 100755
--- a/src/com/stevesoft/pat/RBuffer.java
+++ b/src/com/stevesoft/pat/RBuffer.java
@@ -7,28 +7,41 @@
 //
 package com.stevesoft.pat;
 
-
 /** This class is used internally by RegexReader to
     store blocks of data. */
-class RBuffer {
+class RBuffer
+{
   boolean done = false;
   StringBuffer sb;
-  int pos,epos;
+  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)+"^";
+  RBuffer()
+  {}
+
+  RBuffer(StringBuffer sb)
+  {
+    this.sb = sb;
   }
-  String sp(int n) {
-    if(n<=0)
+
+  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++)
+    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 5d5f9a1..5b740cd 100755
--- a/src/com/stevesoft/pat/Range.java
+++ b/src/com/stevesoft/pat/Range.java
@@ -6,56 +6,93 @@
 //    -- Happy Computing!
 //
 package com.stevesoft.pat;
-import java.util.Hashtable;
+
+import java.util.*;
 
 /** Thrown when one encounters things like [z-a] */
-class BadRangeArgs extends RegSyntax {};
+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+"]";
+ 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;
     }
-    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;
+    if (Masked(pos, pt))
+    {
+      return -1;
     }
-    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;
+    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;
     }
-    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;
-        }
+    catch (RegSyntax rs)
+    {
+      return null;
     }
+  }
 };
diff --git a/src/com/stevesoft/pat/RegOpt.java b/src/com/stevesoft/pat/RegOpt.java
index bf99e36..f70df39 100755
--- a/src/com/stevesoft/pat/RegOpt.java
+++ b/src/com/stevesoft/pat/RegOpt.java
@@ -6,330 +6,464 @@
 //    -- 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);
-    }
+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);
+ * 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()
+  {}
 
-        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;
+  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;
+  // 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;
     }
-    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;
+    else if (h.size() == 0)
+    {
+      return null;
     }
-    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;
+    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;
+  }
 
-    // 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);
-        }
+  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);
     }
-    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);
+    return count;
+  }
 
-            // 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);
+  // 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);
+      }
+    }
+  }
 
-            Pattern optpat = RegOpt.opt(o,igc,dontMinQ);
-            h.put(c,optpat);
-            optpat.setParent(this);
-        }
+  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);
     }
-    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();
+    else if (p instanceof Or)
+    {
+      ( (Or) p).addOr(n);
     }
-    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);
+    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);
+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;
             }
-        } 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;
+          }
+          o.addOr(opt(pp, ignoreCase, dontMinQ));
         }
-        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;
+      }
+      if (b.keys.size() > 0)
+      {
+        Pattern p2 = (Pattern) b.reduce(ignoreCase, dontMinQ);
+        if (p2 != null)
+        {
+          o.addOr(p2);
         }
-        return true;
+      }
+      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;
     }
-    /*
-    public static void setParents(Regex r) {
-      setParents(r.thePattern,null);
+    if (p.next != null)
+    {
+      p.next = opt(p.next, ignoreCase, dontMinQ);
     }
-    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);
+    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;
+          }
         }
       }
-      if(p.next == null)
-        p.parent = x;
-      else {
-        p.parent = null;
-        RegOpt.setParents(p.next,x);
+      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 76ff4ea..d644d0c 100755
--- a/src/com/stevesoft/pat/RegRes.java
+++ b/src/com/stevesoft/pat/RegRes.java
@@ -6,159 +6,271 @@
 //    -- 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();
+ */
+/**
+ 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();
     }
-    public RegRes() {}
-    public RegRes(RegRes r) {
-      copyOutOf(r);
+    for (int i = 0; i < numSubs(); i++)
+    {
+      int n = i + 1;
+      sb.append(" sub(" + n + ")=" + matchedFrom(n) +
+                ":" + charsMatched(n));
     }
-    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_;
+    return sb.toString();
+  }
+
+  public RegRes()
+  {}
+
+  public RegRes(RegRes r)
+  {
+    copyOutOf(r);
+  }
+
+  public void copyOutOf(RegRes r)
+  {
+    if (r.marks == null)
+    {
+      marks = null;
     }
-    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;
+    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];
         }
-        return true;
+        //marks = (int[])r.marks.clone();
+      }
+      catch (Throwable t)
+      {}
     }
-    /** 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);
+    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;
     }
-    /** 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_];
+    if (marks == null && r.marks != null)
+    {
+      return false;
     }
-    /** 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);
+    if (marks != null && r.marks == null)
+    {
+      return false;
     }
-    /** 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);
+    for (int i = 1; i <= numSubs_; i++)
+    {
+      if (matchedFrom(i) != r.matchedFrom(i))
+      {
+        return false;
+      }
+      else if (charsMatched(i) != r.charsMatched(i))
+      {
+        return false;
+      }
     }
-    /** 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);
+    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;
     }
-    /** 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());
+    //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;
     }
-    /** 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());
+    //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;
     }
-    /** 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); }
+    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 1a51d9e..ac47c1a 100755
--- a/src/com/stevesoft/pat/RegSyntax.java
+++ b/src/com/stevesoft/pat/RegSyntax.java
@@ -10,15 +10,20 @@ 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
+ 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);
-    }
+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 c403412..688c906 100755
--- a/src/com/stevesoft/pat/RegSyntaxError.java
+++ b/src/com/stevesoft/pat/RegSyntaxError.java
@@ -17,13 +17,26 @@ package com.stevesoft.pat;
     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);
+ */
+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 665632e..af5cbcc 100755
--- a/src/com/stevesoft/pat/Regex.java
+++ b/src/com/stevesoft/pat/Regex.java
@@ -6,1424 +6,2020 @@
 //    -- Happy Computing!
 //
 package com.stevesoft.pat;
-import java.util.*;
+
 import java.io.*;
-import com.stevesoft.pat.wrap.StringWrap;
+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;
-    }
+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;
-    }
+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;
-    }
+ * 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;
-    }
+ * 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;
-    }
+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;
-    }
+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;
-    }
+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;
-    }
+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;
-    }
+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;
-    }
+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;
-    }
+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;
-    }
+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;
-    }
+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;
-    }
+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;
+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) {
+
+  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;
+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) {
+
+  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 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>
+ </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>
+ </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;
+ </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;
         }
-        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);
-            }
+      }
+    }
+    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;
         }
-        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;
+        charsMatched_ = thePattern.matchAt(s, i, pt);
+        if (charsMatched_ >= 0)
+        {
+          matchFrom_ = thePattern.mfrom;
+          marks = pt.marks;
+          gFlagto = matchFrom_ + charsMatched_;
+          gFlags = s;
+          return didMatch_ = true;
         }
+      }
     }
-    /** 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;
+    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;
+  }
 
-    /** 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");
-        }
+  // 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;
     }
+  }
 
-    // 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;
+  /** 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;
     }
+  }
 
-    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();
+  /** 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();
         }
-        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;
+        else
+        {
+          i2 = sp.getPatInt();
         }
-        return p==null ? new NullPattern() : p;
+      }
+      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");
+      }
     }
+  }
 
-    // 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);
+  // 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
-            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();
+        {
+          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");
         }
-        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();
+        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));
-            }
+  }
+
+  // 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);
         }
-        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;
+        else
+        {
+          sb.append(newEsc);
+          sb.append(s.charAt(i + 1));
         }
-        return true;
+        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(); }
+  /** 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 =
+  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;
+        && ( (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';
     }
-    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;
+    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 0ff33e3..6475dfe 100755
--- a/src/com/stevesoft/pat/RegexReader.java
+++ b/src/com/stevesoft/pat/RegexReader.java
@@ -8,6 +8,7 @@
 package com.stevesoft.pat;
 
 import java.io.*;
+
 import com.stevesoft.pat.wrap.*;
 
 /** This class allows you to replace the text in strings
@@ -15,8 +16,10 @@ import com.stevesoft.pat.wrap.*;
     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 {
+ */
+public class RegexReader
+    extends Reader
+{
   RBuffer rb = new RBuffer(new StringBuffer());
   PartialBuffer wrap = new PartialBuffer(rb.sb);
   boolean moreToRead = true;
@@ -24,185 +27,259 @@ public class RegexReader extends Reader {
   Replacer rp;
 
   // the buffer size
-  int nmax = 2*1024;
+  int nmax = 2 * 1024;
 
-  public RegexReader(Regex rex,Reader r) {
+  public RegexReader(Regex rex, Reader r)
+  {
     this.r = r;
     rp = rex.getReplacer();
   }
-  public RegexReader(Transformer tex,Reader r) {
+
+  public RegexReader(Transformer tex, Reader r)
+  {
     this.r = r;
     rp = tex.getReplacer();
   }
-  public void reset() throws IOException {
+
+  public void reset()
+      throws IOException
+  {
     r.reset();
     rb = new RBuffer(new StringBuffer());
     wrap = new PartialBuffer(rb.sb);
     moreToRead = true;
   }
-  void readData() throws IOException {
+
+  void readData()
+      throws IOException
+  {
     int c;
     int n = 0;
-    while( (c = r.read()) != -1) {
-      rb.sb.append((char)c);
-      if(n++ > nmax)
+    while ( (c = r.read()) != -1)
+    {
+      rb.sb.append( (char) c);
+      if (n++ > nmax)
+      {
         break;
+      }
     }
-    if(c == -1 && n == 0) {
+    if (c == -1 && n == 0)
+    {
       moreToRead = false;
       wrap.allowOverRun = false;
     }
   }
-  void getMoreData() throws IOException {
-    while(rb.pos >= rb.epos) {
+
+  void getMoreData()
+      throws IOException
+  {
+    while (rb.pos >= rb.epos)
+    {
       wrap.overRun = false;
-      if(rb.next != null) {
-	rb = rb.next;
-      } else if(rb.done) {
+      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) {
+      }
+      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;
-	    }
+      }
+      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
+          {
+            rb3.pos = rb3.epos = npos;
+          }
 
         }
-      } else {
-	if(wrap.overRun) {
-	  readData();
-        } else if(rb.epos<rb.sb.length()) {
-	  rb.epos++;
-        } else {
-	  break;
-	}
+      }
+      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) {
+
+  public int read()
+      throws IOException
+  {
+    if (rb.pos >= rb.epos)
+    {
       getMoreData();
-      if(rb.pos >= rb.epos)
+      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
+
+  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++) {
+    int end = off + len;
+    for (int i = off; i < end; i++)
+    {
       c = read();
-      if(c < 0) {
-	if(i == off)
-	  return -1;
-        return i-off;
+      if (c < 0)
+      {
+        if (i == off)
+        {
+          return -1;
+        }
+        return i - off;
       }
-      buf[i] = (char)c;
+      buf[i] = (char) c;
     }
     return len;
   }
+
   public void close()
-    throws IOException
+      throws IOException
   {
     r.close();
   }
 
-  public boolean markSupported() { return false; }
+  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() {
+  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) {
+  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; }
+   */
+  public int getMaxLines()
+  {
+    return max_lines;
+  }
+
   /** This function no longer serves any purpose.
       @deprecated
-      */
-  public void setMaxLines(int ml) { max_lines = ml; }
+   */
+  public void setMaxLines(int ml)
+  {
+    max_lines = ml;
+  }
 
   char EOLchar = '\n';
   /** This function no longer serves any purpose.
       @deprecated
-      */
-  public char getEOLchar() {
+   */
+  public char getEOLchar()
+  {
     return EOLchar;
   }
+
   /** This function no longer serves any purpose.
       @deprecated
-      */
-  public void setEOLchar(char c) {
+   */
+  public void setEOLchar(char c)
+  {
     EOLchar = c;
   }
 
-  public long skip(long d) throws IOException {
+  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)
+    while (n < d && read() != -1)
+    {
       n++;
+    }
     return n;
   }
 
   /*
-  static void test(String re,String inp,int n) throws Exception {
+     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);
@@ -222,8 +299,8 @@ public class RegexReader extends Reader {
       System.out.println("res2="+res2);
       System.exit(255);
     }
-  }
-  public static void main(String[] args) throws Exception {
+     }
+     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);
@@ -243,6 +320,6 @@ public class RegexReader extends Reader {
       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 bc6fe51..76fa005 100755
--- a/src/com/stevesoft/pat/RegexTokenizer.java
+++ b/src/com/stevesoft/pat/RegexTokenizer.java
@@ -6,105 +6,156 @@
 //    -- 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;
+ */
+/**
+ 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();
+  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();
     }
-    /** 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++);
+    else if (s != null)
+    {
+      v.addElement(s);
     }
-    /** 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);
+  }
+
+  /** 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();
     }
-    /** 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();
+    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);
     }
-    /** Tells whether there are more tokens in the pattern. */
-    public boolean hasMoreElements() {
-        if(count >= v.size()) getMore();
-        return count < v.size();
+    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);
     }
-    /** 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;
+    getMore();
+    return nextToken();
+  }
+
+  /** Tells whether there are more tokens in the pattern. */
+  public boolean hasMoreElements()
+  {
+    if (count >= v.size())
+    {
+      getMore();
     }
-    /** Returns all tokens in the String */
-    public String[] allTokens() {
-        countTokens();
-        String[] ret = new String[v.size()];
-        v.copyInto(ret);
-        return ret;
+    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 008f6ac..bcfbd5b 100755
--- a/src/com/stevesoft/pat/RegexWriter.java
+++ b/src/com/stevesoft/pat/RegexWriter.java
@@ -8,6 +8,7 @@
 package com.stevesoft.pat;
 
 import java.io.*;
+
 import com.stevesoft.pat.wrap.*;
 
 /** A basic extension of FilterWriter that uses Transformer
@@ -34,171 +35,232 @@ import com.stevesoft.pat.wrap.*;
  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);
-    }
+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;
 
-    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;
-    }
+  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;
+  }
 
-    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()) {
+  /** 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++;
       }
-      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);
+    }
+    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 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 flush()
+      throws IOException
+  {
+  }
 
-    public void close() throws IOException {
-	wrap.allowOverRun = false;
-	wrap.overRun = false;
-	while(epos < sb.length())
-	  write();
-	write();
-	w.close();
+  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 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); }
+  /** 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;
-    }
+  /** 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 interval at which regex matches are checked. */
+  public int getInterval()
+  {
+    return interval;
+  }
 
-    /** Get the buffer size. */
-    public int getBufferSize() {
-      return bufferSize;
-    }
+  /** Get the buffer size. */
+  public int getBufferSize()
+  {
+    return bufferSize;
+  }
 
-    /** Set the buffer size. */
-    public void setBufferSize(int i) {
-      bufferSize = i;
-    }
+  /** Set the buffer size. */
+  public void setBufferSize(int i)
+  {
+    bufferSize = i;
+  }
 
-  static void test(String re,String inp,int n) throws Exception {
+  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++)
+    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);
+    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/$&/","xxx",n);
+
+  public static void main(String[] args)
+      throws Exception
+  {
+    for (int n = 1; n <= 1; n++)
+    {
+      test("s/x/y/", "-----x123456789", n);
+      test("s/x/y/", "x123456789", n);
+      test("s/x/y/", "-----x", n);
+      test("s/x.*?x/y/", ".xx..x..x...x...x....x....x", n);
+      test("s/x.*x/[$&]/", "--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 002ffa1..d4f09bb 100755
--- a/src/com/stevesoft/pat/ReplaceRule.java
+++ b/src/com/stevesoft/pat/ReplaceRule.java
@@ -26,230 +26,373 @@ import java.util.*;
     @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;
+ */
+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;
     }
-    static ReplaceRule add(ReplaceRule head,ReplaceRule adding) {
-        if(head == null)
-            return head = adding;
-        head.addRule(adding);
-        return head;
+    return xsav;
+  }
+
+  static ReplaceRule add(ReplaceRule head, ReplaceRule adding)
+  {
+    if (head == null)
+    {
+      return head = adding;
     }
-    public ReplaceRule add(ReplaceRule adding) {
-        return add(this,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;
     }
-    /** Add another ReplaceRule to the linked list. */
-    public void addRule(ReplaceRule r) {
-        if(next == null) next = r;
-        else next.addRule(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;
+  }
+
+  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();
     }
-    /** 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("${"+var+"}"));
-                } else if(
-		  (var = gv.stringMatched(7+off)) != null) {
-		  char c = var.charAt(0);
-		  if(c == 'n')
-		    head=add(head,new StringRule("\n"));
-		  else if(c == 't')
-		    head=add(head,new StringRule("\t"));
-		  else if(c == 'r')
-		    head=add(head,new StringRule("\r"));
-		  else if(c == 'b')
-		    head=add(head,new StringRule("\r"));
-		  else if(c == 'a')
-		    head=add(head,new StringRule(""+(char)7));
-		  else if(c == 'e')
-		    head=add(head,new StringRule(""+(char)27));
-		  else if(c == 'f')
-		    head=add(head,new StringRule(""+(char)12));
-		} else if(
-		  (var = gv.stringMatched(8+off)) != null) {
-		  char c = var.charAt(0);
-		  if(c < Ctrl.cmap.length)
-		    c = Ctrl.cmap[c];
-		  head=add(head,new StringRule(""+c));
-		} else if(
-		  (var = gv.stringMatched(9+off)) != null) {
-		  int d =
-		    16*getHexDigit(var.charAt(0))+
-		    getHexDigit(var.charAt(1));
-		  head=add(head,new StringRule(""+(char)d));
-		}
-                mt = gv.matchedTo();
+    getvar =
+        new Regex(
+            "(?:\\\\(\\d+)|" + // ref 1
+            "\\$(?:" +
+            "(\\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("${" + var + "}"));
+            }
+          }
+          else if (var.startsWith("=") && (tmp = defs.get(var.substring(1))) != null)
+          {
+            if (tmp instanceof Regex)
+            {
+              head = add(head, new ChangeRule(var.substring(1), (Regex) tmp));
+            }
+            else if (tmp instanceof Transformer)
+            {
+              head = add(head,
+                         new ChangeRule(var.substring(1), (Transformer) tmp));
             }
-            if(mt <= s.length())
-                head=add(head,new StringRule(s.substring(mt)));
-            return head;
-        } finally {
-            //Regex.backGs = sav_backGs;
-            //Regex.backGto = sav_backGto;
+            else
+            {
+              head = add(head, new StringRule("${" + 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;
     }
-    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;
+    finally
+    {
+      //Regex.backGs = sav_backGs;
+      //Regex.backGto = sav_backGto;
     }
-    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+"}";
+  }
+
+  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 "${" + name + "}";
+  }
+
+  /** Convert to a String. */
+  public final String toString()
+  {
+    StringBuffer sb = new StringBuffer();
+    sb.append(toString1());
+    ReplaceRule rr = this.next;
+    while (rr != null)
+    {
+      sb.append(rr.toString1());
+      rr = rr.next;
     }
-    /** Convert to a String. */
-    public final String toString() {
-        StringBuffer sb = new StringBuffer();
-        sb.append(toString1());
-        ReplaceRule rr = this.next;
-        while(rr != null) {
-            sb.append(rr.toString1());
-            rr = rr.next;
-        }
-        return sb.toString();
+    return sb.toString();
+  }
+
+  /** Modified the behavior of a ReplaceRule by supplying
+      an argument.  If a ReplaceRule named "foo" is defined
+      and the pattern "s/x/${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/${foo}/".
+      @see com.stevesoft.pat.Validator#arg(java.lang.String)
+   */
+  public ReplaceRule arg(String s)
+  {
+    return null;
+  }
+
+  static int getHexDigit(char c)
+  {
+    if (c >= '0' && c <= '9')
+    {
+      return c - '0';
     }
-    /** Modified the behavior of a ReplaceRule by supplying
-        an argument.  If a ReplaceRule named "foo" is defined
-        and the pattern "s/x/${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;
+    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 bdeea39..77570f9 100755
--- a/src/com/stevesoft/pat/Replacer.java
+++ b/src/com/stevesoft/pat/Replacer.java
@@ -7,27 +7,32 @@
 //
 package com.stevesoft.pat;
 
-import com.stevesoft.pat.wrap.StringWrap;
+import com.stevesoft.pat.wrap.*;
 
 /** Internally used class. */
-class RegHolder {
-    Regex me = null;
-    RegHolder prev = null;
+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+")";
-    }
+ * @see CodeRule
+ */
+class CodeVal
+{
+  int pos;
+  char code;
+  CodeVal(int p, char c)
+  {
+    pos = p;
+    code = c;
+  }
+
+  public String toString()
+  {
+    return "(" + pos + "," + code + ")";
+  }
 }
 
 /**
@@ -43,217 +48,310 @@ class CodeVal {
   <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;
+ */
+public class Replacer
+{
+  boolean first;
 
-    /** Instantiate a new Replacer. */
-    public Replacer() {}
+  /** 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);
-    }
+  public StringLike replaceFirstRegion(String s, Regex r,
+                                       int start, int end)
+  {
+    return replaceFirstRegion(new StringWrap(s), r, start, end);
+  }
 
-    RegHolder rh = new RegHolder();
+  /** 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 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 StringLike replaceFirst(StringLike s)
+  {
+    return replaceFirstRegion(s, 0, s.length());
+  }
 
-    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();
-    }
+  public StringLike replaceFirstFrom(StringLike s, int start)
+  {
+    return replaceFirstRegion(s, start, s.length());
+  }
 
-    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_--;
+  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++;
+  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);
             }
-            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;
+            rmn++;
+          }
+          apply(rh.me);
         }
-        return ret;
+      }
+      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));
+      }
 
-    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;
-                    }
-                }
+      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;
             }
-            if(!want_more_text)
-                pos = r.matchedTo();
+          }
+          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;
+  }
+
+  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;
     }
-    public void setPos(int pos) {
-      this.pos = pos;
+    //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 9e6394f..c27d2e4 100755
--- a/src/com/stevesoft/pat/RightRule.java
+++ b/src/com/stevesoft/pat/RightRule.java
@@ -10,13 +10,20 @@ 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 "$'";
-    }
+ */
+public class RightRule
+    extends ReplaceRule
+{
+  public RightRule()
+  {}
+
+  public void apply(StringBufferLike sb, RegRes res)
+  {
+    sb.append(res.right());
+  }
+
+  public String toString1()
+  {
+    return "$'";
+  }
 }
diff --git a/src/com/stevesoft/pat/Rthings.java b/src/com/stevesoft/pat/Rthings.java
index 0868eaa..4c4db39 100755
--- a/src/com/stevesoft/pat/Rthings.java
+++ b/src/com/stevesoft/pat/Rthings.java
@@ -7,38 +7,46 @@
 //
 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 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 e732d58..9b8017d 100755
--- a/src/com/stevesoft/pat/RuleHolder.java
+++ b/src/com/stevesoft/pat/RuleHolder.java
@@ -6,15 +6,37 @@
 //    -- 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)); }
+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 ca2dbb5..16aada1 100755
--- a/src/com/stevesoft/pat/Skip.java
+++ b/src/com/stevesoft/pat/Skip.java
@@ -13,113 +13,174 @@ package com.stevesoft.pat;
     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;
+ */
+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);
     }
-    /** 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);
+    else
+    {
+      mask = 0;
     }
-    /** The same as find(s,0,s.length()) */
-    public final int find(StringLike s) {
-        return find(s,0,s.length());
+    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;
     }
-    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;
+    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;
+          }
         }
-        return -1;
+      }
     }
-    static Skip findSkip(Regex r) {
-        return findSkip(r.thePattern,r.ignoreCase,!r.dontMatchInQuotes);
+    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;
+          }
+        }
+      }
     }
-    // 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 -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 null;
+        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 f2b03ca..ca1c5a8 100755
--- a/src/com/stevesoft/pat/Skip2.java
+++ b/src/com/stevesoft/pat/Skip2.java
@@ -11,28 +11,45 @@ package com.stevesoft.pat;
     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 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);
     }
-    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;
+    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 4fbe381..632418e 100755
--- a/src/com/stevesoft/pat/SkipBMH.java
+++ b/src/com/stevesoft/pat/SkipBMH.java
@@ -7,10 +7,10 @@
 //
 package com.stevesoft.pat;
 
-import com.stevesoft.pat.wrap.StringWrap;
+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">
+ <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
@@ -20,164 +20,252 @@ import com.stevesoft.pat.wrap.StringWrap;
     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;
+ */
+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();
     }
-    final boolean anyc(char c) {
-        return c==uc||c==lc||c==tc;
+
+    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);
+      }
     }
-    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;
-            }
+    // 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;
+          }
         }
+      }
     }
-    /** 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);
+    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;
+          }
+        }
+      }
     }
-    final public int searchFrom(String s,int start) {
-        return find(s,start,s.length());
+
+    return -1;
+  }
+
+  public int find(StringLike s, int start, int end)
+  {
+    if (s instanceof StringWrap)
+    {
+      return find(s.toString(), start, end);
     }
-    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;
-                }
-            }
+    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;
         }
-
-        return -1;
+      }
+      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;
+          }
+        }
+      }
     }
-    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;
-                }
-            }
+    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;
         }
-
-        return -1;
+      }
+      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 9d963ae..9bf2837 100755
--- a/src/com/stevesoft/pat/Skipped.java
+++ b/src/com/stevesoft/pat/Skipped.java
@@ -6,22 +6,49 @@
 //    -- Happy Computing!
 //
 package com.stevesoft.pat;
-import java.util.Hashtable;
+
+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;
+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);
     }
-    public patInt minChars() { return new patInt(s.length()); }
-    public patInt maxChars() { return new patInt(s.length()); }
-    Pattern clone1(Hashtable h) { return new Skipped(s); }
+    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 72df8d2..fbae452 100755
--- a/src/com/stevesoft/pat/SpecialRule.java
+++ b/src/com/stevesoft/pat/SpecialRule.java
@@ -7,7 +7,12 @@
 //
 package com.stevesoft.pat;
 
-public class SpecialRule extends ReplaceRule {
-    public SpecialRule() {}
-    public void apply(StringBufferLike sb,RegRes rr) {}
+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 9784358..c47ee53 100755
--- a/src/com/stevesoft/pat/Start.java
+++ b/src/com/stevesoft/pat/Start.java
@@ -6,26 +6,53 @@
 //    -- Happy Computing!
 //
 package com.stevesoft.pat;
-import java.util.Hashtable;
+
+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;
+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);
     }
-    public String toString() {
-        if(retIsStart)
-            return "^"+nextString();
-        else
-            return "\\A"+nextString();
+    if (pos == 0)
+    {
+      return nextMatch(pos, pt);
+    }
+    return -1;
+  }
+
+  public String toString()
+  {
+    if (retIsStart)
+    {
+      return "^" + nextString();
     }
-    public patInt maxChars() { return new patInt(0); }
-    Pattern clone1(Hashtable h) { return new Start(retIsStart); }
+    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 6043625..d9383dd 100755
--- a/src/com/stevesoft/pat/StrPos.java
+++ b/src/com/stevesoft/pat/StrPos.java
@@ -6,111 +6,170 @@
 //    -- 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; }
+ */
+/**
+ 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;
 
-    /** 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; }
+  /** tell whether we are at end of string */
+  public boolean eos()
+  {
+    return eos;
+  }
 
-    boolean dontMatch,eos;
+  /** initialize a StrPos from another StrPos. */
+  public StrPos(StrPos sp)
+  {
+    dup(sp);
+  }
 
-    /** 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;
     }
-    /** 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;
+    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;
+      }
     }
-    /** 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();
+    else
+    {
+      dontMatch = false;
     }
-    /** 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;
+    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;
     }
-    /** 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;
+    return c == ch;
+  }
+
+  /** As match, but only matches if the character is escaped. */
+  public boolean escMatch(char ch)
+  {
+    if (!dontMatch || eos)
+    {
+      return false;
     }
-    /** As match, but only matches if the character is escaped. */
-    public boolean escMatch(char ch) {
-        if(!dontMatch || eos) return false;
-        return c == ch;
+    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;
+  }
 
-    /** 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();
     }
-    /** 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);
+    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();
     }
-    /** get the string that we are processing. */
-    public String getString() { return s; }
+    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 18fa994..96d2178 100755
--- a/src/com/stevesoft/pat/StringBufferLike.java
+++ b/src/com/stevesoft/pat/StringBufferLike.java
@@ -1,64 +1,90 @@
-package//
+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;
-
+    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 {
+public class StringBufferLike
+    implements BasicStringBufferLike
+{
   BasicStringBufferLike sbl;
-  public StringBufferLike(BasicStringBufferLike sbl) {
+  public StringBufferLike(BasicStringBufferLike sbl)
+  {
     this.sbl = sbl;
   }
+
   char mode = 'E', altMode = ' ';
-  public StringLike toStringLike() {
+  public StringLike toStringLike()
+  {
     return sbl.toStringLike();
   }
-  public String toString() {
+
+  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(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++)
+
+  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;
+
+  public void setMode(char c)
+  {
+    if (c == 'u' || c == 'l')
+    {
+      if (altMode == ' ')
+      {
+        altMode = mode;
+      }
+    }
     mode = c;
   }
-  public Object unwrap() {
+
+  public Object unwrap()
+  {
     return sbl.unwrap();
   }
 }
diff --git a/src/com/stevesoft/pat/StringLike.java b/src/com/stevesoft/pat/StringLike.java
index a6cd318..07bc441 100755
--- a/src/com/stevesoft/pat/StringLike.java
+++ b/src/com/stevesoft/pat/StringLike.java
@@ -1,11 +1,11 @@
-package//
+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;
+    com.stevesoft.pat;
 
 /** Package pat can search anything that implements this
     interface.  Package pat assumes the following:
@@ -18,20 +18,27 @@ com.stevesoft.pat;
     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);
+ */
+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 c37b6bb..e831a14 100755
--- a/src/com/stevesoft/pat/StringRule.java
+++ b/src/com/stevesoft/pat/StringRule.java
@@ -10,13 +10,28 @@ 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); }
+ */
+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 ab5e431..16c3306 100755
--- a/src/com/stevesoft/pat/SubMark.java
+++ b/src/com/stevesoft/pat/SubMark.java
@@ -8,15 +8,24 @@
 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;
+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 125a7bd..4c71c1f 100755
--- a/src/com/stevesoft/pat/TransPat.java
+++ b/src/com/stevesoft/pat/TransPat.java
@@ -7,33 +7,39 @@
 //
 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)";
-    }
+ */
+class TransPat
+    extends Pattern
+{
+  Regex[] ra = new Regex[10];
+  int ra_len = 0;
+  int pn = -1;
+  public String toString()
+  {
+    return "(?#TransPat)";
+  }
 
-    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;
+  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 14f7e38..843fbfa 100755
--- a/src/com/stevesoft/pat/Transformer.java
+++ b/src/com/stevesoft/pat/Transformer.java
@@ -7,20 +7,35 @@
 //
 package com.stevesoft.pat;
 
-import com.stevesoft.pat.wrap.StringWrap;
+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();
-    }
+ */
+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
@@ -42,113 +57,163 @@ class TransRepRule extends ReplaceRule {
   <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;
-    }
+ */
+public class Transformer
+{
+  TransPat tp;
+  Regex rp = new Regex();
+  boolean auto_optimize;
 
-    /** 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_;
-    }
+  /** Get a replacer to that works with the current Regex.
+   @see com.stevesoft.pat.Replacer
+   */
+  public Replacer getReplacer()
+  {
+    return rp.getReplacer();
+  }
 
-    /** Returns the number of Regex's in this Transformer. */
-    public int patterns() { return tp.ra_len; }
+  /** Instantiate a new Transformer object. */
+  public Transformer(boolean auto)
+  {
+    auto_optimize = auto;
+    tp = new TransPat();
+    rp.setReplaceRule(new TransRepRule(this));
+    rp.thePattern = tp;
+  }
 
-    /** 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 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_;
+  }
 
-    /** 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);
-    }
+  /** Returns the number of Regex's in this Transformer. */
+  public int patterns()
+  {
+    return tp.ra_len;
+  }
 
-    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();
-    }
+  /** 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];
+  }
 
-    /** 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);
-    }
+  /** 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 7fbac56..4d86074 100755
--- a/src/com/stevesoft/pat/UniValidator.java
+++ b/src/com/stevesoft/pat/UniValidator.java
@@ -8,9 +8,18 @@
 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); }
+ * 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 facd3f7..34b07da 100755
--- a/src/com/stevesoft/pat/Validator.java
+++ b/src/com/stevesoft/pat/Validator.java
@@ -8,51 +8,63 @@
 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>. */
+ 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.
+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; }
+       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.
 
-    /** 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); }
+       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;
+  }
 
-    /** 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 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 5cc6722..34b73e5 100755
--- a/src/com/stevesoft/pat/WantMoreTextReplaceRule.java
+++ b/src/com/stevesoft/pat/WantMoreTextReplaceRule.java
@@ -10,10 +10,19 @@ 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 "${WANT_MORE_TEXT}"; }
+ */
+public class WantMoreTextReplaceRule
+    extends SpecialRule
+{
+  public WantMoreTextReplaceRule()
+  {}
+
+  public void apply(StringBufferLike sb, RegRes res)
+  {
+  }
+
+  public String toString1()
+  {
+    return "${WANT_MORE_TEXT}";
+  }
 }
diff --git a/src/com/stevesoft/pat/lookAhead.java b/src/com/stevesoft/pat/lookAhead.java
index 112db7c..73be36a 100755
--- a/src/com/stevesoft/pat/lookAhead.java
+++ b/src/com/stevesoft/pat/lookAhead.java
@@ -6,41 +6,94 @@
 //    -- Happy Computing!
 //
 package com.stevesoft.pat;
-import java.util.Hashtable;
+
+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;
+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);
     }
-    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;
-        }
+    else
+    {
+      return pos;
     }
-    String leftForm() {
-        if(reverse)
-            return "(?!";
-        else
-            return "(?=";
+  }
+
+  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;
+      }
     }
-    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;
+  }
+
+  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 f9c8498..da7c6d0 100755
--- a/src/com/stevesoft/pat/oneChar.java
+++ b/src/com/stevesoft/pat/oneChar.java
@@ -6,43 +6,70 @@
 //    -- Happy Computing!
 //
 package com.stevesoft.pat;
-import java.util.Hashtable;
+
+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;
+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;
     }
-    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;
+    else
+    {
+      altc = cl;
+      altc2 = cu;
     }
-    public String toString() {
-        return protect(""+c,PROTECT_THESE,ESC)+nextString();
+    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);
     }
-    public patInt minChars() { return new patInt(1); }
-    public patInt maxChars() { return new patInt(1); }
-    Pattern clone1(Hashtable h) { return new oneChar(c); }
+    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 5cdbabe..5de9f07 100755
--- a/src/com/stevesoft/pat/parsePerl.java
+++ b/src/com/stevesoft/pat/parsePerl.java
@@ -8,259 +8,372 @@
 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;
+ 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 '>';
     }
-
-    final public static String codify(String s,boolean keepbs) {
-        return codify(s,0,s.length(),keepbs);
+    if (c == '[')
+    {
+      return ']';
+    }
+    if (c == '(')
+    {
+      return ')';
+    }
+    if (c == '{')
+    {
+      return '}';
     }
-    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 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('\\');
         }
-        return modified ? sb.toString() : s;
+        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;
     }
-    final static char uc(char c) {
-        return CaseMgr.toUpperCase(c);
+    if (c >= 'A' && c <= 'Z')
+    {
+      return false;
     }
-    final static char lc(char c) {
-        return CaseMgr.toLowerCase(c);
+    if (c >= '0' && c <= '9')
+    {
+      return false;
     }
-    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;
+    if (c == '_')
+    {
+      return false;
     }
-    final static Regex parse(String s) {
-        boolean igncase = false, optim = false, gFlag = false;
-        boolean sFlag = false, mFlag = false, xFlag = false;
+    return true;
+  }
 
-        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));
+  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);
         }
-        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++;
+        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++;
         }
-        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));
-            }
+        else if (s.charAt(i) == cdelim && count == 0)
+        {
+          i++;
+          break;
         }
-        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;
-            }
+        else if (s.charAt(i) == delim && cdelim != delim)
+        {
+          count++;
         }
-        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;
+        else if (s.charAt(i) == cdelim && cdelim != delim)
+        {
+          count--;
         }
-        return r;
+        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));
+      }
     }
-    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);
+    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();
     }
+    return sb.toString();
+  }
 }
diff --git a/src/com/stevesoft/pat/patInf.java b/src/com/stevesoft/pat/patInf.java
index 09da207..28580e2 100755
--- a/src/com/stevesoft/pat/patInf.java
+++ b/src/com/stevesoft/pat/patInf.java
@@ -7,6 +7,11 @@
 //
 package com.stevesoft.pat;
 
-final class patInf extends patInt {
-    patInf() { inf = true; }
+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 e18c627..f997a52 100755
--- a/src/com/stevesoft/pat/patInt.java
+++ b/src/com/stevesoft/pat/patInt.java
@@ -10,79 +10,162 @@ 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;
+ */
+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++;
+  }
+
+  /** 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--;
+  }
+
+  /** 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 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 "";
     }
-    /** Test to see if two patterns are equal. */
-    public final boolean equals(patInt j) {
-        return !j.inf && !inf && i==j.i;
+    else
+    {
+      return "" + 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);
     }
-    /** 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;
+    else
+    {
+      i += p.i;
     }
-    /** 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);
+    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;
     }
-    /** 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;
+    else if (p.i < i)
+    {
+      i = p.i;
     }
-    /** 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;
+    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;
     }
-    /** 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; }
+    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 4e11067..19f268e 100755
--- a/src/com/stevesoft/pat/wrap/CharArrayBufferWrap.java
+++ b/src/com/stevesoft/pat/wrap/CharArrayBufferWrap.java
@@ -1,38 +1,53 @@
-package//
+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;
+    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
-  {
+    implements BasicStringBufferLike
+{
   StringBuffer sb = new StringBuffer();
-  public void append(char c) {
+  public void append(char c)
+  {
     sb.append(c);
   }
-  public void append(String s) {
+
+  public void append(String s)
+  {
     sb.append(s);
   }
-  public StringLike toStringLike() {
+
+  public StringLike toStringLike()
+  {
     char[] ca = new char[sb.length()];
-    for(int i=0;i<ca.length;i++)
+    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() {
+
+  public int length()
+  {
+    return sb.length();
+  }
+
+  public String toString()
+  {
     return sb.toString();
   }
-  public Object unwrap() {
+
+  public Object unwrap()
+  {
     return sb;
   }
 }
diff --git a/src/com/stevesoft/pat/wrap/CharArrayWrap.java b/src/com/stevesoft/pat/wrap/CharArrayWrap.java
index e490cc9..6de78cf 100755
--- a/src/com/stevesoft/pat/wrap/CharArrayWrap.java
+++ b/src/com/stevesoft/pat/wrap/CharArrayWrap.java
@@ -11,29 +11,64 @@ 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 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]);
     }
-    public int indexOf(char c) {
-      for(int i=0;i<ca.length;i++)
-        if(ca[i] == c)
-          return i;
-      return -1;
+    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 23782ad..90e7691 100755
--- a/src/com/stevesoft/pat/wrap/RandomAccessFileWrap.java
+++ b/src/com/stevesoft/pat/wrap/RandomAccessFileWrap.java
@@ -7,110 +7,167 @@
 //
 package com.stevesoft.pat.wrap;
 
-import com.stevesoft.pat.*;
 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 {
+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];
+  long offset = 0;
+  public void setOffset(long o)
+  {
+    offset = o;
+    i0 = iend = 0;
+  }
 
-    public int getBufferSize() {
-      return buf.length;
-    }
+  public long getOffset()
+  {
+    return offset;
+  }
 
-    public void setBufferSize(int bs) {
-      buf = new byte[bs];
-      i0 = iend = 0;
-    }
+  RandomAccessFile raf;
+  int i0 = 0, iend = 0;
+  byte[] buf = new byte[1024];
 
-    public RandomAccessFileWrap(String file) throws IOException {
-        this.raf = new RandomAccessFile(file,"r");
-    }
-    public RandomAccessFileWrap(RandomAccessFile raf) {
-        this.raf = raf;
+  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];
     }
 
-    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);
+    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)
+    {}
 
-    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;
+    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;
     }
-    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();
+    catch (IOException ioe)
+    {
+      return 0;
     }
-    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 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 BasicStringBufferLike newStringBufferLike() {
-      return new StringBufferWrap();
+  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 int indexOf(char c) {
-      for(int i=0;i<length();i++)
-        if(charAt(i)==c)
-          return i;
-      return -1;
+  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 f42cfde..40ddd65 100755
--- a/src/com/stevesoft/pat/wrap/StringBufferWrap.java
+++ b/src/com/stevesoft/pat/wrap/StringBufferWrap.java
@@ -13,24 +13,35 @@ import com.stevesoft.pat.*;
     capture the output of a replacement. */
 public class StringBufferWrap
     implements BasicStringBufferLike
-  {
+{
   StringBuffer sb = new StringBuffer();
-  public void append(char c) {
+  public void append(char c)
+  {
     sb.append(c);
   }
-  public void append(String s) {
+
+  public void append(String s)
+  {
     sb.append(s);
   }
-  public int length() {
+
+  public int length()
+  {
     return sb.length();
   }
-  public String toString() {
+
+  public String toString()
+  {
     return sb.toString();
   }
-  public StringLike toStringLike() {
+
+  public StringLike toStringLike()
+  {
     return new StringWrap(sb.toString());
   }
-  public Object unwrap() {
+
+  public Object unwrap()
+  {
     return sb;
   }
 }
diff --git a/src/com/stevesoft/pat/wrap/StringWrap.java b/src/com/stevesoft/pat/wrap/StringWrap.java
index 6c07ca1..a53d18e 100755
--- a/src/com/stevesoft/pat/wrap/StringWrap.java
+++ b/src/com/stevesoft/pat/wrap/StringWrap.java
@@ -11,23 +11,47 @@ 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);
-    }
+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 a1be479..1b7f6c2 100755
--- a/src/com/stevesoft/pat/wrap/WriterWrap.java
+++ b/src/com/stevesoft/pat/wrap/WriterWrap.java
@@ -7,9 +7,10 @@
 //
 package com.stevesoft.pat.wrap;
 
-import com.stevesoft.pat.*;
 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>
@@ -17,29 +18,42 @@ import java.io.*;
     This means that the return value of replaceAll() will
     be null if this Object is used as the StringBufferLike.*/
 public class WriterWrap
-  implements BasicStringBufferLike
-  {
+    implements BasicStringBufferLike
+{
   Writer w;
-  public WriterWrap(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(char c)
+  {
+    try
+    {
+      w.write( (int) c);
+    }
+    catch (IOException ioe)
+    {}
   }
-  public void append(String s) {
-    try {
+
+  public void append(String s)
+  {
+    try
+    {
       w.write(s);
-    } catch(IOException ioe) {}
+    }
+    catch (IOException ioe)
+    {}
   }
 
   /** This operation can't really be done. */
-  public StringLike toStringLike() {
+  public StringLike toStringLike()
+  {
     return null;
   }
 
-  public Object unwrap() {
+  public Object unwrap()
+  {
     return w;
   }
 }
diff --git a/src/ext/vamsas/IRegistry.java b/src/ext/vamsas/IRegistry.java
index afddded..9300f59 100755
--- a/src/ext/vamsas/IRegistry.java
+++ b/src/ext/vamsas/IRegistry.java
@@ -7,6 +7,9 @@
 
 package ext.vamsas;
 
-public interface IRegistry extends java.rmi.Remote {
-    public ext.vamsas.ServiceHandles getServices() throws java.rmi.RemoteException;
+public interface IRegistry
+    extends java.rmi.Remote
+{
+  public ext.vamsas.ServiceHandles getServices()
+      throws java.rmi.RemoteException;
 }
diff --git a/src/ext/vamsas/IRegistryService.java b/src/ext/vamsas/IRegistryService.java
index 9f09f02..2590314 100755
--- a/src/ext/vamsas/IRegistryService.java
+++ b/src/ext/vamsas/IRegistryService.java
@@ -7,10 +7,14 @@
 
 package ext.vamsas;
 
-public interface IRegistryService extends javax.xml.rpc.Service {
-    public java.lang.String getRegistryServiceAddress();
+public interface IRegistryService
+    extends javax.xml.rpc.Service
+{
+  public java.lang.String getRegistryServiceAddress();
 
-    public ext.vamsas.IRegistry getRegistryService() throws javax.xml.rpc.ServiceException;
+  public ext.vamsas.IRegistry getRegistryService()
+      throws javax.xml.rpc.ServiceException;
 
-    public ext.vamsas.IRegistry getRegistryService(java.net.URL portAddress) throws javax.xml.rpc.ServiceException;
+  public ext.vamsas.IRegistry getRegistryService(java.net.URL portAddress)
+      throws javax.xml.rpc.ServiceException;
 }
diff --git a/src/ext/vamsas/IRegistryServiceLocator.java b/src/ext/vamsas/IRegistryServiceLocator.java
index b3aa85d..0d7c0da 100755
--- a/src/ext/vamsas/IRegistryServiceLocator.java
+++ b/src/ext/vamsas/IRegistryServiceLocator.java
@@ -7,130 +7,175 @@
 
 package ext.vamsas;
 
-public class IRegistryServiceLocator extends org.apache.axis.client.Service implements ext.vamsas.IRegistryService {
-
-    public IRegistryServiceLocator() {
+public class IRegistryServiceLocator
+    extends org.apache.axis.client.Service implements ext.vamsas.
+    IRegistryService
+{
+
+  public IRegistryServiceLocator()
+  {
+  }
+
+  public IRegistryServiceLocator(org.apache.axis.EngineConfiguration config)
+  {
+    super(config);
+  }
+
+  // Use to get a proxy class for RegistryService
+  private java.lang.String RegistryService_address = "http://webservices.compbio.dundee.ac.uk:8080/jalTestWS/services/RegistryService";
+
+  public java.lang.String getRegistryServiceAddress()
+  {
+    return RegistryService_address;
+  }
+
+  // The WSDD service name defaults to the port name.
+  private java.lang.String RegistryServiceWSDDServiceName = "RegistryService";
+
+  public java.lang.String getRegistryServiceWSDDServiceName()
+  {
+    return RegistryServiceWSDDServiceName;
+  }
+
+  public void setRegistryServiceWSDDServiceName(java.lang.String name)
+  {
+    RegistryServiceWSDDServiceName = name;
+  }
+
+  public ext.vamsas.IRegistry getRegistryService()
+      throws javax.xml.rpc.ServiceException
+  {
+    java.net.URL endpoint;
+    try
+    {
+      endpoint = new java.net.URL(RegistryService_address);
     }
-
-
-    public IRegistryServiceLocator(org.apache.axis.EngineConfiguration config) {
-        super(config);
+    catch (java.net.MalformedURLException e)
+    {
+      throw new javax.xml.rpc.ServiceException(e);
     }
-
-    // Use to get a proxy class for RegistryService
-    private java.lang.String RegistryService_address = "http://webservices.compbio.dundee.ac.uk:8080/jalTestWS/services/RegistryService";
-
-    public java.lang.String getRegistryServiceAddress() {
-        return RegistryService_address;
+    return getRegistryService(endpoint);
+  }
+
+  public ext.vamsas.IRegistry getRegistryService(java.net.URL portAddress)
+      throws javax.xml.rpc.ServiceException
+  {
+    try
+    {
+      ext.vamsas.RegistryServiceSoapBindingStub _stub = new ext.vamsas.
+          RegistryServiceSoapBindingStub(portAddress, this);
+      _stub.setPortName(getRegistryServiceWSDDServiceName());
+      return _stub;
     }
-
-    // The WSDD service name defaults to the port name.
-    private java.lang.String RegistryServiceWSDDServiceName = "RegistryService";
-
-    public java.lang.String getRegistryServiceWSDDServiceName() {
-        return RegistryServiceWSDDServiceName;
+    catch (org.apache.axis.AxisFault e)
+    {
+      return null;
     }
-
-    public void setRegistryServiceWSDDServiceName(java.lang.String name) {
-        RegistryServiceWSDDServiceName = name;
+  }
+
+  public void setRegistryServiceEndpointAddress(java.lang.String address)
+  {
+    RegistryService_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.IRegistry.class.isAssignableFrom(serviceEndpointInterface))
+      {
+        ext.vamsas.RegistryServiceSoapBindingStub _stub = new ext.vamsas.
+            RegistryServiceSoapBindingStub(new java.net.URL(
+            RegistryService_address), this);
+        _stub.setPortName(getRegistryServiceWSDDServiceName());
+        return _stub;
+      }
     }
-
-    public ext.vamsas.IRegistry getRegistryService() throws javax.xml.rpc.ServiceException {
-       java.net.URL endpoint;
-        try {
-            endpoint = new java.net.URL(RegistryService_address);
-        }
-        catch (java.net.MalformedURLException e) {
-            throw new javax.xml.rpc.ServiceException(e);
-        }
-        return getRegistryService(endpoint);
+    catch (java.lang.Throwable t)
+    {
+      throw new javax.xml.rpc.ServiceException(t);
     }
-
-    public ext.vamsas.IRegistry getRegistryService(java.net.URL portAddress) throws javax.xml.rpc.ServiceException {
-        try {
-            ext.vamsas.RegistryServiceSoapBindingStub _stub = new ext.vamsas.RegistryServiceSoapBindingStub(portAddress, this);
-            _stub.setPortName(getRegistryServiceWSDDServiceName());
-            return _stub;
-        }
-        catch (org.apache.axis.AxisFault e) {
-            return null;
-        }
-    }
-
-    public void setRegistryServiceEndpointAddress(java.lang.String address) {
-        RegistryService_address = address;
+    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);
     }
-
-    /**
-     * 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.IRegistry.class.isAssignableFrom(serviceEndpointInterface)) {
-                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) {
-            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()));
+    java.lang.String inputPortName = portName.getLocalPart();
+    if ("RegistryService".equals(inputPortName))
+    {
+      return getRegistryService();
     }
-
-    /**
-     * 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 ("RegistryService".equals(inputPortName)) {
-            return getRegistryService();
-        }
-        else  {
-            java.rmi.Remote _stub = getPort(serviceEndpointInterface);
-            ((org.apache.axis.client.Stub) _stub).setPortName(portName);
-            return _stub;
-        }
+    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", "IRegistryService");
-    }
+  public javax.xml.namespace.QName getServiceName()
+  {
+    return new javax.xml.namespace.QName("vamsas", "IRegistryService");
+  }
 
-    private java.util.HashSet ports = null;
+  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", "RegistryService"));
-        }
-        return ports.iterator();
+  public java.util.Iterator getPorts()
+  {
+    if (ports == null)
+    {
+      ports = new java.util.HashSet();
+      ports.add(new javax.xml.namespace.QName("vamsas", "RegistryService"));
     }
-
-    /**
-    * 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 ("RegistryService".equals(portName)) {
-            setRegistryServiceEndpointAddress(address);
-        }
-        else { // Unknown Port Name
-            throw new javax.xml.rpc.ServiceException(" Cannot set Endpoint Address for Unknown Port" + portName);
-        }
+    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 ("RegistryService".equals(portName))
+    {
+      setRegistryServiceEndpointAddress(address);
     }
-
-    /**
-    * 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/Jpred.java b/src/ext/vamsas/Jpred.java
index 4860339..c3ab28b 100755
--- a/src/ext/vamsas/Jpred.java
+++ b/src/ext/vamsas/Jpred.java
@@ -7,9 +7,18 @@
 
 package ext.vamsas;
 
-public interface Jpred extends java.rmi.Remote {
-    public java.lang.String predict(vamsas.objects.simple.Sequence seq) 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.JpredResult getresult(java.lang.String job_id) throws java.rmi.RemoteException;
+public interface Jpred
+    extends java.rmi.Remote
+{
+  public java.lang.String predict(vamsas.objects.simple.Sequence seq)
+      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.JpredResult getresult(java.lang.String job_id)
+      throws java.rmi.RemoteException;
 }
diff --git a/src/ext/vamsas/JpredService.java b/src/ext/vamsas/JpredService.java
index 0b95e68..8917d77 100755
--- a/src/ext/vamsas/JpredService.java
+++ b/src/ext/vamsas/JpredService.java
@@ -7,10 +7,14 @@
 
 package ext.vamsas;
 
-public interface JpredService extends javax.xml.rpc.Service {
-    public java.lang.String getjpredAddress();
+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;
+  public ext.vamsas.Jpred getjpred(java.net.URL portAddress)
+      throws javax.xml.rpc.ServiceException;
 }
diff --git a/src/ext/vamsas/JpredServiceLocator.java b/src/ext/vamsas/JpredServiceLocator.java
index 813c340..433fa70 100755
--- a/src/ext/vamsas/JpredServiceLocator.java
+++ b/src/ext/vamsas/JpredServiceLocator.java
@@ -7,130 +7,174 @@
 
 package ext.vamsas;
 
-public class JpredServiceLocator extends org.apache.axis.client.Service implements ext.vamsas.JpredService {
-
-    public JpredServiceLocator() {
+public class JpredServiceLocator
+    extends org.apache.axis.client.Service implements ext.vamsas.JpredService
+{
+
+  public JpredServiceLocator()
+  {
+  }
+
+  public JpredServiceLocator(org.apache.axis.EngineConfiguration config)
+  {
+    super(config);
+  }
+
+  // Use to get a proxy class for jpred
+  private java.lang.String jpred_address =
+      "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred";
+
+  public java.lang.String getjpredAddress()
+  {
+    return jpred_address;
+  }
+
+  // The WSDD service name defaults to the port name.
+  private java.lang.String jpredWSDDServiceName = "jpred";
+
+  public java.lang.String getjpredWSDDServiceName()
+  {
+    return jpredWSDDServiceName;
+  }
+
+  public void setjpredWSDDServiceName(java.lang.String name)
+  {
+    jpredWSDDServiceName = name;
+  }
+
+  public ext.vamsas.Jpred getjpred()
+      throws javax.xml.rpc.ServiceException
+  {
+    java.net.URL endpoint;
+    try
+    {
+      endpoint = new java.net.URL(jpred_address);
     }
-
-
-    public JpredServiceLocator(org.apache.axis.EngineConfiguration config) {
-        super(config);
+    catch (java.net.MalformedURLException e)
+    {
+      throw new javax.xml.rpc.ServiceException(e);
     }
-
-    // Use to get a proxy class for jpred
-    private java.lang.String jpred_address = "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred";
-
-    public java.lang.String getjpredAddress() {
-        return jpred_address;
+    return getjpred(endpoint);
+  }
+
+  public ext.vamsas.Jpred getjpred(java.net.URL portAddress)
+      throws javax.xml.rpc.ServiceException
+  {
+    try
+    {
+      ext.vamsas.JpredSoapBindingStub _stub = new ext.vamsas.
+          JpredSoapBindingStub(portAddress, this);
+      _stub.setPortName(getjpredWSDDServiceName());
+      return _stub;
     }
-
-    // The WSDD service name defaults to the port name.
-    private java.lang.String jpredWSDDServiceName = "jpred";
-
-    public java.lang.String getjpredWSDDServiceName() {
-        return jpredWSDDServiceName;
+    catch (org.apache.axis.AxisFault e)
+    {
+      return null;
     }
-
-    public void setjpredWSDDServiceName(java.lang.String name) {
-        jpredWSDDServiceName = name;
+  }
+
+  public void setjpredEndpointAddress(java.lang.String address)
+  {
+    jpred_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.Jpred.class.isAssignableFrom(serviceEndpointInterface))
+      {
+        ext.vamsas.JpredSoapBindingStub _stub = new ext.vamsas.
+            JpredSoapBindingStub(new java.net.URL(jpred_address), this);
+        _stub.setPortName(getjpredWSDDServiceName());
+        return _stub;
+      }
     }
-
-    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) {
-            throw new javax.xml.rpc.ServiceException(e);
-        }
-        return getjpred(endpoint);
+    catch (java.lang.Throwable t)
+    {
+      throw new javax.xml.rpc.ServiceException(t);
     }
-
-    public ext.vamsas.Jpred getjpred(java.net.URL portAddress) throws javax.xml.rpc.ServiceException {
-        try {
-            ext.vamsas.JpredSoapBindingStub _stub = new ext.vamsas.JpredSoapBindingStub(portAddress, this);
-            _stub.setPortName(getjpredWSDDServiceName());
-            return _stub;
-        }
-        catch (org.apache.axis.AxisFault e) {
-            return null;
-        }
-    }
-
-    public void setjpredEndpointAddress(java.lang.String address) {
-        jpred_address = address;
+    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);
     }
-
-    /**
-     * 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.Jpred.class.isAssignableFrom(serviceEndpointInterface)) {
-                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) {
-            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()));
+    java.lang.String inputPortName = portName.getLocalPart();
+    if ("jpred".equals(inputPortName))
+    {
+      return getjpred();
     }
-
-    /**
-     * 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 ("jpred".equals(inputPortName)) {
-            return getjpred();
-        }
-        else  {
-            java.rmi.Remote _stub = getPort(serviceEndpointInterface);
-            ((org.apache.axis.client.Stub) _stub).setPortName(portName);
-            return _stub;
-        }
+    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", "jpredService");
-    }
+  public javax.xml.namespace.QName getServiceName()
+  {
+    return new javax.xml.namespace.QName("vamsas", "jpredService");
+  }
 
-    private java.util.HashSet ports = null;
+  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", "jpred"));
-        }
-        return ports.iterator();
+  public java.util.Iterator getPorts()
+  {
+    if (ports == null)
+    {
+      ports = new java.util.HashSet();
+      ports.add(new javax.xml.namespace.QName("vamsas", "jpred"));
     }
-
-    /**
-    * 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 ("jpred".equals(portName)) {
-            setjpredEndpointAddress(address);
-        }
-        else { // Unknown Port Name
-            throw new javax.xml.rpc.ServiceException(" Cannot set Endpoint Address for Unknown Port" + portName);
-        }
+    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 ("jpred".equals(portName))
+    {
+      setjpredEndpointAddress(address);
     }
-
-    /**
-    * 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/JpredSoapBindingStub.java b/src/ext/vamsas/JpredSoapBindingStub.java
index a42bc49..4c8fc7f 100755
--- a/src/ext/vamsas/JpredSoapBindingStub.java
+++ b/src/ext/vamsas/JpredSoapBindingStub.java
@@ -7,293 +7,389 @@
 
 package ext.vamsas;
 
-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();
+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;
+  static org.apache.axis.description.OperationDesc[] _operations;
 
-    static {
-        _operations = new org.apache.axis.description.OperationDesc[4];
-        _initOperationDesc1();
-    }
+  static
+  {
+    _operations = new org.apache.axis.description.OperationDesc[4];
+    _initOperationDesc1();
+  }
 
-    private static void _initOperationDesc1(){
-        org.apache.axis.description.OperationDesc oper;
-        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);
-        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("", "predictReturn"));
-        oper.setStyle(org.apache.axis.constants.Style.RPC);
-        oper.setUse(org.apache.axis.constants.Use.ENCODED);
-        _operations[0] = oper;
+  private static void _initOperationDesc1()
+  {
+    org.apache.axis.description.OperationDesc oper;
+    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);
+    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("", "predictReturn"));
+    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("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);
-        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("", "predictOnMsaReturn"));
-        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("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);
+    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("", "predictOnMsaReturn"));
+    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("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);
-        oper.setReturnType(new javax.xml.namespace.QName("http://simple.objects.vamsas", "Secstructpred"));
-        oper.setReturnClass(vamsas.objects.simple.Secstructpred.class);
-        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;
+    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);
+    oper.setReturnType(new javax.xml.namespace.QName(
+        "http://simple.objects.vamsas", "Secstructpred"));
+    oper.setReturnClass(vamsas.objects.simple.Secstructpred.class);
+    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;
 
-        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("http://simple.objects.vamsas", "JpredResult"));
-        oper.setReturnClass(vamsas.objects.simple.JpredResult.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[3] = 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(
+        "http://simple.objects.vamsas", "JpredResult"));
+    oper.setReturnClass(vamsas.objects.simple.JpredResult.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[3] = oper;
 
-    }
+  }
 
-    public JpredSoapBindingStub() throws org.apache.axis.AxisFault {
-         this(null);
-    }
+  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 {
-         this(service);
-         super.cachedEndpoint = endpointURL;
-    }
+  public JpredSoapBindingStub(java.net.URL endpointURL,
+                              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 {
-        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://simple.objects.vamsas", "JpredResult");
-            cachedSerQNames.add(qName);
-            cls = vamsas.objects.simple.JpredResult.class;
-            cachedSerClasses.add(cls);
-            cachedSerFactories.add(beansf);
-            cachedDeserFactories.add(beandf);
+  public JpredSoapBindingStub(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://simple.objects.vamsas",
+                                          "JpredResult");
+    cachedSerQNames.add(qName);
+    cls = vamsas.objects.simple.JpredResult.class;
+    cachedSerClasses.add(cls);
+    cachedSerFactories.add(beansf);
+    cachedDeserFactories.add(beandf);
 
-            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", "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("http://simple.objects.vamsas", "Secstructpred");
-            cachedSerQNames.add(qName);
-            cls = vamsas.objects.simple.Secstructpred.class;
-            cachedSerClasses.add(cls);
-            cachedSerFactories.add(beansf);
-            cachedDeserFactories.add(beandf);
+    qName = new javax.xml.namespace.QName("http://simple.objects.vamsas",
+                                          "Secstructpred");
+    cachedSerQNames.add(qName);
+    cls = vamsas.objects.simple.Secstructpred.class;
+    cachedSerClasses.add(cls);
+    cachedSerFactories.add(beansf);
+    cachedDeserFactories.add(beandf);
 
-            qName = new javax.xml.namespace.QName("http://simple.objects.vamsas", "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("http://simple.objects.vamsas",
+                                          "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");
-            cachedSerQNames.add(qName);
-            cls = vamsas.objects.simple.Sequence.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);
 
-    }
+  }
 
-    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);
+  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 predict(vamsas.objects.simple.Sequence seq) 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", "predict"));
+  public java.lang.String predict(vamsas.objects.simple.Sequence seq)
+      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", "predict"));
 
-        setRequestHeaders(_call);
-        setAttachments(_call);
-        java.lang.Object _resp = _call.invoke(new java.lang.Object[] {seq});
+    setRequestHeaders(_call);
+    setAttachments(_call);
+    java.lang.Object _resp = _call.invoke(new java.lang.Object[]
+                                          {seq});
 
-        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);
-            }
-        }
+    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);
+      }
     }
+  }
 
-    public java.lang.String predictOnMsa(vamsas.objects.simple.Msfalignment msf) 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", "predictOnMsa"));
+  public java.lang.String predictOnMsa(vamsas.objects.simple.Msfalignment msf)
+      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",
+        "predictOnMsa"));
 
-        setRequestHeaders(_call);
-        setAttachments(_call);
-        java.lang.Object _resp = _call.invoke(new java.lang.Object[] {msf});
+    setRequestHeaders(_call);
+    setAttachments(_call);
+    java.lang.Object _resp = _call.invoke(new java.lang.Object[]
+                                          {msf});
 
-        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);
-            }
-        }
+    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);
+      }
+    }
+  }
 
-    public vamsas.objects.simple.Secstructpred getpredict(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", "getpredict"));
+  public vamsas.objects.simple.Secstructpred getpredict(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", "getpredict"));
 
-        setRequestHeaders(_call);
-        setAttachments(_call);
-        java.lang.Object _resp = _call.invoke(new java.lang.Object[] {job_id});
+    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.Secstructpred) _resp;
-            } catch (java.lang.Exception _exception) {
-                return (vamsas.objects.simple.Secstructpred) org.apache.axis.utils.JavaUtils.convert(_resp, vamsas.objects.simple.Secstructpred.class);
-            }
-        }
+    if (_resp instanceof java.rmi.RemoteException)
+    {
+      throw (java.rmi.RemoteException) _resp;
+    }
+    else
+    {
+      extractAttachments(_call);
+      try
+      {
+        return (vamsas.objects.simple.Secstructpred) _resp;
+      }
+      catch (java.lang.Exception _exception)
+      {
+        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 {
-        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", "getresult"));
+  public vamsas.objects.simple.JpredResult 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[3]);
+    _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});
+    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.JpredResult) _resp;
-            } catch (java.lang.Exception _exception) {
-                return (vamsas.objects.simple.JpredResult) org.apache.axis.utils.JavaUtils.convert(_resp, vamsas.objects.simple.JpredResult.class);
-            }
-        }
+    if (_resp instanceof java.rmi.RemoteException)
+    {
+      throw (java.rmi.RemoteException) _resp;
+    }
+    else
+    {
+      extractAttachments(_call);
+      try
+      {
+        return (vamsas.objects.simple.JpredResult) _resp;
+      }
+      catch (java.lang.Exception _exception)
+      {
+        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 970ec72..db1416e 100755
--- a/src/ext/vamsas/MuscleWS.java
+++ b/src/ext/vamsas/MuscleWS.java
@@ -6,36 +6,38 @@
  */
 
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 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.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.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;
+  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 bf6d26a..a4dc674 100755
--- a/src/ext/vamsas/MuscleWSService.java
+++ b/src/ext/vamsas/MuscleWSService.java
@@ -6,31 +6,33 @@
  */
 
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 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()
+      throws javax.xml.rpc.ServiceException;
 
-    public ext.vamsas.MuscleWS getMuscleWS(java.net.URL portAddress)
-        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 80a2f96..a269029 100755
--- a/src/ext/vamsas/MuscleWSServiceLocator.java
+++ b/src/ext/vamsas/MuscleWSServiceLocator.java
@@ -6,163 +6,203 @@
  */
 
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 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);
     }
-
-    public MuscleWSServiceLocator(org.apache.axis.EngineConfiguration config) {
-        super(config);
+    catch (java.net.MalformedURLException e)
+    {
+      throw new javax.xml.rpc.ServiceException(e);
     }
 
-    public java.lang.String getMuscleWSAddress() {
-        return MuscleWS_address;
-    }
+    return getMuscleWS(endpoint);
+  }
 
-    public java.lang.String getMuscleWSWSDDServiceName() {
-        return MuscleWSWSDDServiceName;
-    }
+  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());
 
-    public void setMuscleWSWSDDServiceName(java.lang.String name) {
-        MuscleWSWSDDServiceName = name;
+      return _stub;
     }
-
-    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);
+    catch (org.apache.axis.AxisFault e)
+    {
+      return null;
     }
-
-    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;
+      }
     }
-
-    public void setMuscleWSEndpointAddress(java.lang.String address) {
-        MuscleWS_address = address;
+    catch (java.lang.Throwable t)
+    {
+      throw new javax.xml.rpc.ServiceException(t);
     }
 
-    /**
- * 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()));
+    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);
     }
 
-    /**
- * 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;
-        }
-    }
+    java.lang.String inputPortName = portName.getLocalPart();
 
-    public javax.xml.namespace.QName getServiceName() {
-        return new javax.xml.namespace.QName("vamsas", "MuscleWSService");
+    if ("MuscleWS".equals(inputPortName))
+    {
+      return getMuscleWS();
     }
+    else
+    {
+      java.rmi.Remote _stub = getPort(serviceEndpointInterface);
+      ( (org.apache.axis.client.Stub) _stub).setPortName(portName);
 
-    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();
+      return _stub;
     }
-
-    /**
-* 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);
-        }
+  }
+
+  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"));
     }
 
-    /**
-* 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);
+    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 ace12f4..de80f9e 100755
--- a/src/ext/vamsas/MuscleWSSoapBindingStub.java
+++ b/src/ext/vamsas/MuscleWSSoapBindingStub.java
@@ -6,389 +6,465 @@
  */
 
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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();
+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();
     }
-
-    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;
+    else
+    {
+      super.service = service;
     }
 
-    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);
+          }
         }
+      }
 
-        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);
+      return _call;
     }
-
-    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;
+    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 vamsas.objects.simple.WsJobId align(
+      vamsas.objects.simple.SequenceSet seqSet)
+      throws java.rmi.RemoteException
+  {
+    if (super.cachedEndpoint == null)
+    {
+      throw new org.apache.axis.NoEndPointException();
     }
 
-    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);
+    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"));
 
-        java.lang.Object _resp = _call.invoke(new java.lang.Object[] { seqSet });
+    setRequestHeaders(_call);
+    setAttachments(_call);
 
-        if (_resp instanceof java.rmi.RemoteException) {
-            throw (java.rmi.RemoteException) _resp;
-        } else {
-            extractAttachments(_call);
+    java.lang.Object _resp = _call.invoke(new java.lang.Object[]
+                                          {seqSet});
 
-            try {
-                return (vamsas.objects.simple.WsJobId) _resp;
-            } catch (java.lang.Exception _exception) {
-                return (vamsas.objects.simple.WsJobId) org.apache.axis.utils.JavaUtils.convert(_resp,
+    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();
     }
 
-    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"));
 
-        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);
-            }
-        }
-    }
+    setRequestHeaders(_call);
+    setAttachments(_call);
 
-    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();
-        }
+    java.lang.Object _resp = _call.invoke(new java.lang.Object[]
+                                          {job_id});
 
-        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);
-            }
-        }
+    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();
     }
 
-    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[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);
 
-        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"));
+    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();
+    }
 
-        setRequestHeaders(_call);
-        setAttachments(_call);
+    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"));
 
-        java.lang.Object _resp = _call.invoke(new java.lang.Object[] { jobId });
+    setRequestHeaders(_call);
+    setAttachments(_call);
 
-        if (_resp instanceof java.rmi.RemoteException) {
-            throw (java.rmi.RemoteException) _resp;
-        } else {
-            extractAttachments(_call);
+    java.lang.Object _resp = _call.invoke(new java.lang.Object[]
+                                          {jobId});
 
-            try {
-                return (vamsas.objects.simple.WsJobId) _resp;
-            } catch (java.lang.Exception _exception) {
-                return (vamsas.objects.simple.WsJobId) org.apache.axis.utils.JavaUtils.convert(_resp,
+    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 6379c0c..22bd8ed 100755
--- a/src/ext/vamsas/RegistryServiceSoapBindingStub.java
+++ b/src/ext/vamsas/RegistryServiceSoapBindingStub.java
@@ -7,164 +7,212 @@
 
 package ext.vamsas;
 
-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;
-
-    static {
-        _operations = new org.apache.axis.description.OperationDesc[1];
-        _initOperationDesc1();
+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;
+
+  static
+  {
+    _operations = new org.apache.axis.description.OperationDesc[1];
+    _initOperationDesc1();
+  }
+
+  private static void _initOperationDesc1()
+  {
+    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.setReturnClass(ext.vamsas.ServiceHandles.class);
+    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
+  {
+    this(null);
+  }
+
+  public RegistryServiceSoapBindingStub(java.net.URL endpointURL,
+                                        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
+  {
+    if (service == null)
+    {
+      super.service = new org.apache.axis.client.Service();
     }
-
-    private static void _initOperationDesc1(){
-        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.setReturnClass(ext.vamsas.ServiceHandles.class);
-        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;
-
+    else
+    {
+      super.service = service;
     }
-
-    public RegistryServiceSoapBindingStub() throws org.apache.axis.AxisFault {
-         this(null);
+    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("vamsas",
+                                          "ArrayOf_tns1_ServiceHandle");
+    cachedSerQNames.add(qName);
+    cls = ext.vamsas.ServiceHandle[].class;
+    cachedSerClasses.add(cls);
+    cachedSerFactories.add(arraysf);
+    cachedDeserFactories.add(arraydf);
+
+    qName = new javax.xml.namespace.QName("registry.objects.vamsas",
+                                          "ServiceHandles");
+    cachedSerQNames.add(qName);
+    cls = ext.vamsas.ServiceHandles.class;
+    cachedSerClasses.add(cls);
+    cachedSerFactories.add(beansf);
+    cachedDeserFactories.add(beandf);
+
+    qName = new javax.xml.namespace.QName("registry.objects.vamsas",
+                                          "ServiceHandle");
+    cachedSerQNames.add(qName);
+    cls = ext.vamsas.ServiceHandle.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);
+          }
+        }
+      }
+      return _call;
     }
-
-    public RegistryServiceSoapBindingStub(java.net.URL endpointURL, javax.xml.rpc.Service service) throws org.apache.axis.AxisFault {
-         this(service);
-         super.cachedEndpoint = endpointURL;
+    catch (java.lang.Throwable _t)
+    {
+      throw new org.apache.axis.AxisFault(
+          "Failure trying to get the Call object", _t);
     }
-
-    public RegistryServiceSoapBindingStub(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("vamsas", "ArrayOf_tns1_ServiceHandle");
-            cachedSerQNames.add(qName);
-            cls = ext.vamsas.ServiceHandle[].class;
-            cachedSerClasses.add(cls);
-            cachedSerFactories.add(arraysf);
-            cachedDeserFactories.add(arraydf);
-
-            qName = new javax.xml.namespace.QName("registry.objects.vamsas", "ServiceHandles");
-            cachedSerQNames.add(qName);
-            cls = ext.vamsas.ServiceHandles.class;
-            cachedSerClasses.add(cls);
-            cachedSerFactories.add(beansf);
-            cachedDeserFactories.add(beandf);
-
-            qName = new javax.xml.namespace.QName("registry.objects.vamsas", "ServiceHandle");
-            cachedSerQNames.add(qName);
-            cls = ext.vamsas.ServiceHandle.class;
-            cachedSerClasses.add(cls);
-            cachedSerFactories.add(beansf);
-            cachedDeserFactories.add(beandf);
-
+  }
+
+  public ext.vamsas.ServiceHandles getServices()
+      throws java.rmi.RemoteException
+  {
+    if (super.cachedEndpoint == null)
+    {
+      throw new org.apache.axis.NoEndPointException();
     }
-
-    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);
-        }
+    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",
+        "getServices"));
+
+    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 ext.vamsas.ServiceHandles getServices() 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", "getServices"));
-
-        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 (ext.vamsas.ServiceHandles) _resp;
-            } catch (java.lang.Exception _exception) {
-                return (ext.vamsas.ServiceHandles) org.apache.axis.utils.JavaUtils.convert(_resp, ext.vamsas.ServiceHandles.class);
-            }
-        }
+    else
+    {
+      extractAttachments(_call);
+      try
+      {
+        return (ext.vamsas.ServiceHandles) _resp;
+      }
+      catch (java.lang.Exception _exception)
+      {
+        return (ext.vamsas.ServiceHandles) org.apache.axis.utils.JavaUtils.
+            convert(_resp, ext.vamsas.ServiceHandles.class);
+      }
     }
+  }
 
 }
diff --git a/src/ext/vamsas/ServiceHandle.java b/src/ext/vamsas/ServiceHandle.java
index 2b662f7..994ea5c 100755
--- a/src/ext/vamsas/ServiceHandle.java
+++ b/src/ext/vamsas/ServiceHandle.java
@@ -7,214 +7,245 @@
 
 package ext.vamsas;
 
-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) {
-           this.abstractName = abstractName;
-           this.description = description;
-           this.endpointURL = endpointURL;
-           this.name = name;
-    }
-
-
-    /**
-     * Gets the abstractName value for this ServiceHandle.
-     * 
-     * @return abstractName
-     */
-    public java.lang.String getAbstractName() {
-        return abstractName;
-    }
-
-
-    /**
-     * Sets the abstractName value for this ServiceHandle.
-     * 
-     * @param abstractName
-     */
-    public void setAbstractName(java.lang.String abstractName) {
-        this.abstractName = abstractName;
-    }
-
-
-    /**
-     * Gets the description value for this ServiceHandle.
-     * 
-     * @return description
-     */
-    public java.lang.String getDescription() {
-        return description;
-    }
-
-
-    /**
-     * Sets the description value for this ServiceHandle.
-     * 
-     * @param description
-     */
-    public void setDescription(java.lang.String description) {
-        this.description = description;
-    }
-
-
-    /**
-     * Gets the endpointURL value for this ServiceHandle.
-     * 
-     * @return endpointURL
-     */
-    public java.lang.String getEndpointURL() {
-        return endpointURL;
-    }
-
-
-    /**
-     * Sets the endpointURL value for this ServiceHandle.
-     * 
-     * @param endpointURL
-     */
-    public void setEndpointURL(java.lang.String endpointURL) {
-        this.endpointURL = endpointURL;
-    }
-
-
-    /**
-     * Gets the name value for this ServiceHandle.
-     * 
-     * @return name
-     */
-    public java.lang.String getName() {
-        return name;
-    }
-
-
-    /**
-     * Sets the name value for this ServiceHandle.
-     * 
-     * @param name
-     */
-    public void setName(java.lang.String name) {
-        this.name = name;
-    }
-
-    private java.lang.Object __equalsCalc = null;
-    public synchronized boolean equals(java.lang.Object obj) {
-        if (!(obj instanceof ServiceHandle)) return false;
-        ServiceHandle other = (ServiceHandle) obj;
-        if (obj == null) return false;
-        if (this == obj) return true;
-        if (__equalsCalc != null) {
-            return (__equalsCalc == obj);
-        }
-        __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())));
-        __equalsCalc = null;
-        return _equals;
-    }
-
-    private boolean __hashCodeCalc = false;
-    public synchronized int hashCode() {
-        if (__hashCodeCalc) {
-            return 0;
-        }
-        __hashCodeCalc = true;
-        int _hashCode = 1;
-        if (getAbstractName() != null) {
-            _hashCode += getAbstractName().hashCode();
-        }
-        if (getDescription() != null) {
-            _hashCode += getDescription().hashCode();
-        }
-        if (getEndpointURL() != null) {
-            _hashCode += getEndpointURL().hashCode();
-        }
-        if (getName() != null) {
-            _hashCode += getName().hashCode();
-        }
-        __hashCodeCalc = false;
-        return _hashCode;
-    }
-
-    // Type metadata
-    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();
-        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"));
-        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"));
-        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"));
-        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"));
-        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(
+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)
+  {
+    this.abstractName = abstractName;
+    this.description = description;
+    this.endpointURL = endpointURL;
+    this.name = name;
+  }
+
+  /**
+   * Gets the abstractName value for this ServiceHandle.
+   *
+   * @return abstractName
+   */
+  public java.lang.String getAbstractName()
+  {
+    return abstractName;
+  }
+
+  /**
+   * Sets the abstractName value for this ServiceHandle.
+   *
+   * @param abstractName
+   */
+  public void setAbstractName(java.lang.String abstractName)
+  {
+    this.abstractName = abstractName;
+  }
+
+  /**
+   * Gets the description value for this ServiceHandle.
+   *
+   * @return description
+   */
+  public java.lang.String getDescription()
+  {
+    return description;
+  }
+
+  /**
+   * Sets the description value for this ServiceHandle.
+   *
+   * @param description
+   */
+  public void setDescription(java.lang.String description)
+  {
+    this.description = description;
+  }
+
+  /**
+   * Gets the endpointURL value for this ServiceHandle.
+   *
+   * @return endpointURL
+   */
+  public java.lang.String getEndpointURL()
+  {
+    return endpointURL;
+  }
+
+  /**
+   * Sets the endpointURL value for this ServiceHandle.
+   *
+   * @param endpointURL
+   */
+  public void setEndpointURL(java.lang.String endpointURL)
+  {
+    this.endpointURL = endpointURL;
+  }
+
+  /**
+   * Gets the name value for this ServiceHandle.
+   *
+   * @return name
+   */
+  public java.lang.String getName()
+  {
+    return name;
+  }
+
+  /**
+   * Sets the name value for this ServiceHandle.
+   *
+   * @param name
+   */
+  public void setName(java.lang.String name)
+  {
+    this.name = name;
+  }
+
+  private java.lang.Object __equalsCalc = null;
+  public synchronized boolean equals(java.lang.Object obj)
+  {
+    if (! (obj instanceof ServiceHandle))
+    {
+      return false;
+    }
+    ServiceHandle other = (ServiceHandle) obj;
+    if (obj == null)
+    {
+      return false;
+    }
+    if (this == obj)
+    {
+      return true;
+    }
+    if (__equalsCalc != null)
+    {
+      return (__equalsCalc == obj);
+    }
+    __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())));
+    __equalsCalc = null;
+    return _equals;
+  }
+
+  private boolean __hashCodeCalc = false;
+  public synchronized int hashCode()
+  {
+    if (__hashCodeCalc)
+    {
+      return 0;
+    }
+    __hashCodeCalc = true;
+    int _hashCode = 1;
+    if (getAbstractName() != null)
+    {
+      _hashCode += getAbstractName().hashCode();
+    }
+    if (getDescription() != null)
+    {
+      _hashCode += getDescription().hashCode();
+    }
+    if (getEndpointURL() != null)
+    {
+      _hashCode += getEndpointURL().hashCode();
+    }
+    if (getName() != null)
+    {
+      _hashCode += getName().hashCode();
+    }
+    __hashCodeCalc = false;
+    return _hashCode;
+  }
+
+  // Type metadata
+  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();
+    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"));
+    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"));
+    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"));
+    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"));
+    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(
+  }
+
+  /**
+   * 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/ext/vamsas/ServiceHandles.java b/src/ext/vamsas/ServiceHandles.java
index 1c4932f..1de1345 100755
--- a/src/ext/vamsas/ServiceHandles.java
+++ b/src/ext/vamsas/ServiceHandles.java
@@ -7,120 +7,147 @@
 
 package ext.vamsas;
 
-public class ServiceHandles  implements java.io.Serializable {
-    private ext.vamsas.ServiceHandle[] services;
-
-    public ServiceHandles() {
+public class ServiceHandles
+    implements java.io.Serializable
+{
+  private ext.vamsas.ServiceHandle[] services;
+
+  public ServiceHandles()
+  {
+  }
+
+  public ServiceHandles(
+      ext.vamsas.ServiceHandle[] services)
+  {
+    this.services = services;
+  }
+
+  /**
+   * Gets the services value for this ServiceHandles.
+   *
+   * @return services
+   */
+  public ext.vamsas.ServiceHandle[] getServices()
+  {
+    return services;
+  }
+
+  /**
+   * Sets the services value for this ServiceHandles.
+   *
+   * @param services
+   */
+  public void setServices(ext.vamsas.ServiceHandle[] services)
+  {
+    this.services = services;
+  }
+
+  private java.lang.Object __equalsCalc = null;
+  public synchronized boolean equals(java.lang.Object obj)
+  {
+    if (! (obj instanceof ServiceHandles))
+    {
+      return false;
     }
-
-    public ServiceHandles(
-           ext.vamsas.ServiceHandle[] services) {
-           this.services = services;
+    ServiceHandles other = (ServiceHandles) obj;
+    if (obj == null)
+    {
+      return false;
     }
-
-
-    /**
-     * Gets the services value for this ServiceHandles.
-     * 
-     * @return services
-     */
-    public ext.vamsas.ServiceHandle[] getServices() {
-        return services;
+    if (this == obj)
+    {
+      return true;
     }
-
-
-    /**
-     * Sets the services value for this ServiceHandles.
-     * 
-     * @param services
-     */
-    public void setServices(ext.vamsas.ServiceHandle[] services) {
-        this.services = services;
+    if (__equalsCalc != null)
+    {
+      return (__equalsCalc == obj);
     }
-
-    private java.lang.Object __equalsCalc = null;
-    public synchronized boolean equals(java.lang.Object obj) {
-        if (!(obj instanceof ServiceHandles)) return false;
-        ServiceHandles other = (ServiceHandles) obj;
-        if (obj == null) return false;
-        if (this == obj) return true;
-        if (__equalsCalc != null) {
-            return (__equalsCalc == obj);
-        }
-        __equalsCalc = obj;
-        boolean _equals;
-        _equals = true && 
-            ((this.services==null && other.getServices()==null) || 
-             (this.services!=null &&
-              java.util.Arrays.equals(this.services, other.getServices())));
-        __equalsCalc = null;
-        return _equals;
+    __equalsCalc = obj;
+    boolean _equals;
+    _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)
+    {
+      return 0;
     }
-
-    private boolean __hashCodeCalc = false;
-    public synchronized int hashCode() {
-        if (__hashCodeCalc) {
-            return 0;
-        }
-        __hashCodeCalc = true;
-        int _hashCode = 1;
-        if (getServices() != null) {
-            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()) {
-                    _hashCode += obj.hashCode();
-                }
-            }
+    __hashCodeCalc = true;
+    int _hashCode = 1;
+    if (getServices() != null)
+    {
+      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())
+        {
+          _hashCode += obj.hashCode();
         }
-        __hashCodeCalc = false;
-        return _hashCode;
+      }
     }
-
-    // Type metadata
-    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();
-        elemField.setFieldName("services");
-        elemField.setXmlName(new javax.xml.namespace.QName("", "services"));
-        elemField.setXmlType(new javax.xml.namespace.QName("registry.objects.vamsas", "ServiceHandle"));
-        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(
+    __hashCodeCalc = false;
+    return _hashCode;
+  }
+
+  // Type metadata
+  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();
+    elemField.setFieldName("services");
+    elemField.setXmlName(new javax.xml.namespace.QName("", "services"));
+    elemField.setXmlType(new javax.xml.namespace.QName(
+        "registry.objects.vamsas", "ServiceHandle"));
+    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(
+  }
+
+  /**
+   * 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/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 4a68f81..03cdc15 100755
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -1,27 +1,26 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 jalview.analysis;
 
-import jalview.datamodel.*;
-
 import java.util.*;
 
+import jalview.datamodel.*;
 
 /**
  * Takes in a vector or array of sequences and column start and column end
@@ -36,115 +35,122 @@ 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 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;
+  public static final String PID_NOGAPS = "N";
 
-  int[] values = new int[255];
+  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();
+      }
+    }
 
-  char [] seq;
+    Hashtable[] reply = new Hashtable[width];
 
-  for (i = start; i < end; i++)
+    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)
   {
-    residueHash = new Hashtable();
-    maxCount = 0;
-    maxResidue = "";
-    nongap = 0;
-    values = new int[255];
+    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 (j = 0; j < jSize; j++)
+    for (i = start; i < end; i++)
     {
-      seq = sequences[j].getSequence();
-      if (seq.length > i)
-      {
-        c = seq[i];
+      residueHash = new Hashtable();
+      maxCount = 0;
+      maxResidue = "";
+      nongap = 0;
+      values = new int[255];
 
-        if(c == '.' || c==' ')
-          c = '-';
+      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]++;
 
-        if(c=='-')
+        }
+        else
         {
           values['-']++;
-          continue;
         }
-        else if ('a' <= c && c <= 'z')
+      }
+
+      for (v = 'A'; v < 'Z'; v++)
+      {
+        if (values[v] < 2 || values[v] < maxCount)
         {
-          c -= 32 ;//('a' - 'A');
+          continue;
         }
 
-        nongap++;
-        values[c]++;
-
-      }
-      else
-      {
-        values['-']++;
+        if (values[v] > maxCount)
+        {
+          maxResidue = String.valueOf( (char) v);
+        }
+        else if (values[v] == maxCount)
+        {
+          maxResidue += String.valueOf( (char) v);
+        }
+        maxCount = values[v];
       }
-    }
-
-    for (v = 'A'; v < 'Z'; v++)
-    {
-      if (values[v] < 2 || values[v] < maxCount)
-        continue;
 
-      if (values[v] > maxCount)
+      if (maxResidue.length() == 0)
       {
-        maxResidue = String.valueOf( (char) v);
+        maxResidue = "-";
       }
-      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);
 
-    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) jSize;
-    residueHash.put(PID_GAPS, new Float(percentage));
-
-    percentage = ( (float) maxCount * 100) / (float) nongap;
-    residueHash.put(PID_NOGAPS, new Float(percentage));
-    result[i] = residueHash;
+      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 db549a4..2fcc593 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -1,33 +1,30 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 jalview.analysis;
 
-import jalview.datamodel.SequenceI;
-
-import jalview.schemes.*;
-
-import jalview.util.*;
+import java.util.*;
 
 import java.awt.*;
 
-import java.util.*;
-
+import jalview.datamodel.*;
+import jalview.schemes.*;
+import jalview.util.*;
 
 /**
  *
@@ -37,841 +34,853 @@ import java.util.*;
  */
 public class AlignSeq
 {
-    public static final String PEP = "pep";
-    public static final String DNA = "dna";
-    /** DOCUMENT ME!! */
-    public static java.util.Hashtable dnaHash = new java.util.Hashtable();
-
-    static
-    {
-        dnaHash.put("C", new Integer(0));
-        dnaHash.put("T", new Integer(1));
-        dnaHash.put("A", new Integer(2));
-        dnaHash.put("G", new Integer(3));
-        dnaHash.put("-", new Integer(4));
-    }
-
-    static String[] dna = { "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", "-"
-    };
-    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!! */
-    public int seq1start;
-
-    /** DOCUMENT ME!! */
-    public int seq1end;
-
-    /** DOCUMENT ME!! */
-    public int seq2start;
-
-    /** 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!
-     */
-    public AlignSeq(SequenceI s1, SequenceI s2, String 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!
-     */
-    public AlignSeq(SequenceI s1,
-                    String string1,
-                    SequenceI s2,
-                    String string2,
-                    String type)
+  public static final String PEP = "pep";
+  public static final String DNA = "dna";
+  /** DOCUMENT ME!! */
+  public static java.util.Hashtable dnaHash = new java.util.Hashtable();
+
+  static
+  {
+    dnaHash.put("C", new Integer(0));
+    dnaHash.put("T", new Integer(1));
+    dnaHash.put("A", new Integer(2));
+    dnaHash.put("G", new Integer(3));
+    dnaHash.put("-", new Integer(4));
+  }
+
+  static String[] dna =
+      {
+      "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", "-"
+  };
+  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!! */
+  public int seq1start;
+
+  /** DOCUMENT ME!! */
+  public int seq1end;
+
+  /** DOCUMENT ME!! */
+  public int seq2start;
+
+  /** 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!
+   */
+  public AlignSeq(SequenceI s1, SequenceI s2, String 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!
+   */
+  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()
+  {
+    return maxscore;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public int getSeq2Start()
+  {
+    return seq2start;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public int getSeq2End()
+  {
+    return seq2end;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public int getSeq1Start()
+  {
+    return seq1start;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public int getSeq1End()
+  {
+    return seq1end;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public String getOutput()
+  {
+    return output.toString();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public String getAStr1()
+  {
+    return astr1;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public String getAStr2()
+  {
+    return astr2;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public int[] getASeq1()
+  {
+    return aseq1;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public int[] getASeq2()
+  {
+    return aseq2;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public SequenceI getS1()
+  {
+    return s1;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public SequenceI getS2()
+  {
+    return s2;
+  }
+
+  /**
+   * 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
+   */
+  public void SeqInit(SequenceI s1,
+                      String string1,
+                      SequenceI s2,
+                      String string2,
+                      String type)
+  {
+    this.s1 = s1;
+    this.s2 = s2;
+    setDefaultParams(type);
+    SeqInit(string1, string2);
+  }
+
+  public void SeqInit(SequenceI s1,
+                      String string1,
+                      SequenceI s2,
+                      String string2,
+                      ScoreMatrix scoreMatrix)
+  {
+    this.s1 = s1;
+    this.s2 = s2;
+    setType(scoreMatrix.isDNA() ? AlignSeq.DNA : AlignSeq.PEP);
+    lookup = scoreMatrix.getMatrix();
+  }
+
+  /**
+   * construct score matrix for string1 and string2 (after removing any existing gaps
+   * @param string1
+   * @param string2
+   */
+  private void SeqInit(String string1, String string2)
+  {
+    s1str = extractGaps(jalview.util.Comparison.GapChars, string1);
+    s2str = extractGaps(jalview.util.Comparison.GapChars, string2);
+
+    if (s1str.length() == 0 || s2str.length() == 0)
     {
-        SeqInit(s1, string1, s2,  string2,  type);
+      output.append("ALL GAPS: " +
+                    (s1str.length() == 0 ? s1.getName() : " ")
+                    + (s2str.length() == 0 ? s2.getName() : ""));
+      return;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getMaxScore()
+    //System.out.println("lookuip " + rt.freeMemory() + " "+  rt.totalMemory());
+    seq1 = new int[s1str.length()];
+
+    //System.out.println("seq1 " + rt.freeMemory() +" "  + rt.totalMemory());
+    seq2 = new int[s2str.length()];
+
+    //System.out.println("seq2 " + rt.freeMemory() + " " + rt.totalMemory());
+    score = new int[s1str.length()][s2str.length()];
+
+    //System.out.println("score " + rt.freeMemory() + " " + rt.totalMemory());
+    E = new int[s1str.length()][s2str.length()];
+
+    //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());
+    seq1 = stringToInt(s1str, type);
+
+    //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();
+    // tstart = System.currentTimeMillis();
+    //traceAlignment();
+    //tend = System.currentTimeMillis();
+    //System.out.println("Time take to traceback alignment = " + (tend-tstart) + " ms");
+  }
+
+  private void setDefaultParams(String type)
+  {
+    setType(type);
+
+    if (type.equals(AlignSeq.PEP))
     {
-        return maxscore;
+      lookup = ResidueProperties.getDefaultPeptideMatrix();
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getSeq2Start()
+    else if (type.equals(AlignSeq.DNA))
     {
-        return seq2start;
+      lookup = ResidueProperties.getDefaultDnaMatrix();
     }
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getSeq2End()
+  private void setType(String type2)
+  {
+    this.type = type2;
+    if (type.equals(AlignSeq.PEP))
     {
-        return seq2end;
+      intToStr = pep;
+      defInt = 23;
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getSeq1Start()
+    else if (type.equals(AlignSeq.DNA))
     {
-        return seq1start;
+      intToStr = dna;
+      defInt = 4;
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getSeq1End()
+    else
     {
-        return seq1end;
+      output.append("Wrong type = dna or pep only");
+      throw new Error("Unknown Type " + type2 +
+                      " - dna or pep are the only allowed values.");
     }
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String getOutput()
-    {
-        return output.toString();
-    }
+  /**
+   * DOCUMENT ME!
+   */
+  public void traceAlignment()
+  {
+    // Find the maximum score along the rhs or bottom row
+    int max = -9999;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String getAStr1()
+    for (int i = 0; i < seq1.length; i++)
     {
-        return astr1;
+      if (score[i][seq2.length - 1] > max)
+      {
+        max = score[i][seq2.length - 1];
+        maxi = i;
+        maxj = seq2.length - 1;
+      }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String getAStr2()
+    for (int j = 0; j < seq2.length; j++)
     {
-        return astr2;
+      if (score[seq1.length - 1][j] > max)
+      {
+        max = score[seq1.length - 1][j];
+        maxi = seq1.length - 1;
+        maxj = j;
+      }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int[] getASeq1()
-    {
-        return aseq1;
-    }
+    //  System.out.println(maxi + " " + maxj + " " + score[maxi][maxj]);
+    int i = maxi;
+    int j = maxj;
+    int trace;
+    maxscore = score[i][j] / 10;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int[] getASeq2()
-    {
-        return aseq2;
-    }
+    seq1end = maxi + 1;
+    seq2end = maxj + 1;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public SequenceI getS1()
-    {
-        return s1;
-    }
+    aseq1 = new int[seq1.length + seq2.length];
+    aseq2 = new int[seq1.length + seq2.length];
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public SequenceI getS2()
-    {
-        return s2;
-    }
+    count = (seq1.length + seq2.length) - 1;
 
-    /**
-     * 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
-     */
-    public void SeqInit(SequenceI s1,
-                        String string1,
-                        SequenceI s2,
-                        String string2,
-                        String type)
+    while ( (i > 0) && (j > 0))
     {
-      this.s1 = s1;
-      this.s2 = s2;
-      setDefaultParams(type);
-      SeqInit(string1,string2);
-    }
-    public void SeqInit(SequenceI s1,
-        String string1,
-        SequenceI s2,
-        String string2,
-        ScoreMatrix scoreMatrix) { 
-      this.s1=s1;
-      this.s2=s2;
-      setType(scoreMatrix.isDNA() ? AlignSeq.DNA : AlignSeq.PEP);
-      lookup=scoreMatrix.getMatrix();
-    }
-    /**
-     * construct score matrix for string1 and string2 (after removing any existing gaps
-     * @param string1
-     * @param string2
-     */
-    private void SeqInit(String string1, String string2) {
-      s1str = extractGaps(jalview.util.Comparison.GapChars, string1);
-      s2str = extractGaps(jalview.util.Comparison.GapChars, string2);
-
-      if(s1str.length()==0 || s2str.length()==0)
+      if ( (aseq1[count] != defInt) && (i >= 0))
       {
-        output.append("ALL GAPS: " +
-                           (s1str.length()==0?s1.getName():" ")
-                           +(s2str.length()==0?s2.getName():""));
-        return;
+        aseq1[count] = seq1[i];
+        astr1 = intToStr[seq1[i]] + astr1;
       }
 
-      //System.out.println("lookuip " + rt.freeMemory() + " "+  rt.totalMemory());
-      seq1 = new int[s1str.length()];
-
-      //System.out.println("seq1 " + rt.freeMemory() +" "  + rt.totalMemory());
-      seq2 = new int[s2str.length()];
-
-      //System.out.println("seq2 " + rt.freeMemory() + " " + rt.totalMemory());
-      score = new int[s1str.length()][s2str.length()];
-
-      //System.out.println("score " + rt.freeMemory() + " " + rt.totalMemory());
-      E = new int[s1str.length()][s2str.length()];
-
-      //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());
-      seq1 = stringToInt(s1str, type);
-
-      //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();
-      // tstart = System.currentTimeMillis();
-      //traceAlignment();
-      //tend = System.currentTimeMillis();
-      //System.out.println("Time take to traceback alignment = " + (tend-tstart) + " ms");
-    }
+      if ( (aseq2[count] != defInt) && (j > 0))
+      {
+        aseq2[count] = seq2[j];
+        astr2 = intToStr[seq2[j]] + astr2;
+      }
 
-    private void setDefaultParams(String type) {
-        setType(type);
-        
-        if (type.equals(AlignSeq.PEP))
-        {
-            lookup = ResidueProperties.getDefaultPeptideMatrix();
-        }
-        else if (type.equals(AlignSeq.DNA))
-        {
-            lookup = ResidueProperties.getDefaultDnaMatrix();
-        }
-    }
+      trace = findTrace(i, j);
 
-    private void setType(String type2) {
-      this.type = type2;
-      if (type.equals(AlignSeq.PEP))
+      if (trace == 0)
       {
-          intToStr = pep;
-          defInt = 23;
+        i--;
+        j--;
       }
-      else if (type.equals(AlignSeq.DNA))
+      else if (trace == 1)
       {
-          intToStr = dna;
-          defInt = 4;
+        j--;
+        aseq1[count] = defInt;
+        astr1 = "-" + astr1.substring(1);
       }
-      else
+      else if (trace == -1)
       {
-          output.append("Wrong type = dna or pep only");
-          throw new Error("Unknown Type "+type2+" - dna or pep are the only allowed values.");
+        i--;
+        aseq2[count] = defInt;
+        astr2 = "-" + astr2.substring(1);
       }
-    }
 
-    /**
-     * DOCUMENT ME!
-     */
-    public void traceAlignment()
-    {
-        // Find the maximum score along the rhs or bottom row
-        int max = -9999;
+      count--;
+    }
 
-        for (int i = 0; i < seq1.length; i++)
-        {
-            if (score[i][seq2.length - 1] > max)
-            {
-                max = score[i][seq2.length - 1];
-                maxi = i;
-                maxj = seq2.length - 1;
-            }
-        }
+    seq1start = i + 1;
+    seq2start = j + 1;
 
-        for (int j = 0; j < seq2.length; j++)
-        {
-            if (score[seq1.length - 1][j] > max)
-            {
-                max = score[seq1.length - 1][j];
-                maxi = seq1.length - 1;
-                maxj = j;
-            }
-        }
+    if (aseq1[count] != defInt)
+    {
+      aseq1[count] = seq1[i];
+      astr1 = intToStr[seq1[i]] + astr1;
+    }
 
-        //  System.out.println(maxi + " " + maxj + " " + score[maxi][maxj]);
-        int i = maxi;
-        int j = maxj;
-        int trace;
-        maxscore = score[i][j] / 10;
+    if (aseq2[count] != defInt)
+    {
+      aseq2[count] = seq2[j];
+      astr2 = intToStr[seq2[j]] + astr2;
+    }
+  }
 
-        seq1end = maxi + 1;
-        seq2end = maxj + 1;
+  /**
+   * DOCUMENT ME!
+   */
+  public void printAlignment(java.io.PrintStream os)
+  {
+    // Find the biggest id length for formatting purposes
+    int maxid = s1.getName().length();
 
-        aseq1 = new int[seq1.length + seq2.length];
-        aseq2 = new int[seq1.length + seq2.length];
+    if (s2.getName().length() > maxid)
+    {
+      maxid = s2.getName().length();
+    }
 
-        count = (seq1.length + seq2.length) - 1;
+    int len = 72 - maxid - 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("Sequence ");
+    output.append(new Format("%" + maxid + "s").form(s2.getName()));
+    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()) + " ");
 
-        while ((i > 0) && (j > 0))
+      for (int i = 0; i < len; i++)
+      {
+        if ( (count + i + (j * len)) < aseq1.length)
         {
-            if ((aseq1[count] != defInt) && (i >= 0))
-            {
-                aseq1[count] = seq1[i];
-                astr1 = intToStr[seq1[i]] + astr1;
-            }
-
-            if ((aseq2[count] != defInt) && (j > 0))
-            {
-                aseq2[count] = seq2[j];
-                astr2 = intToStr[seq2[j]] + astr2;
-            }
+          output.append(new Format("%s").form(intToStr[aseq1[count + i +
+                                              (j * len)]]));
+        }
+      }
 
-            trace = findTrace(i, j);
+      output.append("\n");
+      output.append(new Format("%" + (maxid) + "s").form(" ") + " ");
 
-            if (trace == 0)
-            {
-                i--;
-                j--;
-            }
-            else if (trace == 1)
+      // Print out the matching chars
+      for (int i = 0; i < len; i++)
+      {
+        if ( (count + i + (j * len)) < aseq1.length)
+        {
+          if (intToStr[aseq1[count + i + (j * len)]].equals(
+              intToStr[aseq2[count + i + (j * len)]]) &&
+              !intToStr[aseq1[count + i + (j * len)]].equals("-"))
+          {
+            pid++;
+            output.append("|");
+          }
+          else if (type.equals("pep"))
+          {
+            if (ResidueProperties.getPAM250(
+                intToStr[aseq1[count + i + (j * len)]],
+                intToStr[aseq2[count + i + (j * len)]]) > 0)
             {
-                j--;
-                aseq1[count] = defInt;
-                astr1 = "-" + astr1.substring(1);
+              output.append(".");
             }
-            else if (trace == -1)
+            else
             {
-                i--;
-                aseq2[count] = defInt;
-                astr2 = "-" + astr2.substring(1);
+              output.append(" ");
             }
-
-            count--;
+          }
+          else
+          {
+            output.append(" ");
+          }
         }
+      }
 
-        seq1start = i + 1;
-        seq2start = j + 1;
+      // Now print the second aligned sequence
+      output = output.append("\n");
+      output = output.append(new Format("%" + (maxid) + "s").form(s2.getName()) +
+                             " ");
 
-        if (aseq1[count] != defInt)
+      for (int i = 0; i < len; i++)
+      {
+        if ( (count + i + (j * len)) < aseq1.length)
         {
-            aseq1[count] = seq1[i];
-            astr1 = intToStr[seq1[i]] + astr1;
+          output.append(new Format("%s").form(intToStr[aseq2[count + i +
+                                              (j * len)]]));
         }
+      }
 
-        if (aseq2[count] != defInt)
-        {
-            aseq2[count] = seq2[j];
-            astr2 = intToStr[seq2[j]] + astr2;
-        }
+      output = output.append("\n\n");
     }
 
-    /**
-     * DOCUMENT ME!
-     */
-    public void printAlignment(java.io.PrintStream os)
+    pid = pid / (float) (aseq1.length - count) * 100;
+    output = output.append(new Format("Percentage ID = %2.2f\n\n").form(pid));
+
+    try
+    {
+      os.print(output.toString());
+    }
+    catch (Exception ex)
+    {}
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param mat DOCUMENT ME!
+   */
+  public void printScoreMatrix(int[][] mat)
+  {
+    int n = seq1.length;
+    int m = seq2.length;
+
+    for (int i = 0; i < n; i++)
     {
-        // Find the biggest id length for formatting purposes
-        int maxid = s1.getName().length();
+      // Print the top sequence
+      if (i == 0)
+      {
+        Format.print(System.out, "%8s", s2str.substring(0, 1));
 
-        if (s2.getName().length() > maxid)
+        for (int jj = 1; jj < m; jj++)
         {
-            maxid = s2.getName().length();
+          Format.print(System.out, "%5s", s2str.substring(jj, jj + 1));
         }
 
-        int len = 72 - maxid - 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("Sequence ");
-        output.append(new Format("%" + maxid + "s").form(s2.getName()));
-        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()) + " ");
-
-            for (int i = 0; i < len; i++)
-            {
-                if ((count + i + (j * len)) < aseq1.length)
-                {
-                    output.append(new Format("%s").form(intToStr[aseq1[count + i +
-                            (j * len)]]));
-                }
-            }
-
-            output.append("\n");
-            output.append(new Format("%" + (maxid) + "s").form(" ") + " ");
-
-            // Print out the matching chars
-            for (int i = 0; i < len; i++)
-            {
-                if ((count + i + (j * len)) < aseq1.length)
-                {
-                    if (intToStr[aseq1[count + i + (j * len)]].equals(
-                                intToStr[aseq2[count + i + (j * len)]]) &&
-                            !intToStr[aseq1[count + i + (j * len)]].equals("-"))
-                    {
-                        pid++;
-                        output.append("|");
-                    }
-                    else if (type.equals("pep"))
-                    {
-                        if (ResidueProperties.getPAM250(
-                                    intToStr[aseq1[count + i + (j * len)]],
-                                    intToStr[aseq2[count + i + (j * len)]]) > 0)
-                        {
-                            output.append(".");
-                        }
-                        else
-                        {
-                            output.append(" ");
-                        }
-                    }
-                    else
-                    {
-                        output.append(" ");
-                    }
-                }
-            }
-
-            // Now print the second aligned sequence
-            output = output.append("\n");
-            output = output.append(new Format("%" + (maxid) + "s").form(s2.getName()) + " ");
-
-            for (int i = 0; i < len; i++)
-            {
-                if ((count + i + (j * len)) < aseq1.length)
-                {
-                    output .append(new Format("%s").form(intToStr[aseq2[count + i +
-                            (j * len)]]));
-                }
-            }
+        System.out.println();
+      }
 
-            output = output .append("\n\n");
+      for (int j = 0; j < m; j++)
+      {
+        if (j == 0)
+        {
+          Format.print(System.out, "%3s", s1str.substring(i, i + 1));
         }
 
-        pid = pid / (float) (aseq1.length - count) * 100;
-        output = output.append(new Format("Percentage ID = %2.2f\n\n").form(pid));
+        Format.print(System.out, "%3d ", mat[i][j] / 10);
+      }
 
-        try{
-          os.print(output.toString());
-        }catch(Exception ex){}
+      System.out.println();
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param mat DOCUMENT ME!
-     */
-    public void printScoreMatrix(int[][] mat)
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param i DOCUMENT ME!
+   * @param j DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public int findTrace(int i, int j)
+  {
+    int t = 0;
+    int max = score[i - 1][j - 1] + (lookup[seq1[i]][seq2[j]] * 10);
+
+    if (F[i][j] > max)
     {
-        int n = seq1.length;
-        int m = seq2.length;
-
-        for (int i = 0; i < n; i++)
-        {
-            // Print the top sequence
-            if (i == 0)
-            {
-                Format.print(System.out, "%8s", s2str.substring(0, 1));
+      max = F[i][j];
+      t = -1;
+    }
+    else if (F[i][j] == max)
+    {
+      if (prev == -1)
+      {
+        max = F[i][j];
+        t = -1;
+      }
+    }
 
-                for (int jj = 1; jj < m; jj++)
-                {
-                    Format.print(System.out, "%5s", s2str.substring(jj, jj + 1));
-                }
+    if (E[i][j] >= max)
+    {
+      max = E[i][j];
+      t = 1;
+    }
+    else if (E[i][j] == max)
+    {
+      if (prev == 1)
+      {
+        max = E[i][j];
+        t = 1;
+      }
+    }
 
-                System.out.println();
-            }
+    prev = t;
 
-            for (int j = 0; j < m; j++)
-            {
-                if (j == 0)
-                {
-                    Format.print(System.out, "%3s", s1str.substring(i, i + 1));
-                }
+    return t;
+  }
 
-                Format.print(System.out, "%3d ", mat[i][j] / 10);
-            }
+  /**
+   * DOCUMENT ME!
+   */
+  public void calcScoreMatrix()
+  {
+    int n = seq1.length;
+    int m = seq2.length;
 
-            System.out.println();
-        }
-    }
+    // top left hand element
+    score[0][0] = lookup[seq1[0]][seq2[0]] * 10;
+    E[0][0] = -gapExtend;
+    F[0][0] = 0;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     * @param j DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int findTrace(int i, int j)
+    // Calculate the top row first
+    for (int j = 1; j < m; j++)
     {
-        int t = 0;
-        int max = score[i - 1][j - 1] + (lookup[seq1[i]][seq2[j]] * 10);
+      // What should these values be? 0 maybe
+      E[0][j] = max(score[0][j - 1] - gapOpen, E[0][j - 1] - gapExtend);
+      F[0][j] = -gapExtend;
 
-        if (F[i][j] > max)
-        {
-            max = F[i][j];
-            t = -1;
-        }
-        else if (F[i][j] == max)
-        {
-            if (prev == -1)
-            {
-                max = F[i][j];
-                t = -1;
-            }
-        }
+      score[0][j] = max(lookup[seq1[0]][seq2[j]] * 10, -gapOpen,
+                        -gapExtend);
 
-        if (E[i][j] >= max)
-        {
-            max = E[i][j];
-            t = 1;
-        }
-        else if (E[i][j] == max)
-        {
-            if (prev == 1)
-            {
-                max = E[i][j];
-                t = 1;
-            }
-        }
+      traceback[0][j] = 1;
+    }
 
-        prev = t;
+    // Now do the left hand column
+    for (int i = 1; i < n; i++)
+    {
+      E[i][0] = -gapOpen;
+      F[i][0] = max(score[i - 1][0] - gapOpen, F[i - 1][0] - gapExtend);
 
-        return t;
+      score[i][0] = max(lookup[seq1[i]][seq2[0]] * 10, E[i][0], F[i][0]);
+      traceback[i][0] = -1;
     }
 
-    /**
-     * DOCUMENT ME!
-     */
-    public void calcScoreMatrix()
+    // Now do all the other rows
+    for (int i = 1; i < n; i++)
+    {
+      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);
+
+        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);
+      }
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param gapChar DOCUMENT ME!
+   * @param seq DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public static String extractGaps(String gapChar, String seq)
+  {
+    StringTokenizer str = new StringTokenizer(seq, gapChar);
+    StringBuffer newString = new StringBuffer();
+
+    while (str.hasMoreTokens())
     {
-        int n = seq1.length;
-        int m = seq2.length;
+      newString.append(str.nextToken());
+    }
 
-        // top left hand element
-        score[0][0] = lookup[seq1[0]][seq2[0]] * 10;
-        E[0][0] = -gapExtend;
-        F[0][0] = 0;
+    return newString.toString();
+  }
+
+  /**
+   * 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)
+  {
+    int max = i1;
+
+    if (i2 > i1)
+    {
+      max = i2;
+    }
 
-        // Calculate the top row first
-        for (int j = 1; j < m; j++)
-        {
-            // What should these values be? 0 maybe
-            E[0][j] = max(score[0][j - 1] - gapOpen, E[0][j - 1] - gapExtend);
-            F[0][j] = -gapExtend;
+    if (i3 > max)
+    {
+      max = i3;
+    }
 
-            score[0][j] = max(lookup[seq1[0]][seq2[j]] * 10, -gapOpen,
-                    -gapExtend);
+    return max;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param i1 DOCUMENT ME!
+   * @param i2 DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public int max(int i1, int i2)
+  {
+    int max = i1;
+
+    if (i2 > i1)
+    {
+      max = i2;
+    }
 
-            traceback[0][j] = 1;
-        }
+    return max;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param s DOCUMENT ME!
+   * @param type DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public int[] stringToInt(String s, String type)
+  {
+    int[] seq1 = new int[s.length()];
+
+    for (int i = 0; i < s.length(); i++)
+    {
+      // String ss = s.substring(i, i + 1).toUpperCase();
+      char c = s.charAt(i);
+      if ('a' <= c && c <= 'z')
+      {
+        // TO UPPERCASE !!!
+        c -= ('a' - 'A');
+      }
 
-        // Now do the left hand column
-        for (int i = 1; i < n; i++)
+      try
+      {
+        if (type.equals("pep"))
         {
-            E[i][0] = -gapOpen;
-            F[i][0] = max(score[i - 1][0] - gapOpen, F[i - 1][0] - gapExtend);
-
-            score[i][0] = max(lookup[seq1[i]][seq2[0]] * 10, E[i][0], F[i][0]);
-            traceback[i][0] = -1;
+          seq1[i] = ResidueProperties.aaIndex[c];
         }
-
-        // Now do all the other rows
-        for (int i = 1; i < n; i++)
+        else if (type.equals("dna"))
         {
-            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);
-
-                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);
-            }
+          seq1[i] = ResidueProperties.nucleotideIndex[c];
         }
-    }
 
-
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param gapChar DOCUMENT ME!
-     * @param seq DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public static String extractGaps(String gapChar, String seq)
-    {
-        StringTokenizer str = new StringTokenizer(seq, gapChar);
-        StringBuffer newString = new StringBuffer();
-
-        while (str.hasMoreTokens())
+        if (seq1[i] > 23)
         {
-            newString.append( str.nextToken() );
+          seq1[i] = 23;
         }
-
-        return newString.toString();
-    }
-
-    /**
-     * 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)
-    {
-        int max = i1;
-
-        if (i2 > i1)
+      }
+      catch (Exception e)
+      {
+        if (type.equals("dna"))
         {
-            max = i2;
+          seq1[i] = 4;
         }
-
-        if (i3 > max)
+        else
         {
-            max = i3;
+          seq1[i] = 23;
         }
-
-        return max;
+      }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i1 DOCUMENT ME!
-     * @param i2 DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int max(int i1, int i2)
+    return seq1;
+  }
+
+  /**
+   * 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 max = -1000;
+    int min = 1000;
+
+    for (int i = 0; i < n; i++)
     {
-        int max = i1;
-
-        if (i2 > i1)
+      for (int j = 0; j < m; j++)
+      {
+        if (mat[i][j] >= max)
         {
-            max = i2;
+          max = mat[i][j];
         }
 
-        return max;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param s DOCUMENT ME!
-     * @param type DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int[] stringToInt(String s, String type)
-    {
-        int[] seq1 = new int[s.length()];
-
-        for (int i = 0; i < s.length(); i++)
+        if (mat[i][j] <= min)
         {
-           // String ss = s.substring(i, i + 1).toUpperCase();
-            char c = s.charAt(i);
-            if ('a' <= c && c <= 'z')
-            {
-              // TO UPPERCASE !!!
-              c -= ('a' - 'A');
-            }
-
-
-            try
-            {
-                if (type.equals("pep"))
-                {
-                    seq1[i] = ResidueProperties.aaIndex[c];
-                }
-                else if (type.equals("dna"))
-                {
-                    seq1[i] = ResidueProperties.nucleotideIndex[c];
-                }
-
-                if (seq1[i] > 23)
-                {
-                    seq1[i] = 23;
-                }
-            }
-            catch (Exception e)
-            {
-                if (type.equals("dna"))
-                {
-                    seq1[i] = 4;
-                }
-                else
-                {
-                    seq1[i] = 23;
-                }
-            }
+          min = mat[i][j];
         }
-
-        return seq1;
+      }
     }
 
-    /**
-     * 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 max = -1000;
-        int min = 1000;
+    System.out.println(max + " " + min);
 
-        for (int i = 0; i < n; i++)
-        {
-            for (int j = 0; j < m; j++)
-            {
-                if (mat[i][j] >= max)
-                {
-                    max = mat[i][j];
-                }
-
-                if (mat[i][j] <= min)
-                {
-                    min = mat[i][j];
-                }
-            }
-        }
-
-        System.out.println(max + " " + min);
-
-        for (int i = 0; i < n; i++)
-        {
-            for (int j = 0; j < m; j++)
-            {
-                int x = psize * i;
-                int y = psize * j;
+    for (int i = 0; i < n; i++)
+    {
+      for (int j = 0; j < m; j++)
+      {
+        int x = psize * i;
+        int y = psize * 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(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 778142c..ea8d4e5 100755
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -1,483 +1,486 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 jalview.analysis;
 
-import jalview.datamodel.*;
-
-import jalview.util.*;
-
 import java.util.*;
 
+import jalview.datamodel.*;
+import jalview.util.*;
 
 /** Data structure to hold and manipulate a multiple sequence alignment
  */
 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;
-
-    /**
-     * Sort by Percentage Identity
-     *
-     * @param align AlignmentI
-     * @param s SequenceI
-     */
-    public static void sortByPID(AlignmentI align, SequenceI s)
-    {
-        int nSeq = align.getHeight();
-
-        float[] scores = new float[nSeq];
-        SequenceI[] seqs = new SequenceI[nSeq];
-
-        for (int i = 0; i < nSeq; i++)
-        {
-            scores[i] = Comparison.PID(align.getSequenceAt(i).getSequenceAsString(),
-                                       s.getSequenceAsString());
-            seqs[i] = align.getSequenceAt(i);
-        }
-
-        QuickSort.sort(scores, 0, scores.length - 1, seqs);
-
-        setReverseOrder(align, seqs);
+  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;
+
+  /**
+   * Sort by Percentage Identity
+   *
+   * @param align AlignmentI
+   * @param s SequenceI
+   */
+  public static void sortByPID(AlignmentI align, SequenceI s)
+  {
+    int nSeq = align.getHeight();
+
+    float[] scores = new float[nSeq];
+    SequenceI[] seqs = new SequenceI[nSeq];
+
+    for (int i = 0; i < nSeq; i++)
+    {
+      scores[i] = Comparison.PID(align.getSequenceAt(i).getSequenceAsString(),
+                                 s.getSequenceAsString());
+      seqs[i] = align.getSequenceAt(i);
     }
 
-    /**
-     * Reverse the order of the sort
-     *
-     * @param align DOCUMENT ME!
-     * @param seqs DOCUMENT ME!
-     */
-    private static void setReverseOrder(AlignmentI align, SequenceI[] seqs)
-    {
-        int nSeq = seqs.length;
+    QuickSort.sort(scores, 0, scores.length - 1, seqs);
 
-        int len = 0;
+    setReverseOrder(align, seqs);
+  }
 
-        if ((nSeq % 2) == 0)
-        {
-            len = nSeq / 2;
-        }
-        else
-        {
-            len = (nSeq + 1) / 2;
-        }
+  /**
+   * Reverse the order of the sort
+   *
+   * @param align DOCUMENT ME!
+   * @param seqs DOCUMENT ME!
+   */
+  private static void setReverseOrder(AlignmentI align, SequenceI[] seqs)
+  {
+    int nSeq = seqs.length;
 
-        // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
-        for (int i = 0; i < len; i++)
-        {
-            //SequenceI tmp = seqs[i];
-            align.getSequences().setElementAt(seqs[nSeq - i - 1], i);
-            align.getSequences().setElementAt(seqs[i], nSeq - i - 1);
-        }
+    int len = 0;
+
+    if ( (nSeq % 2) == 0)
+    {
+      len = nSeq / 2;
+    }
+    else
+    {
+      len = (nSeq + 1) / 2;
     }
 
-    /**
-     * Sets the Alignment object with the given sequences
-     *
-     * @param align Alignment object to be updated
-     * @param tmp sequences as a vector
-     */
-    private static void setOrder(AlignmentI align, Vector tmp)
+    // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
+    for (int i = 0; i < len; i++)
+    {
+      //SequenceI tmp = seqs[i];
+      align.getSequences().setElementAt(seqs[nSeq - i - 1], i);
+      align.getSequences().setElementAt(seqs[i], nSeq - i - 1);
+    }
+  }
+
+  /**
+   * Sets the Alignment object with the given sequences
+   *
+   * @param align Alignment object to be updated
+   * @param tmp sequences as a vector
+   */
+  private static void setOrder(AlignmentI align, Vector tmp)
+  {
+    setOrder(align, vectorSubsetToArray(tmp, align.getSequences()));
+  }
+
+  /**
+   * Sets the Alignment object with the given sequences
+   *
+   * @param align DOCUMENT ME!
+   * @param seqs sequences as an array
+   */
+  public static void setOrder(AlignmentI align, SequenceI[] seqs)
+  {
+    // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
+    Vector algn = align.getSequences();
+    Vector tmp = new Vector();
+
+    for (int i = 0; i < seqs.length; i++)
     {
-        setOrder(align, vectorSubsetToArray(tmp, align.getSequences()));
+      if (algn.contains(seqs[i]))
+      {
+        tmp.addElement(seqs[i]);
+      }
     }
 
-    /**
-     * Sets the Alignment object with the given sequences
-     *
-     * @param align DOCUMENT ME!
-     * @param seqs sequences as an array
-     */
-    public static void setOrder(AlignmentI align, SequenceI[] seqs)
+    algn.removeAllElements();
+    //User may have hidden seqs, then clicked undo or redo
+    for (int i = 0; i < tmp.size(); i++)
     {
-        // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
-        Vector algn = align.getSequences();
-        Vector tmp = new Vector();
+      algn.addElement(tmp.elementAt(i));
+    }
 
-        for (int i = 0; i < seqs.length; i++)
-        {
-          if(algn.contains(seqs[i]))
-            tmp.addElement(seqs[i]);
-        }
+  }
 
-        algn.removeAllElements();
-        //User may have hidden seqs, then clicked undo or redo
-        for (int i = 0; i < tmp.size(); i++)
-        {
-          algn.addElement(tmp.elementAt(i));
-        }
+  /**
+   * Sorts by ID. Numbers are sorted before letters.
+   *
+   * @param align The alignment object to sort
+   */
+  public static void sortByID(AlignmentI align)
+  {
+    int nSeq = align.getHeight();
 
+    String[] ids = new String[nSeq];
+    SequenceI[] seqs = new SequenceI[nSeq];
 
+    for (int i = 0; i < nSeq; i++)
+    {
+      ids[i] = align.getSequenceAt(i).getName();
+      seqs[i] = align.getSequenceAt(i);
+    }
 
+    QuickSort.sort(ids, seqs);
 
+    if (sortIdAscending)
+    {
+      setReverseOrder(align, seqs);
     }
-
-    /**
-     * Sorts by ID. Numbers are sorted before letters.
-     *
-     * @param align The alignment object to sort
-     */
-    public static void sortByID(AlignmentI align)
+    else
     {
-        int nSeq = align.getHeight();
-
-        String[] ids = new String[nSeq];
-        SequenceI[] seqs = new SequenceI[nSeq];
-
-        for (int i = 0; i < nSeq; i++)
-        {
-            ids[i] = align.getSequenceAt(i).getName();
-            seqs[i] = align.getSequenceAt(i);
-        }
-
-        QuickSort.sort(ids, seqs);
-
-        if (sortIdAscending)
-        {
-            setReverseOrder(align, seqs);
-        }
-        else
-        {
-            setOrder(align, seqs);
-        }
+      setOrder(align, seqs);
+    }
 
-        sortIdAscending = !sortIdAscending;
+    sortIdAscending = !sortIdAscending;
+  }
+
+  /**
+   * 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
+    Vector groups = new Vector();
+
+    if (groups.hashCode() != lastGroupHash)
+    {
+      sortGroupAscending = true;
+      lastGroupHash = groups.hashCode();
+    }
+    else
+    {
+      sortGroupAscending = !sortGroupAscending;
     }
 
-    /**
-     * 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)
+    //SORTS GROUPS BY SIZE
+    //////////////////////
+    for (int i = 0; i < align.getGroups().size(); i++)
     {
-        //MAINTAINS ORIGNAL SEQUENCE ORDER,
-        //ORDERS BY GROUP SIZE
-        Vector groups = new Vector();
+      SequenceGroup sg = (SequenceGroup) align.getGroups().elementAt(i);
 
-        if (groups.hashCode() != lastGroupHash)
-        {
-            sortGroupAscending = true;
-            lastGroupHash = groups.hashCode();
-        }
-        else
-        {
-            sortGroupAscending = !sortGroupAscending;
-        }
+      for (int j = 0; j < groups.size(); j++)
+      {
+        SequenceGroup sg2 = (SequenceGroup) groups.elementAt(j);
 
-        //SORTS GROUPS BY SIZE
-        //////////////////////
-        for (int i = 0; i < align.getGroups().size(); i++)
+        if (sg.getSize() > sg2.getSize())
         {
-            SequenceGroup sg = (SequenceGroup) align.getGroups().elementAt(i);
-
-            for (int j = 0; j < groups.size(); j++)
-            {
-                SequenceGroup sg2 = (SequenceGroup) groups.elementAt(j);
-
-                if (sg.getSize() > sg2.getSize())
-                {
-                    groups.insertElementAt(sg, j);
+          groups.insertElementAt(sg, j);
 
-                    break;
-                }
-            }
-
-            if (!groups.contains(sg))
-            {
-                groups.addElement(sg);
-            }
+          break;
         }
+      }
 
-        //NOW ADD SEQUENCES MAINTAINING ALIGNMENT ORDER
-        ///////////////////////////////////////////////
-        Vector seqs = new Vector();
+      if (!groups.contains(sg))
+      {
+        groups.addElement(sg);
+      }
+    }
 
-        for (int i = 0; i < groups.size(); i++)
-        {
-            SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
-            SequenceI[] orderedseqs = sg.getSequencesInOrder(align);
+    //NOW ADD SEQUENCES MAINTAINING ALIGNMENT ORDER
+    ///////////////////////////////////////////////
+    Vector seqs = new Vector();
 
-            for (int j = 0; j < orderedseqs.length; j++)
-            {
-                seqs.addElement(orderedseqs[j]);
-            }
-        }
+    for (int i = 0; i < groups.size(); i++)
+    {
+      SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
+      SequenceI[] orderedseqs = sg.getSequencesInOrder(align);
 
-        if (sortGroupAscending)
-        {
-            setOrder(align, seqs);
-        }
-        else
-        {
-            setReverseOrder(align,
-                vectorSubsetToArray(seqs, align.getSequences()));
-        }
+      for (int j = 0; j < orderedseqs.length; j++)
+      {
+        seqs.addElement(orderedseqs[j]);
+      }
     }
 
-    /**
-     * 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)
+    if (sortGroupAscending)
     {
-        SequenceI[] seqs = new SequenceI[tmp.size()];
-
-        for (int i = 0; i < tmp.size(); i++)
-        {
-            seqs[i] = (SequenceI) tmp.elementAt(i);
-        }
-
-        return seqs;
+      setOrder(align, seqs);
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param tmp DOCUMENT ME!
-     * @param mask DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    private static SequenceI[] vectorSubsetToArray(Vector tmp, Vector mask)
+    else
     {
-        Vector seqs = new Vector();
-        int i;
-        boolean[] tmask = new boolean[mask.size()];
-
-        for (i = 0; i < mask.size(); i++)
-            tmask[i] = true;
-
-        for (i = 0; i < tmp.size(); i++)
-        {
-            Object sq = tmp.elementAt(i);
+      setReverseOrder(align,
+                      vectorSubsetToArray(seqs, align.getSequences()));
+    }
+  }
+
+  /**
+   * 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)
+  {
+    SequenceI[] seqs = new SequenceI[tmp.size()];
+
+    for (int i = 0; i < tmp.size(); i++)
+    {
+      seqs[i] = (SequenceI) tmp.elementAt(i);
+    }
 
-            if (mask.contains(sq) && tmask[mask.indexOf(sq)])
-            {
-                tmask[mask.indexOf(sq)] = false;
-                seqs.addElement(sq);
-            }
-        }
+    return seqs;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param tmp DOCUMENT ME!
+   * @param mask DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  private static SequenceI[] vectorSubsetToArray(Vector tmp, Vector mask)
+  {
+    Vector seqs = new Vector();
+    int i;
+    boolean[] tmask = new boolean[mask.size()];
+
+    for (i = 0; i < mask.size(); i++)
+    {
+      tmask[i] = true;
+    }
 
-        for (i = 0; i < tmask.length; i++)
-            if (tmask[i])
-            {
-                seqs.addElement(mask.elementAt(i));
-            }
+    for (i = 0; i < tmp.size(); i++)
+    {
+      Object sq = tmp.elementAt(i);
 
-        return vectorToArray(seqs);
+      if (mask.contains(sq) && tmask[mask.indexOf(sq)])
+      {
+        tmask[mask.indexOf(sq)] = false;
+        seqs.addElement(sq);
+      }
     }
 
-    /**
-     * Sorts by a given AlignmentOrder object
-     *
-     * @param align Alignment to order
-     * @param order specified order for alignment
-     */
-    public static void sortBy(AlignmentI align, AlignmentOrder order)
+    for (i = 0; i < tmask.length; i++)
     {
-        // Get an ordered vector of sequences which may also be present in align
-        Vector tmp = order.getOrder();
-
-        if (lastOrder == order)
-        {
-            sortOrderAscending = !sortOrderAscending;
-        }
-        else
-        {
-            sortOrderAscending = true;
-        }
+      if (tmask[i])
+      {
+        seqs.addElement(mask.elementAt(i));
+      }
+    }
 
-        if (sortOrderAscending)
-        {
-            setOrder(align, tmp);
-        }
-        else
-        {
-            setReverseOrder(align,
-                vectorSubsetToArray(tmp, align.getSequences()));
-        }
+    return vectorToArray(seqs);
+  }
+
+  /**
+   * Sorts by a given AlignmentOrder object
+   *
+   * @param align Alignment to order
+   * @param order specified order for alignment
+   */
+  public static void sortBy(AlignmentI align, AlignmentOrder order)
+  {
+    // Get an ordered vector of sequences which may also be present in align
+    Vector tmp = order.getOrder();
+
+    if (lastOrder == order)
+    {
+      sortOrderAscending = !sortOrderAscending;
+    }
+    else
+    {
+      sortOrderAscending = true;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param align alignment to order
-     * @param tree tree which has
-     *
-     * @return DOCUMENT ME!
-     */
-    private static Vector getOrderByTree(AlignmentI align, NJTree tree)
+    if (sortOrderAscending)
     {
-        int nSeq = align.getHeight();
+      setOrder(align, tmp);
+    }
+    else
+    {
+      setReverseOrder(align,
+                      vectorSubsetToArray(tmp, align.getSequences()));
+    }
+  }
 
-        Vector tmp = new Vector();
+  /**
+   * DOCUMENT ME!
+   *
+   * @param align alignment to order
+   * @param tree tree which has
+   *
+   * @return DOCUMENT ME!
+   */
+  private static Vector getOrderByTree(AlignmentI align, NJTree tree)
+  {
+    int nSeq = align.getHeight();
 
-        tmp = _sortByTree(tree.getTopNode(), tmp, align.getSequences());
+    Vector tmp = new Vector();
 
-        if (tmp.size() != nSeq)
-        {
-            // TODO: JBPNote - decide if this is always an error
-            // (eg. not when a tree is associated to another alignment which has more
-            //  sequences)
-            if (tmp.size() < nSeq)
-            {
-                addStrays(align, tmp);
-            }
-
-            if (tmp.size() != nSeq)
-            {
-                System.err.println("ERROR: tmp.size()=" + tmp.size() +
-                    " != nseq=" + nSeq + " in getOrderByTree");
-            }
-        }
+    tmp = _sortByTree(tree.getTopNode(), tmp, align.getSequences());
 
-        return tmp;
+    if (tmp.size() != nSeq)
+    {
+      // TODO: JBPNote - decide if this is always an error
+      // (eg. not when a tree is associated to another alignment which has more
+      //  sequences)
+      if (tmp.size() < nSeq)
+      {
+        addStrays(align, tmp);
+      }
+
+      if (tmp.size() != nSeq)
+      {
+        System.err.println("ERROR: tmp.size()=" + tmp.size() +
+                           " != nseq=" + nSeq + " in getOrderByTree");
+      }
     }
 
-    /**
-     * Sorts the alignment by a given tree
-     *
-     * @param align alignment to order
-     * @param tree tree which has
-     */
-    public static void sortByTree(AlignmentI align, NJTree tree)
+    return tmp;
+  }
+
+  /**
+   * Sorts the alignment by a given tree
+   *
+   * @param align alignment to order
+   * @param tree tree which has
+   */
+  public static void sortByTree(AlignmentI align, NJTree tree)
+  {
+    Vector tmp = getOrderByTree(align, tree);
+
+    // tmp should properly permute align with tree.
+    if (lastTree != tree)
     {
-        Vector tmp = getOrderByTree(align, tree);
-
-        // tmp should properly permute align with tree.
-        if (lastTree != tree)
-        {
-            sortTreeAscending = true;
-            lastTree = tree;
-        }
-        else
-        {
-            sortTreeAscending = !sortTreeAscending;
-        }
-
-        if (sortTreeAscending)
-        {
-            setOrder(align, tmp);
-        }
-        else
-        {
-            setReverseOrder(align,
-                vectorSubsetToArray(tmp, align.getSequences()));
-        }
+      sortTreeAscending = true;
+      lastTree = tree;
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param align DOCUMENT ME!
-     * @param seqs DOCUMENT ME!
-     */
-    private static void addStrays(AlignmentI align, Vector seqs)
+    else
     {
-        int nSeq = align.getHeight();
-
-        for (int i = 0; i < nSeq; i++)
-        {
-            if (!seqs.contains(align.getSequenceAt(i)))
-            {
-                seqs.addElement(align.getSequenceAt(i));
-            }
-        }
+      sortTreeAscending = !sortTreeAscending;
+    }
 
-        if (nSeq != seqs.size())
-        {
-            System.err.println(
-                "ERROR: Size still not right even after addStrays");
-        }
+    if (sortTreeAscending)
+    {
+      setOrder(align, tmp);
+    }
+    else
+    {
+      setReverseOrder(align,
+                      vectorSubsetToArray(tmp, align.getSequences()));
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param align DOCUMENT ME!
+   * @param seqs DOCUMENT ME!
+   */
+  private static void addStrays(AlignmentI align, Vector seqs)
+  {
+    int nSeq = align.getHeight();
+
+    for (int i = 0; i < nSeq; i++)
+    {
+      if (!seqs.contains(align.getSequenceAt(i)))
+      {
+        seqs.addElement(align.getSequenceAt(i));
+      }
     }
 
-    /**
-     * 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)
+    if (nSeq != seqs.size())
     {
-        if (node == null)
-        {
-            return tmp;
-        }
+      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!
+   *
+   * @return DOCUMENT ME!
+   */
+  private static Vector _sortByTree(SequenceNode node, Vector tmp,
+                                    Vector seqset)
+  {
+    if (node == null)
+    {
+      return tmp;
+    }
 
-        SequenceNode left = (SequenceNode) node.left();
-        SequenceNode right = (SequenceNode) node.right();
+    SequenceNode left = (SequenceNode) node.left();
+    SequenceNode right = (SequenceNode) node.right();
 
-        if ((left == null) && (right == null))
-        {
-            if (!node.isPlaceholder() && (node.element() != null))
-            {
-                if (node.element() instanceof SequenceI)
-                {
-                    if (!tmp.contains(node.element()))
-                    {
-                        tmp.addElement((SequenceI) node.element());
-                    }
-                }
-            }
-
-            return tmp;
-        }
-        else
+    if ( (left == null) && (right == null))
+    {
+      if (!node.isPlaceholder() && (node.element() != null))
+      {
+        if (node.element() instanceof SequenceI)
         {
-            _sortByTree(left, tmp, seqset);
-            _sortByTree(right, tmp, seqset);
+          if (!tmp.contains(node.element()))
+          {
+            tmp.addElement( (SequenceI) node.element());
+          }
         }
+      }
 
-        return tmp;
+      return tmp;
+    }
+    else
+    {
+      _sortByTree(left, tmp, seqset);
+      _sortByTree(right, tmp, seqset);
     }
 
-    // Ordering Objects
-    // Alignment.sortBy(OrderObj) - sequence of sequence pointer refs in appropriate order
-    //
+    return tmp;
+  }
 
-    /**
-     * recover the order of sequences given by the safe numbering scheme introducd
-     * SeqsetUtils.uniquify.
-     */
-    public static void recoverOrder(SequenceI[] alignment)
-    {
-        float[] ids = new float[alignment.length];
+  // Ordering Objects
+  // Alignment.sortBy(OrderObj) - sequence of sequence pointer refs in appropriate order
+  //
 
-        for (int i = 0; i < alignment.length; i++)
-            ids[i] = (new Float(alignment[i].getName().substring(8))).floatValue();
+  /**
+   * recover the order of sequences given by the safe numbering scheme introducd
+   * SeqsetUtils.uniquify.
+   */
+  public static void recoverOrder(SequenceI[] alignment)
+  {
+    float[] ids = new float[alignment.length];
 
-        jalview.util.QuickSort.sort(ids, alignment);
+    for (int i = 0; i < alignment.length; i++)
+    {
+      ids[i] = (new Float(alignment[i].getName().substring(8))).floatValue();
     }
+
+    jalview.util.QuickSort.sort(ids, alignment);
+  }
 }
diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index b1cc250..4eb1218 100755
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -1,27 +1,26 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 jalview.analysis;
 
-import jalview.datamodel.*;
-
 import java.util.*;
 
+import jalview.datamodel.*;
 
 /**
  * Calculates conservation values for a given set of sequences
@@ -31,516 +30,521 @@ import java.util.*;
  */
 public class Conservation
 {
-    SequenceI [] sequences;
-    int start;
-    int end;
-    Vector seqNums; // vector of int vectors where first is sequence checksum
-    int maxLength = 0; //  used by quality calcs
-    boolean seqNumsChanged = false; // updated after any change via calcSeqNum;
-    Hashtable [] total;
-
-    /** Stores calculated quality values */
-    public Vector quality;
-
-    /** Stores maximum and minimum values of quality values  */
-    public Double[] qualityRange = new Double[2];
-    String consString = "";
-    Sequence consSequence;
-    Hashtable propHash;
-    int threshold;
-    String name = "";
-    int[][] cons2;
-
-    /**
-     * Creates a new Conservation object.
-     *
-     * @param name Name of conservation
-     * @param propHash DOCUMENT ME!
-     * @param threshold to count the residues in residueHash(). commonly used value is 3
-     * @param sequences sequences to be used in calculation
-     * @param start start residue position
-     * @param end end residue position
-     */
-    public Conservation(String name, Hashtable propHash, int threshold,
-        Vector sequences, int start, int end)
+  SequenceI[] sequences;
+  int start;
+  int end;
+  Vector seqNums; // vector of int vectors where first is sequence checksum
+  int maxLength = 0; //  used by quality calcs
+  boolean seqNumsChanged = false; // updated after any change via calcSeqNum;
+  Hashtable[] total;
+
+  /** Stores calculated quality values */
+  public Vector quality;
+
+  /** Stores maximum and minimum values of quality values  */
+  public Double[] qualityRange = new Double[2];
+  String consString = "";
+  Sequence consSequence;
+  Hashtable propHash;
+  int threshold;
+  String name = "";
+  int[][] cons2;
+
+  /**
+   * Creates a new Conservation object.
+   *
+   * @param name Name of conservation
+   * @param propHash DOCUMENT ME!
+   * @param threshold to count the residues in residueHash(). commonly used value is 3
+   * @param sequences sequences to be used in calculation
+   * @param start start residue position
+   * @param end end residue position
+   */
+  public Conservation(String name, Hashtable propHash, int threshold,
+                      Vector sequences, int start, int end)
+  {
+
+    this.name = name;
+    this.propHash = propHash;
+    this.threshold = threshold;
+    this.start = start;
+    this.end = end;
+
+    maxLength = end - start + 1; // default width includes bounds of calculation
+
+    int s, sSize = sequences.size();
+    SequenceI[] sarray = new SequenceI[sSize];
+    this.sequences = sarray;
+
+    for (s = 0; s < sSize; s++)
     {
-
-        this.name = name;
-        this.propHash = propHash;
-        this.threshold = threshold;
-        this.start = start;
-        this.end = end;
-
-        maxLength=end-start+1; // default width includes bounds of calculation
-
-        int s, sSize = sequences.size();
-        SequenceI[] sarray = new SequenceI[sSize];
-        this.sequences = sarray;
-
-        for (s = 0; s < sSize; s++)
-        {
-          sarray[s] = (SequenceI) sequences.elementAt(s);
-          if(sarray[s].getLength()>maxLength)
-            maxLength = sarray[s].getLength();
-        }
+      sarray[s] = (SequenceI) sequences.elementAt(s);
+      if (sarray[s].getLength() > maxLength)
+      {
+        maxLength = sarray[s].getLength();
+      }
     }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param i DOCUMENT ME!
+   */
+  private void calcSeqNum(int i)
+  {
+    String sq = null; // for dumb jbuilder not-inited exception warning
+    int[] sqnum = null;
 
+    int sSize = sequences.length;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     */
-    private void calcSeqNum(int i)
+    if ( (i > -1) && (i < sSize))
     {
-        String sq = null; // for dumb jbuilder not-inited exception warning
-        int[] sqnum = null;
+      sq = sequences[i].getSequenceAsString();
+
+      if (seqNums.size() <= i)
+      {
+        seqNums.addElement(new int[sq.length() + 1]);
+      }
 
-        int sSize = sequences.length;
+      if (sq.hashCode() != ( (int[]) seqNums.elementAt(i))[0])
+      {
+        int j;
+        int len;
+        seqNumsChanged = true;
+        len = sq.length();
 
-        if ((i > -1) && (i < sSize))
+        if (maxLength < len)
         {
-            sq = sequences[i].getSequenceAsString();
+          maxLength = len;
+        }
 
-            if (seqNums.size() <= i)
-            {
-                seqNums.addElement(new int[sq.length() + 1]);
-            }
+        sqnum = new int[len + 1]; // better to always make a new array - sequence can change its length
+        sqnum[0] = sq.hashCode();
 
-            if (sq.hashCode() != ((int[]) seqNums.elementAt(i))[0])
-            {
-                int j;
-                int len;
-                seqNumsChanged = true;
-                len = sq.length();
+        for (j = 1; j <= len; j++)
+        {
+          sqnum[j] = jalview.schemes.ResidueProperties.aaIndex[sq.charAt(j - 1)];
+        }
 
-                if (maxLength < len)
-                {
-                    maxLength = len;
-                }
+        seqNums.setElementAt(sqnum, i);
+      }
+      else
+      {
+        System.out.println("SEQUENCE HAS BEEN DELETED!!!");
+      }
+    }
+    else
+    {
+      // JBPNote INFO level debug
+      System.err.println(
+          "ERROR: calcSeqNum called with out of range sequence index for Alignment\n");
+    }
+  }
+
+  /**
+   * Calculates the conservation values for given set of sequences
+   */
+  public void calculate()
+  {
+    Hashtable resultHash, ht;
+    int thresh, j, jSize = sequences.length;
+    int[] values; // Replaces residueHash
+    String type, res = null;
+    char c;
+    Enumeration enumeration2;
+
+    total = new Hashtable[maxLength];
+
+    for (int i = start; i <= end; i++)
+    {
+      values = new int[255];
 
-                sqnum = new int[len + 1]; // better to always make a new array - sequence can change its length
-                sqnum[0] = sq.hashCode();
+      for (j = 0; j < jSize; j++)
+      {
+        if (sequences[j].getLength() > i)
+        {
+          c = sequences[j].getCharAt(i);
 
-                for (j = 1; j <= len; j++)
-                {
-                    sqnum[j] = jalview.schemes.ResidueProperties.aaIndex[sq.charAt(j-1)];
-                }
+          // No need to check if its a '-'
+          if (c == '.' || c == ' ')
+          {
+            c = '-';
+          }
 
+          if ('a' <= c && c <= 'z')
+          {
+            c -= (32); // 32 = 'a' - 'A'
+          }
 
-                seqNums.setElementAt(sqnum, i);
-            }
-            else
-              System.out.println("SEQUENCE HAS BEEN DELETED!!!");
+          values[c]++;
         }
         else
         {
-            // JBPNote INFO level debug
-            System.err.println(
-                "ERROR: calcSeqNum called with out of range sequence index for Alignment\n");
+          values['-']++;
         }
-    }
+      }
 
-    /**
-     * Calculates the conservation values for given set of sequences
-     */
-    public void calculate()
-    {
-      Hashtable resultHash, ht;
-      int thresh, j, jSize = sequences.length;
-      int[] values; // Replaces residueHash
-      String type, res=null;
-      char c;
-      Enumeration enumeration2;
+      //What is the count threshold to count the residues in residueHash()
+      thresh = (threshold * (jSize)) / 100;
 
-      total = new Hashtable[maxLength];
+      //loop over all the found residues
+      resultHash = new Hashtable();
+      for (char v = '-'; v < 'Z'; v++)
+      {
 
-      for (int i = start; i <= end; i++)
+        if (values[v] > thresh)
         {
-            values = new int[255];
+          res = String.valueOf(v);
 
-            for (j = 0; j < jSize; j++)
-            {
-              if (sequences[j].getLength() > i)
-              {
-                c = sequences[j].getCharAt(i);
-
-                // No need to check if its a '-'
-                if (c == '.' || c == ' ')
-                  c = '-';
+          //Now loop over the properties
+          enumeration2 = propHash.keys();
 
-                if ('a' <= c && c <= 'z')
-                {
-                  c -= (32);// 32 = 'a' - 'A'
-                }
+          while (enumeration2.hasMoreElements())
+          {
+            type = (String) enumeration2.nextElement();
+            ht = (Hashtable) propHash.get(type);
 
-                values[c]++;
+            //Have we ticked this before?
+            if (!resultHash.containsKey(type))
+            {
+              if (ht.containsKey(res))
+              {
+                resultHash.put(type, ht.get(res));
               }
               else
               {
-                values['-']++;
+                resultHash.put(type, ht.get("-"));
               }
             }
-
-            //What is the count threshold to count the residues in residueHash()
-            thresh = (threshold * (jSize)) / 100;
-
-            //loop over all the found residues
-            resultHash = new Hashtable();
-            for (char v = '-'; v < 'Z'; v++)
+            else if ( ( (Integer) resultHash.get(type)).equals(
+                (Integer) ht.get(res)) == false)
             {
-
-                if (values[v] > thresh)
-                {
-                  res =  String.valueOf( v );
-
-                    //Now loop over the properties
-                    enumeration2 = propHash.keys();
-
-                    while (enumeration2.hasMoreElements())
-                    {
-                        type = (String) enumeration2.nextElement();
-                        ht = (Hashtable) propHash.get(type);
-
-                        //Have we ticked this before?
-                        if (!resultHash.containsKey(type))
-                        {
-                            if (ht.containsKey(res))
-                            {
-                                resultHash.put(type, ht.get(res));
-                            }
-                            else
-                            {
-                                resultHash.put(type, ht.get("-"));
-                            }
-                        }
-                        else if (((Integer) resultHash.get(type)).equals(
-                                    (Integer) ht.get(res)) == false)
-                        {
-                            resultHash.put(type, new Integer(-1));
-                        }
-                    }
-                }
+              resultHash.put(type, new Integer( -1));
             }
-
-            total[i-start] = resultHash;
+          }
         }
-    }
-
+      }
 
-    /***
-     * countConsNGaps
-     * returns gap count in int[0], and conserved residue count in int[1]
-     */
-    public int[] countConsNGaps(int j)
+      total[i - start] = resultHash;
+    }
+  }
+
+  /***
+   * countConsNGaps
+   * returns gap count in int[0], and conserved residue count in int[1]
+   */
+  public int[] countConsNGaps(int j)
+  {
+    int count = 0;
+    int cons = 0;
+    int nres = 0;
+    int[] r = new int[2];
+    char f = '$';
+    int i, iSize = sequences.length;
+    char c;
+
+    for (i = 0; i < iSize; i++)
     {
-        int count = 0;
-        int cons = 0;
-        int nres = 0;
-        int[] r = new int[2];
-        char f = '$';
-        int i, iSize = sequences.length;
-        char c;
-
-        for (i = 0; i < iSize; i++)
-        {
-            if (j >= sequences[i].getLength())
-            {
-                count++;
-                continue;
-            }
+      if (j >= sequences[i].getLength())
+      {
+        count++;
+        continue;
+      }
 
-            c = sequences[i].getCharAt(j); // gaps do not have upper/lower case
+      c = sequences[i].getCharAt(j); // gaps do not have upper/lower case
 
-            if (jalview.util.Comparison.isGap((c)))
-            {
-                count++;
-            }
-            else
-            {
-                nres++;
-
-                if (nres == 1)
-                {
-                    f = c;
-                    cons++;
-                }
-                else if (f == c)
-                {
-                    cons++;
-                }
-            }
-        }
+      if (jalview.util.Comparison.isGap( (c)))
+      {
+        count++;
+      }
+      else
+      {
+        nres++;
 
-        r[0] = (nres == cons) ? 1 : 0;
-        r[1] = count;
+        if (nres == 1)
+        {
+          f = c;
+          cons++;
+        }
+        else if (f == c)
+        {
+          cons++;
+        }
+      }
+    }
 
-        return r;
+    r[0] = (nres == cons) ? 1 : 0;
+    r[1] = count;
+
+    return r;
+  }
+
+  /**
+   * Calculates the conservation sequence
+   *
+   * @param consflag if true, poitiveve conservation; false calculates negative conservation
+   * @param percentageGaps commonly used value is 25
+   */
+  public void verdict(boolean consflag, float percentageGaps)
+  {
+    StringBuffer consString = new StringBuffer();
+    String type;
+    Integer result;
+    int[] gapcons;
+    int totGaps, count;
+    float pgaps;
+    Hashtable resultHash;
+    Enumeration enumeration;
+
+    //NOTE THIS SHOULD CHECK IF THE CONSEQUENCE ALREADY
+    //EXISTS AND NOT OVERWRITE WITH '-', BUT THIS CASE
+    //DOES NOT EXIST IN JALVIEW 2.1.2
+    for (int i = 0; i < start; i++)
+    {
+      consString.append('-');
     }
 
-    /**
-     * Calculates the conservation sequence
-     *
-     * @param consflag if true, poitiveve conservation; false calculates negative conservation
-     * @param percentageGaps commonly used value is 25
-     */
-    public void verdict(boolean consflag, float percentageGaps)
+    for (int i = start; i <= end; i++)
     {
-        StringBuffer consString = new StringBuffer();
-        String type;
-        Integer result;
-        int[] gapcons;
-        int totGaps, count;
-        float pgaps;
-        Hashtable resultHash ;
-        Enumeration enumeration;
-
-        //NOTE THIS SHOULD CHECK IF THE CONSEQUENCE ALREADY
-        //EXISTS AND NOT OVERWRITE WITH '-', BUT THIS CASE
-        //DOES NOT EXIST IN JALVIEW 2.1.2
-        for(int i=0; i<start; i++)
-          consString.append('-');
-
-
-        for (int i = start; i <= end; i++)
+      gapcons = countConsNGaps(i);
+      totGaps = gapcons[1];
+      pgaps = ( (float) totGaps * 100) / (float) sequences.length;
+
+      if (percentageGaps > pgaps)
+      {
+        resultHash = total[i - start];
+
+        //Now find the verdict
+        count = 0;
+        enumeration = resultHash.keys();
+
+        while (enumeration.hasMoreElements())
         {
-            gapcons = countConsNGaps(i);
-            totGaps = gapcons[1];
-            pgaps = ((float) totGaps * 100) / (float) sequences.length;
+          type = (String) enumeration.nextElement();
+          result = (Integer) resultHash.get(type);
 
-            if (percentageGaps > pgaps)
+          //Do we want to count +ve conservation or +ve and -ve cons.?
+          if (consflag)
+          {
+            if (result.intValue() == 1)
             {
-                resultHash =  total[i - start];
-
-                //Now find the verdict
-                count = 0;
-                enumeration = resultHash.keys();
-
-                while (enumeration.hasMoreElements())
-                {
-                   type = (String) enumeration.nextElement();
-                   result = (Integer) resultHash.get(type);
-
-                    //Do we want to count +ve conservation or +ve and -ve cons.?
-                    if (consflag)
-                    {
-                        if (result.intValue() == 1)
-                        {
-                            count++;
-                        }
-                    }
-                    else
-                    {
-                        if (result.intValue() != -1)
-                        {
-                            count++;
-                        }
-                    }
-                }
-
-                if (count < 10)
-                {
-                    consString.append(count); // Conserved props!=Identity
-                }
-                else
-                {
-                    consString.append((gapcons[0] == 1) ? "*" : "+");
-                }
+              count++;
             }
-            else
+          }
+          else
+          {
+            if (result.intValue() != -1)
             {
-                consString.append('-');
+              count++;
             }
+          }
         }
 
-        consSequence = new Sequence(name, consString.toString(), start, end);
+        if (count < 10)
+        {
+          consString.append(count); // Conserved props!=Identity
+        }
+        else
+        {
+          consString.append( (gapcons[0] == 1) ? "*" : "+");
+        }
+      }
+      else
+      {
+        consString.append('-');
+      }
     }
 
-    /**
-     *
-     *
-     * @return Conservation sequence
-     */
-    public Sequence getConsSequence()
+    consSequence = new Sequence(name, consString.toString(), start, end);
+  }
+
+  /**
+   *
+   *
+   * @return Conservation sequence
+   */
+  public Sequence getConsSequence()
+  {
+    return consSequence;
+  }
+
+  // From Alignment.java in jalview118
+  public void findQuality()
+  {
+    findQuality(0, maxLength - 1);
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  private void percentIdentity2()
+  {
+    seqNums = new Vector();
+    // calcSeqNum(s);
+    int i = 0, iSize = sequences.length;
+    //Do we need to calculate this again?
+    for (i = 0; i < iSize; i++)
     {
-        return consSequence;
+      calcSeqNum(i);
     }
 
-    // From Alignment.java in jalview118
-    public void findQuality()
+    if ( (cons2 == null) || seqNumsChanged)
     {
-        findQuality(0, maxLength - 1);
-    }
+      cons2 = new int[maxLength][24];
 
-    /**
-     * DOCUMENT ME!
-     */
-    private void percentIdentity2()
-    {
-      seqNums = new Vector();
-     // calcSeqNum(s);
-      int i = 0, iSize = sequences.length;
-    //Do we need to calculate this again?
-      for (i = 0; i < iSize; i++)
+      // Initialize the array
+      for (int j = 0; j < 24; j++)
       {
-       calcSeqNum(i);
-      }
-
-
-        if ((cons2 == null) || seqNumsChanged)
+        for (i = 0; i < maxLength; i++)
         {
-            cons2 = new int[maxLength][24];
-
-            // Initialize the array
-            for (int j = 0; j < 24; j++)
-            {
-                for (i = 0; i < maxLength; i++)
-                {
-                    cons2[i][j] = 0;
-                }
-            }
+          cons2[i][j] = 0;
+        }
+      }
 
-            int[] sqnum;
-            int j = 0;
+      int[] sqnum;
+      int j = 0;
 
-            while (j < sequences.length)
-            {
-                sqnum = (int[]) seqNums.elementAt(j);
+      while (j < sequences.length)
+      {
+        sqnum = (int[]) seqNums.elementAt(j);
 
-                for (i = 1; i < sqnum.length; i++)
-                {
-                    cons2[i - 1][sqnum[i]]++;
-                }
+        for (i = 1; i < sqnum.length; i++)
+        {
+          cons2[i - 1][sqnum[i]]++;
+        }
 
-                for (i = sqnum.length - 1; i < maxLength; i++)
-                {
-                    cons2[i][23]++; // gap count
-                }
+        for (i = sqnum.length - 1; i < maxLength; i++)
+        {
+          cons2[i][23]++; // gap count
+        }
 
-                j++;
-            }
+        j++;
+      }
 
-            // unnecessary ?
+      // unnecessary ?
 
-            /* for (int i=start; i <= end; i++) {
-                 int max = -1000;
-            int maxi = -1;
-            int maxj = -1;
+      /* for (int i=start; i <= end; i++) {
+           int max = -1000;
+                   int maxi = -1;
+                   int maxj = -1;
 
-            for (int j=0;j<24;j++) {
-              if (cons2[i][j] > max) {
-              max = cons2[i][j];
-              maxi = i;
-              maxj = j;
-            }
+                   for (int j=0;j<24;j++) {
+        if (cons2[i][j] > max) {
+        max = cons2[i][j];
+        maxi = i;
+        maxj = j;
+                   }
 
-            }
-            } */
-        }
+                   }
+                   } */
     }
-
-    /**
-     * Calculates the quality of the set of sequences
-     *
-     * @param start Start residue
-     * @param end End residue
-     */
-    public void findQuality(int start, int end)
+  }
+
+  /**
+   * Calculates the quality of the set of sequences
+   *
+   * @param start Start residue
+   * @param end End residue
+   */
+  public void findQuality(int start, int end)
+  {
+    quality = new Vector();
+
+    double max = -10000;
+    int[][] BLOSUM62 = jalview.schemes.ResidueProperties.getBLOSUM62();
+
+    //Loop over columns // JBPNote Profiling info
+    //long ts = System.currentTimeMillis();
+    //long te = System.currentTimeMillis();
+    percentIdentity2();
+
+    int size = seqNums.size();
+    int[] lengths = new int[size];
+    double tot, bigtot, sr, tmp;
+    double[] x, xx;
+    int l, j, i, ii, i2, k, seqNum;
+
+    for (l = 0; l < size; l++)
     {
-        quality = new Vector();
-
-        double max = -10000;
-        int[][] BLOSUM62 = jalview.schemes.ResidueProperties.getBLOSUM62();
+      lengths[l] = ( (int[]) seqNums.elementAt(l)).length - 1;
+    }
 
-        //Loop over columns // JBPNote Profiling info
-        //long ts = System.currentTimeMillis();
-        //long te = System.currentTimeMillis();
-        percentIdentity2();
+    for (j = start; j <= end; j++)
+    {
+      bigtot = 0;
 
-        int size = seqNums.size();
-        int[] lengths = new int[size];
-        double tot, bigtot, sr, tmp;
-        double [] x, xx;
-        int l, j, i, ii, i2, k, seqNum;
+      // First Xr = depends on column only
+      x = new double[24];
 
-        for (l = 0; l < size; l++)
-            lengths[l] = ((int[]) seqNums.elementAt(l)).length - 1;
+      for (ii = 0; ii < 24; ii++)
+      {
+        x[ii] = 0;
 
-        for (j = start; j <= end; j++)
+        for (i2 = 0; i2 < 24; i2++)
         {
-            bigtot = 0;
-
-            // First Xr = depends on column only
-            x = new double[24];
-
-            for (ii = 0; ii < 24; ii++)
-            {
-                x[ii] = 0;
-
-                for (i2 = 0; i2 < 24; i2++)
-                {
-                  x[ii] += ( ( (double) cons2[j][i2] * BLOSUM62[ii][i2]) +
-                            4);
-                }
-
-                x[ii] /= size;
-            }
+          x[ii] += ( ( (double) cons2[j][i2] * BLOSUM62[ii][i2]) +
+                    4);
+        }
 
-            // Now calculate D for each position and sum
-            for (k = 0; k < size; k++)
-            {
-                tot = 0;
-                xx = new double[24];
-                seqNum = (j < lengths[k])
-                    ? ((int[]) seqNums.elementAt(k))[j + 1] : 23; // Sequence, or gap at the end
+        x[ii] /= size;
+      }
 
-                // This is a loop over r
-                for (i = 0; i < 23; i++)
-                {
-                    sr = 0;
+      // Now calculate D for each position and sum
+      for (k = 0; k < size; k++)
+      {
+        tot = 0;
+        xx = new double[24];
+        seqNum = (j < lengths[k])
+            ? ( (int[]) seqNums.elementAt(k))[j + 1] : 23; // Sequence, or gap at the end
 
-                    sr = (double) BLOSUM62[i][seqNum] + 4;
+        // This is a loop over r
+        for (i = 0; i < 23; i++)
+        {
+          sr = 0;
 
-                    //Calculate X with another loop over residues
-                    //  System.out.println("Xi " + i + " " + x[i] + " " + sr);
-                    xx[i] = x[i] - sr;
+          sr = (double) BLOSUM62[i][seqNum] + 4;
 
-                    tot += (xx[i] * xx[i]);
-                }
+          //Calculate X with another loop over residues
+          //  System.out.println("Xi " + i + " " + x[i] + " " + sr);
+          xx[i] = x[i] - sr;
 
-                bigtot += Math.sqrt(tot);
-            }
+          tot += (xx[i] * xx[i]);
+        }
 
-            // This is the quality for one column
-            if (max < bigtot)
-            {
-                max = bigtot;
-            }
+        bigtot += Math.sqrt(tot);
+      }
 
-            //      bigtot  = bigtot * (size-cons2[j][23])/size;
-            quality.addElement(new Double(bigtot));
+      // This is the quality for one column
+      if (max < bigtot)
+      {
+        max = bigtot;
+      }
 
-            // Need to normalize by gaps
-        }
+      //      bigtot  = bigtot * (size-cons2[j][23])/size;
+      quality.addElement(new Double(bigtot));
 
-        double newmax = -10000;
+      // Need to normalize by gaps
+    }
 
-        for (j = start; j <= end; j++)
-        {
-            tmp = ((Double) quality.elementAt(j)).doubleValue();
-            tmp = ((max - tmp) * (size - cons2[j][23])) / size;
+    double newmax = -10000;
 
-            //     System.out.println(tmp+ " " + j);
-            quality.setElementAt(new Double(tmp), j);
+    for (j = start; j <= end; j++)
+    {
+      tmp = ( (Double) quality.elementAt(j)).doubleValue();
+      tmp = ( (max - tmp) * (size - cons2[j][23])) / size;
 
-            if (tmp > newmax)
-            {
-                newmax = tmp;
-            }
-        }
+      //     System.out.println(tmp+ " " + j);
+      quality.setElementAt(new Double(tmp), j);
 
-        //    System.out.println("Quality " + s);
-        qualityRange[0] = new Double(0);
-        qualityRange[1] = new Double(newmax);
+      if (tmp > newmax)
+      {
+        newmax = tmp;
+      }
     }
+
+    //    System.out.println("Quality " + s);
+    qualityRange[0] = new Double(0);
+    qualityRange[1] = new Double(newmax);
+  }
 }
diff --git a/src/jalview/analysis/Finder.java b/src/jalview/analysis/Finder.java
index 479c8561..2fa09aa 100644
--- a/src/jalview/analysis/Finder.java
+++ b/src/jalview/analysis/Finder.java
@@ -1,273 +1,308 @@
 package jalview.analysis;
-import java.util.Vector;
+
+import java.util.*;
 
 import jalview.datamodel.*;
 
-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;
-        this.selection = selection;
+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;
+    this.selection = selection;
+  }
+
+  public Finder(AlignmentI alignment, SequenceGroup selectionGroup,
+                int seqIndex, int resIndex)
+  {
+    this(alignment, selectionGroup);
+    this.seqIndex = seqIndex;
+    this.resIndex = resIndex;
+  }
+
+  public boolean find(String searchString)
+  {
+    boolean hasResults = false;
+    if (!caseSensitive)
+    {
+      searchString = searchString.toUpperCase();
+    }
+    regex = new com.stevesoft.pat.Regex(searchString);
+    searchResults = new SearchResults();
+    idMatch = new Vector();
+    Sequence seq;
+    String item = null;
+    boolean found = false;
+
+    ////// is the searchString a residue number?
+    try
+    {
+      int res = Integer.parseInt(searchString);
+      found = true;
+      if (selection == null || selection.getSize() < 1)
+      {
+        seq = (Sequence) alignment.getSequenceAt(0);
+      }
+      else
+      {
+        seq = (Sequence) (selection.getSequenceAt(0));
+      }
+
+      searchResults.addResult(seq, res, res);
+      hasResults = true;
     }
+    catch (NumberFormatException ex)
+    {
+    }
+
+    ///////////////////////////////////////////////
 
-    public Finder(AlignmentI alignment, SequenceGroup selectionGroup, int seqIndex, int resIndex) {
-        this(alignment, selectionGroup);
-        this.seqIndex=seqIndex;
-        this.resIndex=resIndex;
+    int end = alignment.getHeight();
+
+    if (selection != null)
+    {
+      if ( (selection.getSize() < 1) ||
+          ( (selection.getEndRes() - selection.getStartRes()) < 2))
+      {
+        selection = null;
+      }
     }
 
-    public boolean find(String searchString) {
-        boolean hasResults=false;
-        if(!caseSensitive)
-            searchString = searchString.toUpperCase();
-        regex = new com.stevesoft.pat.Regex(searchString);
-        searchResults = new SearchResults();
-        idMatch = new Vector();
-        Sequence seq;
-        String item = null;
-        boolean found = false;
-
-        ////// is the searchString a residue number?
-        try
+    while (!found && (seqIndex < end))
+    {
+      seq = (Sequence) alignment.getSequenceAt(seqIndex);
+
+      if ( (selection != null) && !selection.getSequences(null).contains(seq))
+      {
+        seqIndex++;
+        resIndex = 0;
+
+        continue;
+      }
+
+      item = seq.getSequenceAsString();
+      // JBPNote - check if this toUpper which is present in the application implementation makes a difference
+      //if(!caseSensitive)
+      //  item = item.toUpperCase();
+
+      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
+      StringBuffer noGapsSB = new StringBuffer();
+      int insertCount = 0;
+      Vector spaces = new Vector();
+
+      for (int j = 0; j < item.length(); j++)
+      {
+        if (!jalview.util.Comparison.isGap(item.charAt(j)))
         {
-            int res = Integer.parseInt(searchString);
-            found = true;
-            if (selection == null || selection.getSize() < 1)
-            {
-              seq = (Sequence) alignment.getSequenceAt(0);
-            }
-            else
-            {
-              seq = (Sequence) (selection.getSequenceAt(0));
-            }
-
-            searchResults.addResult(seq, res, res);
-            hasResults=true;
+          noGapsSB.append(item.charAt(j));
+          spaces.addElement(new Integer(insertCount));
         }
-        catch (NumberFormatException ex)
+        else
         {
+          insertCount++;
         }
+      }
 
-        ///////////////////////////////////////////////
-
-        int end = alignment.getHeight();
+      String noGaps = noGapsSB.toString();
 
+      for (int r = resIndex; r < noGaps.length(); r++)
+      {
 
-        if (selection != null)
+        if (regex.searchFrom(noGaps, r))
         {
-            if ((selection.getSize() < 1) ||
-                    ((selection.getEndRes() - selection.getStartRes()) < 2))
-            {
-                selection = null;
-            }
-        }
+          resIndex = regex.matchedFrom();
+
+          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()));
+
+          searchResults.addResult(seq, sres, eres);
+          hasResults = true;
+          if (!findAll)
+          {
+            // thats enough, break and display the result
+            found = true;
+            resIndex++;
 
-        while (!found && (seqIndex < end))
-        {
-            seq = (Sequence) alignment.getSequenceAt(seqIndex);
-
-            if ((selection != null) && !selection.getSequences(null).contains(seq))
-            {
-                seqIndex++;
-                resIndex = 0;
-
-                continue;
-            }
-
-            item = seq.getSequenceAsString();
-            // JBPNote - check if this toUpper which is present in the application implementation makes a difference
-            //if(!caseSensitive)
-            //  item = item.toUpperCase();
-
-            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
-            StringBuffer noGapsSB = new StringBuffer();
-            int insertCount = 0;
-            Vector spaces = new Vector();
-
-            for (int j = 0; j < item.length(); j++)
-            {
-                if (!jalview.util.Comparison.isGap(item.charAt(j)))
-                {
-                    noGapsSB.append(item.charAt(j));
-                    spaces.addElement(new Integer(insertCount));
-                }
-                else
-                {
-                    insertCount++;
-                }
-            }
-
-            String noGaps = noGapsSB.toString();
-
-            for (int r = resIndex; r < noGaps.length(); r++)
-            {
-
-                if (regex.searchFrom(noGaps, r))
-                {
-                    resIndex = regex.matchedFrom();
-
-                    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()));
-
-                    searchResults.addResult(seq, sres, eres);
-                    hasResults=true;
-                    if (!findAll)
-                    {
-                        // thats enough, break and display the result
-                        found = true;
-                        resIndex++;
-
-                        break;
-                    }
-
-                    r = resIndex;
-                }
-                else
-                {
-                  break;
-                }
-            }
-
-            if (!found)
-            {
-                seqIndex++;
-                resIndex = 0;
-            }
-        }
+            break;
+          }
 
-        for (int id = 0; id < alignment.getHeight(); id++)
+          r = resIndex;
+        }
+        else
         {
-            if (regex.search(alignment.getSequenceAt(id).getName()))
-            {
-                idMatch.addElement(alignment.getSequenceAt(id));
-                hasResults=true;
-            }
+          break;
         }
-        return hasResults;
-    }
-    /**
-     * @return the alignment
-     */
-    public AlignmentI getAlignment() {
-        return alignment;
-    }
-    /**
-     * @param alignment the alignment to set
-     */
-    public void setAlignment(AlignmentI alignment) {
-        this.alignment = alignment;
-    }
-    /**
-     * @return the caseSensitive
-     */
-    public boolean isCaseSensitive() {
-        return caseSensitive;
-    }
-    /**
-     * @param caseSensitive the caseSensitive to set
-     */
-    public void setCaseSensitive(boolean caseSensitive) {
-        this.caseSensitive = caseSensitive;
-    }
-    /**
-     * @return the findAll
-     */
-    public boolean isFindAll() {
-        return findAll;
-    }
-    /**
-     * @param findAll the findAll to set
-     */
-    public void setFindAll(boolean findAll) {
-        this.findAll = findAll;
-    }
-    /**
-     * @return the selection
-     */
-    public jalview.datamodel.SequenceGroup getSelection() {
-        return selection;
-    }
-    /**
-     * @param selection the selection to set
-     */
-    public void setSelection(jalview.datamodel.SequenceGroup selection) {
-        this.selection = selection;
-    }
-    /**
-     * @return the idMatch
-     */
-    public Vector getIdMatch() {
-        return idMatch;
-    }
-    /**
-     * @return the regex
-     */
-    public com.stevesoft.pat.Regex getRegex() {
-        return regex;
-    }
-    /**
-     * @return the searchResults
-     */
-    public SearchResults getSearchResults() {
-        return searchResults;
-    }
-
-    /**
-     * @return the resIndex
-     */
-    public int getResIndex() {
-        return resIndex;
-    }
-
-    /**
-     * @param resIndex the resIndex to set
-     */
-    public void setResIndex(int resIndex) {
-        this.resIndex = resIndex;
-    }
+      }
 
-    /**
-     * @return the seqIndex
-     */
-    public int getSeqIndex() {
-        return seqIndex;
+      if (!found)
+      {
+        seqIndex++;
+        resIndex = 0;
+      }
     }
 
-    /**
-     * @param seqIndex the seqIndex to set
-     */
-    public void setSeqIndex(int seqIndex) {
-        this.seqIndex = seqIndex;
+    for (int id = 0; id < alignment.getHeight(); id++)
+    {
+      if (regex.search(alignment.getSequenceAt(id).getName()))
+      {
+        idMatch.addElement(alignment.getSequenceAt(id));
+        hasResults = true;
+      }
     }
+    return hasResults;
+  }
+
+  /**
+   * @return the alignment
+   */
+  public AlignmentI getAlignment()
+  {
+    return alignment;
+  }
+
+  /**
+   * @param alignment the alignment to set
+   */
+  public void setAlignment(AlignmentI alignment)
+  {
+    this.alignment = alignment;
+  }
+
+  /**
+   * @return the caseSensitive
+   */
+  public boolean isCaseSensitive()
+  {
+    return caseSensitive;
+  }
+
+  /**
+   * @param caseSensitive the caseSensitive to set
+   */
+  public void setCaseSensitive(boolean caseSensitive)
+  {
+    this.caseSensitive = caseSensitive;
+  }
+
+  /**
+   * @return the findAll
+   */
+  public boolean isFindAll()
+  {
+    return findAll;
+  }
+
+  /**
+   * @param findAll the findAll to set
+   */
+  public void setFindAll(boolean findAll)
+  {
+    this.findAll = findAll;
+  }
+
+  /**
+   * @return the selection
+   */
+  public jalview.datamodel.SequenceGroup getSelection()
+  {
+    return selection;
+  }
+
+  /**
+   * @param selection the selection to set
+   */
+  public void setSelection(jalview.datamodel.SequenceGroup selection)
+  {
+    this.selection = selection;
+  }
+
+  /**
+   * @return the idMatch
+   */
+  public Vector getIdMatch()
+  {
+    return idMatch;
+  }
+
+  /**
+   * @return the regex
+   */
+  public com.stevesoft.pat.Regex getRegex()
+  {
+    return regex;
+  }
+
+  /**
+   * @return the searchResults
+   */
+  public SearchResults getSearchResults()
+  {
+    return searchResults;
+  }
+
+  /**
+   * @return the resIndex
+   */
+  public int getResIndex()
+  {
+    return resIndex;
+  }
+
+  /**
+   * @param resIndex the resIndex to set
+   */
+  public void setResIndex(int resIndex)
+  {
+    this.resIndex = resIndex;
+  }
+
+  /**
+   * @return the seqIndex
+   */
+  public int getSeqIndex()
+  {
+    return seqIndex;
+  }
+
+  /**
+   * @param seqIndex the seqIndex to set
+   */
+  public void setSeqIndex(int seqIndex)
+  {
+    this.seqIndex = seqIndex;
+  }
 }
diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index b882ba7..4d0bb93 100755
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -1,34 +1,29 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 jalview.analysis;
 
-import jalview.datamodel.*;
-
-import jalview.io.NewickFile;
-
-import jalview.schemes.ResidueProperties;
-import jalview.schemes.ScoreMatrix;
-
-import jalview.util.*;
-
 import java.util.*;
 
+import jalview.datamodel.*;
+import jalview.io.*;
+import jalview.schemes.*;
+import jalview.util.*;
 
 /**
  * DOCUMENT ME!
@@ -38,1213 +33,1239 @@ import java.util.*;
  */
 public class NJTree
 {
-    Vector cluster;
-    SequenceI[] sequence;
-
-    //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;
-
-    /**
-     * 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
-     */
-    public NJTree(SequenceI[] seqs, AlignmentView odata, NewickFile treefile) {
-      this(seqs, treefile);
-      if (odata!=null)
-        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();
-      } */
+  Vector cluster;
+  SequenceI[] sequence;
+
+  //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;
+
+  /**
+   * 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
+   */
+  public NJTree(SequenceI[] seqs, AlignmentView odata, NewickFile treefile)
+  {
+    this(seqs, treefile);
+    if (odata != null)
+    {
+      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();
+           } */
+  }
+
+  /**
+   * 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
+   */
+  public NJTree(SequenceI[] seqs, NewickFile treefile)
+  {
+    this.sequence = seqs;
+    top = treefile.getTree();
 
     /**
-     * Creates a new NJTree object from a tree from an external source
+     * There is no dependent alignment to be recovered from an
+     * imported tree.
      *
-     * @param seqs SequenceI which should be associated with leafs of treefile
-     * @param treefile A parsed tree
+             if (sequenceString == null)
+             {
+      sequenceString = new String[seqs.length];
+      for (int i = 0; i < seqs.length; i++)
+      {
+        sequenceString[i] = seqs[i].getSequence();
+      }
+             }
      */
-    public NJTree(SequenceI[] seqs,  NewickFile treefile)
-    {
-        this.sequence = seqs;
-        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();
-          }
-        }
-        */
 
-        hasDistances = treefile.HasDistances();
-        hasBootstrap = treefile.HasBootstrap();
-        hasRootDistance = treefile.HasRootDistance();
+    hasDistances = treefile.HasDistances();
+    hasBootstrap = treefile.HasBootstrap();
+    hasRootDistance = treefile.HasRootDistance();
 
-        maxheight = findHeight(top);
+    maxheight = findHeight(top);
 
-        SequenceIdMatcher algnIds = new SequenceIdMatcher(seqs);
-
-        Vector leaves = new Vector();
-        findLeaves(top, leaves);
-
-        int i = 0;
-        int namesleft = seqs.length;
-
-        SequenceNode j;
-        SequenceI nam;
-        String realnam;
-        Vector one2many=new Vector();
-        int countOne2Many=0;
-        while (i < leaves.size())
-        {
-            j = (SequenceNode) leaves.elementAt(i++);
-            realnam = j.getName();
-            nam = null;
+    SequenceIdMatcher algnIds = new SequenceIdMatcher(seqs);
 
-            if (namesleft > -1)
-            {
-                nam = algnIds.findIdMatch(realnam);
-            }
+    Vector leaves = new Vector();
+    findLeaves(top, leaves);
 
-            if (nam != null)
-            {
-                j.setElement(nam);
-                if (one2many.contains(nam)) {
-                  countOne2Many++;
-                //  if (jalview.bin.Cache.log.isDebugEnabled())
-                //    jalview.bin.Cache.log.debug("One 2 many relationship for "+nam.getName());
-                } else {
-                  one2many.addElement(nam);
-                  namesleft--;
-                }
-            }
-            else
-            {
-                j.setElement(new Sequence(realnam, "THISISAPLACEHLDER"));
-                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();
-    }
+    int i = 0;
+    int namesleft = seqs.length;
 
-    /**
-     * 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!
-     */
-    public NJTree(SequenceI[] sequence,
-                  AlignmentView seqData,
-                  String type,
-                  String pwtype,
-                  int start, int end)
+    SequenceNode j;
+    SequenceI nam;
+    String realnam;
+    Vector one2many = new Vector();
+    int countOne2Many = 0;
+    while (i < leaves.size())
     {
-        this.sequence = sequence;
-        this.node = new Vector();
-        this.type = type;
-        this.pwtype = pwtype;
-        if (seqData!=null) {
-          this.seqData = seqData;
-        } else {
-          SeqCigar[] seqs = new SeqCigar[sequence.length];
-          for(int i=0; i<sequence.length; i++)
-            {
-              seqs[i] = new SeqCigar(sequence[i], start, end);
-            }
-            CigarArray sdata = new CigarArray(seqs);
-            sdata.addOperation(CigarArray.M, end-start+1);
-            this.seqData = new AlignmentView(sdata, start);
-        }
+      j = (SequenceNode) leaves.elementAt(i++);
+      realnam = j.getName();
+      nam = null;
 
-        if (!(type.equals("NJ")))
-        {
-            type = "AV";
-        }
+      if (namesleft > -1)
+      {
+        nam = algnIds.findIdMatch(realnam);
+      }
 
-        if (!(pwtype.equals("PID")))
+      if (nam != null)
+      {
+        j.setElement(nam);
+        if (one2many.contains(nam))
         {
-          if (ResidueProperties.getScoreMatrix(pwtype)==null) {
-            type = "BLOSUM62";
-          }
+          countOne2Many++;
+          //  if (jalview.bin.Cache.log.isDebugEnabled())
+          //    jalview.bin.Cache.log.debug("One 2 many relationship for "+nam.getName());
         }
-
-        int i = 0;
-
-        done = new int[sequence.length];
-
-        while ((i < sequence.length) && (sequence[i] != null))
+        else
         {
-            done[i] = 0;
-            i++;
+          one2many.addElement(nam);
+          namesleft--;
         }
-
-        noseqs = i++;
-
-        distance = findDistances(this.seqData.getSequenceStrings(Comparison.GapChars.charAt(0)));
-
-        makeLeaves();
-
-        noClus = cluster.size();
-
-        cluster();
+      }
+      else
+      {
+        j.setElement(new Sequence(realnam, "THISISAPLACEHLDER"));
+        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();
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String toString()
+  /**
+   * 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!
+   */
+  public NJTree(SequenceI[] sequence,
+                AlignmentView seqData,
+                String type,
+                String pwtype,
+                int start, int end)
+  {
+    this.sequence = sequence;
+    this.node = new Vector();
+    this.type = type;
+    this.pwtype = pwtype;
+    if (seqData != null)
     {
-        jalview.io.NewickFile fout = new jalview.io.NewickFile(getTopNode());
-
-        return fout.print(false, true); // distances only
+      this.seqData = seqData;
+    }
+    else
+    {
+      SeqCigar[] seqs = new SeqCigar[sequence.length];
+      for (int i = 0; i < sequence.length; i++)
+      {
+        seqs[i] = new SeqCigar(sequence[i], start, end);
+      }
+      CigarArray sdata = new CigarArray(seqs);
+      sdata.addOperation(CigarArray.M, end - start + 1);
+      this.seqData = new AlignmentView(sdata, start);
     }
 
-    /**
-     *
-     * used when the alignment associated to a tree has changed.
-     *
-     * @param alignment Vector
-     */
-    public void UpdatePlaceHolders(Vector alignment)
+    if (! (type.equals("NJ")))
     {
-        Vector leaves = new Vector();
-        findLeaves(top, leaves);
+      type = "AV";
+    }
 
-        int sz = leaves.size();
-        SequenceIdMatcher seqmatcher = null;
-        int i = 0;
+    if (! (pwtype.equals("PID")))
+    {
+      if (ResidueProperties.getScoreMatrix(pwtype) == null)
+      {
+        type = "BLOSUM62";
+      }
+    }
 
-        while (i < sz)
-        {
-            SequenceNode leaf = (SequenceNode) leaves.elementAt(i++);
+    int i = 0;
 
-            if (alignment.contains(leaf.element()))
-            {
-                leaf.setPlaceholder(false);
-            }
-            else
-            {
-                if (seqmatcher == null)
-                {
-                    // Only create this the first time we need it
-                    SequenceI[] seqs = new SequenceI[alignment.size()];
-
-                    for (int j = 0; j < seqs.length; j++)
-                        seqs[j] = (SequenceI) alignment.elementAt(j);
-
-                    seqmatcher = new SequenceIdMatcher(seqs);
-                }
-
-                SequenceI nam = seqmatcher.findIdMatch(leaf.getName());
-
-                if (nam != null)
-                {
-                    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)
-                    }
-                    leaf.setPlaceholder(false);
-                    leaf.setElement(nam);
-                }
-                else
-                {
-                    if (!leaf.isPlaceholder()) {
-                        // Construct a new placeholder sequence object for this leaf
-                        leaf.setElement(new Sequence(leaf.getName(), "THISISAPLACEHLDER"));
-                    }
-                    leaf.setPlaceholder(true);
-                    
-                }
-            }
-        }
-    }
+    done = new int[sequence.length];
 
-    /**
-     * DOCUMENT ME!
-     */
-    public void cluster()
+    while ( (i < sequence.length) && (sequence[i] != null))
     {
-        while (noClus > 2)
-        {
-            if (type.equals("NJ"))
-            {
-                findMinNJDistance();
-            }
-            else
-            {
-                findMinDistance();
-            }
+      done[i] = 0;
+      i++;
+    }
 
-            Cluster c = joinClusters(mini, minj);
+    noseqs = i++;
 
-            done[minj] = 1;
+    distance = findDistances(this.seqData.getSequenceStrings(Comparison.
+        GapChars.charAt(0)));
 
-            cluster.setElementAt(null, minj);
-            cluster.setElementAt(c, mini);
+    makeLeaves();
 
-            noClus--;
-        }
+    noClus = cluster.size();
 
-        boolean onefound = false;
+    cluster();
+  }
 
-        int one = -1;
-        int two = -1;
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public String toString()
+  {
+    jalview.io.NewickFile fout = new jalview.io.NewickFile(getTopNode());
 
-        for (int i = 0; i < noseqs; i++)
-        {
-            if (done[i] != 1)
-            {
-                if (onefound == false)
-                {
-                    two = i;
-                    onefound = true;
-                }
-                else
-                {
-                    one = i;
-                }
-            }
-        }
+    return fout.print(false, true); // distances only
+  }
 
-        joinClusters(one, two);
-        top = (SequenceNode) (node.elementAt(one));
+  /**
+   *
+   * used when the alignment associated to a tree has changed.
+   *
+   * @param alignment Vector
+   */
+  public void UpdatePlaceHolders(Vector alignment)
+  {
+    Vector leaves = new Vector();
+    findLeaves(top, leaves);
 
-        reCount(top);
-        findHeight(top);
-        findMaxDist(top);
-    }
+    int sz = leaves.size();
+    SequenceIdMatcher seqmatcher = null;
+    int i = 0;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     * @param j DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Cluster joinClusters(int i, int j)
+    while (i < sz)
     {
-        float dist = distance[i][j];
+      SequenceNode leaf = (SequenceNode) leaves.elementAt(i++);
 
-        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++)
+      if (alignment.contains(leaf.element()))
+      {
+        leaf.setPlaceholder(false);
+      }
+      else
+      {
+        if (seqmatcher == null)
         {
-            value[ii] = ((Cluster) cluster.elementAt(i)).value[ii];
-        }
+          // Only create this the first time we need it
+          SequenceI[] seqs = new SequenceI[alignment.size()];
 
-        for (int ii = noi; ii < (noi + noj); ii++)
-        {
-            value[ii] = ((Cluster) cluster.elementAt(j)).value[ii - noi];
-        }
+          for (int j = 0; j < seqs.length; j++)
+          {
+            seqs[j] = (SequenceI) alignment.elementAt(j);
+          }
 
-        Cluster c = new Cluster(value);
+          seqmatcher = new SequenceIdMatcher(seqs);
+        }
 
-        ri = findr(i, j);
-        rj = findr(j, i);
+        SequenceI nam = seqmatcher.findIdMatch(leaf.getName());
 
-        if (type.equals("NJ"))
+        if (nam != null)
         {
-            findClusterNJDistance(i, j);
+          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)
+          }
+          leaf.setPlaceholder(false);
+          leaf.setElement(nam);
         }
         else
         {
-            findClusterDistance(i, j);
+          if (!leaf.isPlaceholder())
+          {
+            // Construct a new placeholder sequence object for this leaf
+            leaf.setElement(new Sequence(leaf.getName(), "THISISAPLACEHLDER"));
+          }
+          leaf.setPlaceholder(true);
+
         }
+      }
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void cluster()
+  {
+    while (noClus > 2)
+    {
+      if (type.equals("NJ"))
+      {
+        findMinNJDistance();
+      }
+      else
+      {
+        findMinDistance();
+      }
+
+      Cluster c = joinClusters(mini, minj);
+
+      done[minj] = 1;
 
-        SequenceNode sn = new SequenceNode();
+      cluster.setElementAt(null, minj);
+      cluster.setElementAt(c, mini);
 
-        sn.setLeft((SequenceNode) (node.elementAt(i)));
-        sn.setRight((SequenceNode) (node.elementAt(j)));
+      noClus--;
+    }
+
+    boolean onefound = false;
 
-        SequenceNode tmpi = (SequenceNode) (node.elementAt(i));
-        SequenceNode tmpj = (SequenceNode) (node.elementAt(j));
+    int one = -1;
+    int two = -1;
 
-        if (type.equals("NJ"))
+    for (int i = 0; i < noseqs; i++)
+    {
+      if (done[i] != 1)
+      {
+        if (onefound == false)
         {
-            findNewNJDistances(tmpi, tmpj, dist);
+          two = i;
+          onefound = true;
         }
         else
         {
-            findNewDistances(tmpi, tmpj, dist);
+          one = i;
         }
+      }
+    }
+
+    joinClusters(one, two);
+    top = (SequenceNode) (node.elementAt(one));
+
+    reCount(top);
+    findHeight(top);
+    findMaxDist(top);
+  }
+
+  /**
+   * 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];
 
-        tmpi.setParent(sn);
-        tmpj.setParent(sn);
+    int noi = ( (Cluster) cluster.elementAt(i)).value.length;
+    int noj = ( (Cluster) cluster.elementAt(j)).value.length;
 
-        node.setElementAt(sn, i);
+    int[] value = new int[noi + noj];
 
-        return c;
+    for (int ii = 0; ii < noi; ii++)
+    {
+      value[ii] = ( (Cluster) cluster.elementAt(i)).value[ii];
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param tmpi DOCUMENT ME!
-     * @param tmpj DOCUMENT ME!
-     * @param dist DOCUMENT ME!
-     */
-    public void findNewNJDistances(SequenceNode tmpi, SequenceNode tmpj,
-        float dist)
+    for (int ii = noi; ii < (noi + noj); ii++)
     {
+      value[ii] = ( (Cluster) cluster.elementAt(j)).value[ii - noi];
+    }
 
-        tmpi.dist = ((dist + ri) - rj) / 2;
-        tmpj.dist = (dist - tmpi.dist);
+    Cluster c = new Cluster(value);
 
-        if (tmpi.dist < 0)
-        {
-            tmpi.dist = 0;
-        }
+    ri = findr(i, j);
+    rj = findr(j, i);
 
-        if (tmpj.dist < 0)
-        {
-            tmpj.dist = 0;
-        }
+    if (type.equals("NJ"))
+    {
+      findClusterNJDistance(i, j);
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param tmpi DOCUMENT ME!
-     * @param tmpj DOCUMENT ME!
-     * @param dist DOCUMENT ME!
-     */
-    public void findNewDistances(SequenceNode tmpi, SequenceNode tmpj,
-        float dist)
+    else
     {
-        float ih = 0;
-        float jh = 0;
+      findClusterDistance(i, j);
+    }
 
-        SequenceNode sni = tmpi;
-        SequenceNode snj = tmpj;
+    SequenceNode sn = new SequenceNode();
 
-        while (sni != null)
-        {
-            ih = ih + sni.dist;
-            sni = (SequenceNode) sni.left();
-        }
+    sn.setLeft( (SequenceNode) (node.elementAt(i)));
+    sn.setRight( (SequenceNode) (node.elementAt(j)));
 
-        while (snj != null)
-        {
-            jh = jh + snj.dist;
-            snj = (SequenceNode) snj.left();
-        }
+    SequenceNode tmpi = (SequenceNode) (node.elementAt(i));
+    SequenceNode tmpj = (SequenceNode) (node.elementAt(j));
 
-        tmpi.dist = ((dist / 2) - ih);
-        tmpj.dist = ((dist / 2) - jh);
+    if (type.equals("NJ"))
+    {
+      findNewNJDistances(tmpi, tmpj, dist);
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     * @param j DOCUMENT ME!
-     */
-    public void findClusterDistance(int i, int j)
+    else
     {
-        int noi = ((Cluster) cluster.elementAt(i)).value.length;
-        int noj = ((Cluster) cluster.elementAt(j)).value.length;
+      findNewDistances(tmpi, tmpj, dist);
+    }
 
-        // New distances from cluster to others
-        float[] newdist = new float[noseqs];
+    tmpi.setParent(sn);
+    tmpj.setParent(sn);
 
-        for (int l = 0; l < noseqs; l++)
-        {
-            if ((l != i) && (l != j))
-            {
-                newdist[l] = ((distance[i][l] * noi) + (distance[j][l] * noj)) / (noi +
-                    noj);
-            }
-            else
-            {
-                newdist[l] = 0;
-            }
-        }
+    node.setElementAt(sn, i);
 
-        for (int ii = 0; ii < noseqs; ii++)
-        {
-            distance[i][ii] = newdist[ii];
-            distance[ii][i] = newdist[ii];
-        }
+    return c;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param tmpi DOCUMENT ME!
+   * @param tmpj DOCUMENT ME!
+   * @param dist DOCUMENT ME!
+   */
+  public void findNewNJDistances(SequenceNode tmpi, SequenceNode tmpj,
+                                 float dist)
+  {
+
+    tmpi.dist = ( (dist + ri) - rj) / 2;
+    tmpj.dist = (dist - tmpi.dist);
+
+    if (tmpi.dist < 0)
+    {
+      tmpi.dist = 0;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     * @param j DOCUMENT ME!
-     */
-    public void findClusterNJDistance(int i, int j)
+    if (tmpj.dist < 0)
     {
+      tmpj.dist = 0;
+    }
+  }
 
-        // New distances from cluster to others
-        float[] newdist = new float[noseqs];
+  /**
+   * DOCUMENT ME!
+   *
+   * @param tmpi DOCUMENT ME!
+   * @param tmpj DOCUMENT ME!
+   * @param dist DOCUMENT ME!
+   */
+  public void findNewDistances(SequenceNode tmpi, SequenceNode tmpj,
+                               float dist)
+  {
+    float ih = 0;
+    float jh = 0;
 
-        for (int l = 0; l < noseqs; l++)
-        {
-            if ((l != i) && (l != j))
-            {
-                newdist[l] = ((distance[i][l] + distance[j][l]) -
-                    distance[i][j]) / 2;
-            }
-            else
-            {
-                newdist[l] = 0;
-            }
-        }
+    SequenceNode sni = tmpi;
+    SequenceNode snj = tmpj;
 
-        for (int ii = 0; ii < noseqs; ii++)
-        {
-            distance[i][ii] = newdist[ii];
-            distance[ii][i] = newdist[ii];
-        }
+    while (sni != null)
+    {
+      ih = ih + sni.dist;
+      sni = (SequenceNode) sni.left();
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     * @param j DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public float findr(int i, int j)
+    while (snj != null)
     {
-        float tmp = 1;
+      jh = jh + snj.dist;
+      snj = (SequenceNode) snj.left();
+    }
 
-        for (int k = 0; k < noseqs; k++)
-        {
-            if ((k != i) && (k != j) && (done[k] != 1))
-            {
-                tmp = tmp + distance[i][k];
-            }
-        }
+    tmpi.dist = ( (dist / 2) - ih);
+    tmpj.dist = ( (dist / 2) - jh);
+  }
 
-        if (noClus > 2)
-        {
-            tmp = tmp / (noClus - 2);
-        }
+  /**
+   * 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;
 
-        return tmp;
+    // New distances from cluster to others
+    float[] newdist = new float[noseqs];
+
+    for (int l = 0; l < noseqs; l++)
+    {
+      if ( (l != i) && (l != j))
+      {
+        newdist[l] = ( (distance[i][l] * noi) + (distance[j][l] * noj)) / (noi +
+            noj);
+      }
+      else
+      {
+        newdist[l] = 0;
+      }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public float findMinNJDistance()
+    for (int ii = 0; ii < noseqs; ii++)
     {
-        float min = 100000;
+      distance[i][ii] = newdist[ii];
+      distance[ii][i] = newdist[ii];
+    }
+  }
 
-        for (int i = 0; i < (noseqs - 1); i++)
-        {
-            for (int j = i + 1; j < noseqs; j++)
-            {
-                if ((done[i] != 1) && (done[j] != 1))
-                {
-                    float tmp = distance[i][j] - (findr(i, j) + findr(j, i));
-
-                    if (tmp < min)
-                    {
-                        mini = i;
-                        minj = j;
-
-                        min = tmp;
-                    }
-                }
-            }
-        }
+  /**
+   * DOCUMENT ME!
+   *
+   * @param i DOCUMENT ME!
+   * @param j DOCUMENT ME!
+   */
+  public void findClusterNJDistance(int i, int j)
+  {
 
-        return min;
+    // New distances from cluster to others
+    float[] newdist = new float[noseqs];
+
+    for (int l = 0; l < noseqs; l++)
+    {
+      if ( (l != i) && (l != j))
+      {
+        newdist[l] = ( (distance[i][l] + distance[j][l]) -
+                      distance[i][j]) / 2;
+      }
+      else
+      {
+        newdist[l] = 0;
+      }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public float findMinDistance()
+    for (int ii = 0; ii < noseqs; ii++)
     {
-        float min = 100000;
+      distance[i][ii] = newdist[ii];
+      distance[ii][i] = newdist[ii];
+    }
+  }
 
-        for (int i = 0; i < (noseqs - 1); i++)
-        {
-            for (int j = i + 1; j < noseqs; j++)
-            {
-                if ((done[i] != 1) && (done[j] != 1))
-                {
-                    if (distance[i][j] < min)
-                    {
-                        mini = i;
-                        minj = j;
-
-                        min = distance[i][j];
-                    }
-                }
-            }
-        }
+  /**
+   * DOCUMENT ME!
+   *
+   * @param i DOCUMENT ME!
+   * @param j DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public float findr(int i, int j)
+  {
+    float tmp = 1;
 
-        return min;
+    for (int k = 0; k < noseqs; k++)
+    {
+      if ( (k != i) && (k != j) && (done[k] != 1))
+      {
+        tmp = tmp + distance[i][k];
+      }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public float[][] findDistances(String[] sequenceString)
+    if (noClus > 2)
     {
-        float[][] distance = new float[noseqs][noseqs];
+      tmp = tmp / (noClus - 2);
+    }
+
+    return tmp;
+  }
 
-        if (pwtype.equals("PID"))
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public float findMinNJDistance()
+  {
+    float min = 100000;
+
+    for (int i = 0; i < (noseqs - 1); i++)
+    {
+      for (int j = i + 1; j < noseqs; j++)
+      {
+        if ( (done[i] != 1) && (done[j] != 1))
         {
-            for (int i = 0; i < (noseqs - 1); i++)
-            {
-                for (int j = i; j < noseqs; j++)
-                {
-                    if (j == i)
-                    {
-                        distance[i][i] = 0;
-                    }
-                    else
-                    {
-                        distance[i][j] = 100 -
-                             Comparison.PID(sequenceString[i], sequenceString[j]);
-
-                        distance[j][i] = distance[i][j];
-                    }
-                }
-            }
+          float tmp = distance[i][j] - (findr(i, j) + findr(j, i));
+
+          if (tmp < min)
+          {
+            mini = i;
+            minj = j;
+
+            min = tmp;
+          }
         }
-        else {
-          // Pairwise substitution score (with no gap penalties)
-          ScoreMatrix pwmatrix=ResidueProperties.getScoreMatrix(pwtype);
-          if (pwmatrix==null) {
-            pwmatrix=ResidueProperties.getScoreMatrix("BLOSUM62");
+      }
+    }
+
+    return min;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public float findMinDistance()
+  {
+    float min = 100000;
+
+    for (int i = 0; i < (noseqs - 1); i++)
+    {
+      for (int j = i + 1; j < noseqs; j++)
+      {
+        if ( (done[i] != 1) && (done[j] != 1))
+        {
+          if (distance[i][j] < min)
+          {
+            mini = i;
+            minj = j;
+
+            min = distance[i][j];
           }
-          int maxscore = 0;
-          int end = sequenceString[0].length();
-          for (int i = 0; i < (noseqs - 1); i++)
+        }
+      }
+    }
+
+    return min;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public float[][] findDistances(String[] sequenceString)
+  {
+    float[][] distance = new float[noseqs][noseqs];
+
+    if (pwtype.equals("PID"))
+    {
+      for (int i = 0; i < (noseqs - 1); i++)
+      {
+        for (int j = i; j < noseqs; j++)
+        {
+          if (j == i)
           {
-            for (int j = i; j < noseqs; j++)
-            {
-              int score = 0;
-              
-              for (int k = 0; k < end; k++)
-              {
-                try
-                {
-                  score += pwmatrix.getPairwiseScore(sequenceString[i].charAt(k),
-                      sequenceString[j].charAt(k));
-                }
-                catch (Exception ex)
-                {
-                  System.err.println("err creating BLOSUM62 tree");
-                  ex.printStackTrace();
-                }
-              }
-              
-              distance[i][j] = (float) score;
-              
-              if (score > maxscore)
-              {
-                maxscore = score;
-              }
-            }
+            distance[i][i] = 0;
           }
-          
-          for (int i = 0; i < (noseqs - 1); i++)
+          else
           {
-            for (int j = i; j < noseqs; j++)
-            {
-              distance[i][j] = (float) maxscore - distance[i][j];
-              distance[j][i] = distance[i][j];
-            }
+            distance[i][j] = 100 -
+                Comparison.PID(sequenceString[i], sequenceString[j]);
+
+            distance[j][i] = distance[i][j];
           }
-          
         }
-        return distance;
-    
-          //   else
-      /*  else if (pwtype.equals("SW"))
+      }
+    }
+    else
+    {
+      // Pairwise substitution score (with no gap penalties)
+      ScoreMatrix pwmatrix = ResidueProperties.getScoreMatrix(pwtype);
+      if (pwmatrix == null)
+      {
+        pwmatrix = ResidueProperties.getScoreMatrix("BLOSUM62");
+      }
+      int maxscore = 0;
+      int end = sequenceString[0].length();
+      for (int i = 0; i < (noseqs - 1); i++)
+      {
+        for (int j = i; j < noseqs; j++)
         {
-            float max = -1;
+          int score = 0;
 
-            for (int i = 0; i < (noseqs - 1); i++)
+          for (int k = 0; k < end; k++)
+          {
+            try
             {
-                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];
-                    }
-                }
+              score += pwmatrix.getPairwiseScore(sequenceString[i].charAt(k),
+                                                 sequenceString[j].charAt(k));
             }
-
-            for (int i = 0; i < (noseqs - 1); i++)
+            catch (Exception ex)
             {
-                for (int j = i; j < noseqs; j++)
-                {
-                    distance[i][j] = max - distance[i][j];
-                    distance[j][i] = distance[i][j];
-                }
+              System.err.println("err creating BLOSUM62 tree");
+              ex.printStackTrace();
             }
-        }/*/
-    }
+          }
 
-    /**
-     * DOCUMENT ME!
-     */
-    public void makeLeaves()
-    {
-        cluster = new Vector();
+          distance[i][j] = (float) score;
 
-        for (int i = 0; i < noseqs; i++)
+          if (score > maxscore)
+          {
+            maxscore = score;
+          }
+        }
+      }
+
+      for (int i = 0; i < (noseqs - 1); i++)
+      {
+        for (int j = i; j < noseqs; j++)
         {
-            SequenceNode sn = new SequenceNode();
+          distance[i][j] = (float) maxscore - distance[i][j];
+          distance[j][i] = distance[i][j];
+        }
+      }
 
-            sn.setElement(sequence[i]);
-            sn.setName(sequence[i].getName());
-            node.addElement(sn);
+    }
+    return distance;
 
-            int[] value = new int[1];
-            value[0] = i;
+    //   else
+    /*  else if (pwtype.equals("SW"))
+      {
+          float max = -1;
 
-            Cluster c = new Cluster(value);
-            cluster.addElement(c);
-        }
-    }
+          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];
+                  }
+              }
+          }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param node DOCUMENT ME!
-     * @param leaves DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Vector findLeaves(SequenceNode node, Vector leaves)
+          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];
+              }
+          }
+      }/*/
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void makeLeaves()
+  {
+    cluster = new Vector();
+
+    for (int i = 0; i < noseqs; i++)
     {
-        if (node == null)
-        {
-            return leaves;
-        }
+      SequenceNode sn = new SequenceNode();
 
-        if ((node.left() == null) && (node.right() == null))
-        {
-            leaves.addElement(node);
+      sn.setElement(sequence[i]);
+      sn.setName(sequence[i].getName());
+      node.addElement(sn);
 
-            return leaves;
-        }
-        else
-        {
-            findLeaves((SequenceNode) node.left(), leaves);
-            findLeaves((SequenceNode) node.right(), leaves);
-        }
+      int[] value = new int[1];
+      value[0] = i;
 
-        return leaves;
+      Cluster c = new Cluster(value);
+      cluster.addElement(c);
     }
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param node DOCUMENT ME!
-     * @param count DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Object findLeaf(SequenceNode node, int count)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param node DOCUMENT ME!
+   * @param leaves DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Vector findLeaves(SequenceNode node, Vector leaves)
+  {
+    if (node == null)
     {
-        found = _findLeaf(node, count);
-
-        return found;
+      return leaves;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param node DOCUMENT ME!
-     * @param count DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Object _findLeaf(SequenceNode node, int count)
+    if ( (node.left() == null) && (node.right() == null))
     {
-        if (node == null)
-        {
-            return null;
-        }
+      leaves.addElement(node);
 
-        if (node.ycount == count)
-        {
-            found = node.element();
+      return leaves;
+    }
+    else
+    {
+      findLeaves( (SequenceNode) node.left(), leaves);
+      findLeaves( (SequenceNode) node.right(), leaves);
+    }
 
-            return found;
-        }
-        else
-        {
-            _findLeaf((SequenceNode) node.left(), count);
-            _findLeaf((SequenceNode) node.right(), count);
-        }
+    return leaves;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param node DOCUMENT ME!
+   * @param count DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Object findLeaf(SequenceNode node, int count)
+  {
+    found = _findLeaf(node, count);
+
+    return found;
+  }
 
-        return found;
+  /**
+   * DOCUMENT ME!
+   *
+   * @param node DOCUMENT ME!
+   * @param count DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Object _findLeaf(SequenceNode node, int count)
+  {
+    if (node == null)
+    {
+      return null;
     }
 
-    /**
-     * printNode is mainly for debugging purposes.
-     *
-     * @param node SequenceNode
-     */
-    public void printNode(SequenceNode node)
+    if (node.ycount == count)
     {
-        if (node == null)
-        {
-            return;
-        }
+      found = node.element();
 
-        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("Boot " + node.getBootstrap());
-        }
-        else
-        {
-            System.out.println("Dist " + ((SequenceNode) node).dist);
-            printNode((SequenceNode) node.left());
-            printNode((SequenceNode) node.right());
-        }
+      return found;
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param node DOCUMENT ME!
-     */
-    public void findMaxDist(SequenceNode node)
+    else
     {
-        if (node == null)
-        {
-            return;
-        }
+      _findLeaf( (SequenceNode) node.left(), count);
+      _findLeaf( (SequenceNode) node.right(), count);
+    }
 
-        if ((node.left() == null) && (node.right() == null))
-        {
-            float dist = ((SequenceNode) node).dist;
+    return found;
+  }
 
-            if (dist > maxDistValue)
-            {
-                maxdist = (SequenceNode) node;
-                maxDistValue = dist;
-            }
-        }
-        else
-        {
-            findMaxDist((SequenceNode) node.left());
-            findMaxDist((SequenceNode) node.right());
-        }
+  /**
+   * printNode is mainly for debugging purposes.
+   *
+   * @param node SequenceNode
+   */
+  public void printNode(SequenceNode node)
+  {
+    if (node == null)
+    {
+      return;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Vector getGroups()
+    if ( (node.left() == null) && (node.right() == null))
     {
-        return groups;
+      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());
+    }
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public float getMaxHeight()
+  /**
+   * DOCUMENT ME!
+   *
+   * @param node DOCUMENT ME!
+   */
+  public void findMaxDist(SequenceNode node)
+  {
+    if (node == null)
     {
-        return maxheight;
+      return;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param node DOCUMENT ME!
-     * @param threshold DOCUMENT ME!
-     */
-    public void groupNodes(SequenceNode node, float threshold)
+    if ( (node.left() == null) && (node.right() == null))
     {
-        if (node == null)
-        {
-            return;
-        }
+      float dist = ( (SequenceNode) node).dist;
 
-        if ((node.height / maxheight) > threshold)
-        {
-            groups.addElement(node);
-        }
-        else
-        {
-            groupNodes((SequenceNode) node.left(), threshold);
-            groupNodes((SequenceNode) node.right(), threshold);
-        }
+      if (dist > maxDistValue)
+      {
+        maxdist = (SequenceNode) node;
+        maxDistValue = dist;
+      }
+    }
+    else
+    {
+      findMaxDist( (SequenceNode) node.left());
+      findMaxDist( (SequenceNode) node.right());
     }
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param node DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public float findHeight(SequenceNode node)
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Vector getGroups()
+  {
+    return groups;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public float getMaxHeight()
+  {
+    return maxheight;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param node DOCUMENT ME!
+   * @param threshold DOCUMENT ME!
+   */
+  public void groupNodes(SequenceNode node, float threshold)
+  {
+    if (node == null)
     {
-        if (node == null)
-        {
-            return maxheight;
-        }
+      return;
+    }
 
-        if ((node.left() == null) && (node.right() == null))
-        {
-            node.height = ((SequenceNode) node.parent()).height + node.dist;
+    if ( (node.height / maxheight) > threshold)
+    {
+      groups.addElement(node);
+    }
+    else
+    {
+      groupNodes( (SequenceNode) node.left(), threshold);
+      groupNodes( (SequenceNode) node.right(), threshold);
+    }
+  }
 
-            if (node.height > maxheight)
-            {
-                return node.height;
-            }
-            else
-            {
-                return maxheight;
-            }
-        }
-        else
-        {
-            if (node.parent() != null)
-            {
-                node.height = ((SequenceNode) node.parent()).height +
-                    node.dist;
-            }
-            else
-            {
-                maxheight = 0;
-                node.height = (float) 0.0;
-            }
+  /**
+   * DOCUMENT ME!
+   *
+   * @param node DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public float findHeight(SequenceNode node)
+  {
+    if (node == null)
+    {
+      return maxheight;
+    }
 
-            maxheight = findHeight((SequenceNode) (node.left()));
-            maxheight = findHeight((SequenceNode) (node.right()));
-        }
+    if ( (node.left() == null) && (node.right() == null))
+    {
+      node.height = ( (SequenceNode) node.parent()).height + node.dist;
 
+      if (node.height > maxheight)
+      {
+        return node.height;
+      }
+      else
+      {
         return maxheight;
+      }
     }
+    else
+    {
+      if (node.parent() != null)
+      {
+        node.height = ( (SequenceNode) node.parent()).height +
+            node.dist;
+      }
+      else
+      {
+        maxheight = 0;
+        node.height = (float) 0.0;
+      }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public SequenceNode reRoot()
+      maxheight = findHeight( (SequenceNode) (node.left()));
+      maxheight = findHeight( (SequenceNode) (node.right()));
+    }
+
+    return maxheight;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public SequenceNode reRoot()
+  {
+    if (maxdist != null)
     {
-        if (maxdist != null)
-        {
-            ycount = 0;
+      ycount = 0;
 
-            float tmpdist = maxdist.dist;
+      float tmpdist = maxdist.dist;
 
-            // New top
-            SequenceNode sn = new SequenceNode();
-            sn.setParent(null);
+      // New top
+      SequenceNode sn = new SequenceNode();
+      sn.setParent(null);
 
-            // New right hand of top
-            SequenceNode snr = (SequenceNode) maxdist.parent();
-            changeDirection(snr, maxdist);
-            System.out.println("Printing reversed tree");
-            printN(snr);
-            snr.dist = tmpdist / 2;
-            maxdist.dist = tmpdist / 2;
+      // New right hand of top
+      SequenceNode snr = (SequenceNode) maxdist.parent();
+      changeDirection(snr, maxdist);
+      System.out.println("Printing reversed tree");
+      printN(snr);
+      snr.dist = tmpdist / 2;
+      maxdist.dist = tmpdist / 2;
 
-            snr.setParent(sn);
-            maxdist.setParent(sn);
+      snr.setParent(sn);
+      maxdist.setParent(sn);
 
-            sn.setRight(snr);
-            sn.setLeft(maxdist);
+      sn.setRight(snr);
+      sn.setLeft(maxdist);
 
-            top = sn;
+      top = sn;
 
-            ycount = 0;
-            reCount(top);
-            findHeight(top);
-        }
+      ycount = 0;
+      reCount(top);
+      findHeight(top);
+    }
 
-        return top;
+    return top;
+  }
+
+  /**
+   *
+   * @return true if original sequence data can be recovered
+   */
+  public boolean hasOriginalSequenceData()
+  {
+    return seqData != null;
+  }
+
+  /**
+   * Returns original alignment data used for calculation - or null where
+   * not available.
+   *
+   * @return null or cut'n'pasteable alignment
+   */
+  public String printOriginalSequenceData(char gapChar)
+  {
+    if (seqData == null)
+    {
+      return null;
     }
-    /**
-     *
-     * @return true if original sequence data can be recovered
-     */
-    public boolean hasOriginalSequenceData() {
-      return seqData!=null;
+
+    StringBuffer sb = new StringBuffer();
+    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(" " + seqdatas[i] + "\n");
     }
-    /**
-     * Returns original alignment data used for calculation - or null where
-     * not available.
-     *
-     * @return null or cut'n'pasteable alignment
-     */
-    public String printOriginalSequenceData(char gapChar)
+    return sb.toString();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param node DOCUMENT ME!
+   */
+  public void printN(SequenceNode node)
+  {
+    if (node == null)
     {
-      if (seqData==null)
-        return null;
+      return;
+    }
 
-      StringBuffer sb = new StringBuffer();
-      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(" "+seqdatas[i]+"\n");
-      }
-      return sb.toString();
+    if ( (node.left() != null) && (node.right() != null))
+    {
+      printN( (SequenceNode) node.left());
+      printN( (SequenceNode) node.right());
     }
-    /**
-     * DOCUMENT ME!
-     *
-     * @param node DOCUMENT ME!
-     */
-    public void printN(SequenceNode node)
+    else
     {
-        if (node == null)
-        {
-            return;
-        }
+      System.out.println(" name = " +
+                         ( (SequenceI) node.element()).getName());
+    }
 
-        if ((node.left() != null) && (node.right() != null))
-        {
-            printN((SequenceNode) node.left());
-            printN((SequenceNode) node.right());
-        }
-        else
-        {
-            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!
+   */
+  public void reCount(SequenceNode node)
+  {
+    ycount = 0;
+    _reCount(node);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param node DOCUMENT ME!
+   */
+  public void _reCount(SequenceNode node)
+  {
+    if (node == null)
+    {
+      return;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param node DOCUMENT ME!
-     */
-    public void reCount(SequenceNode node)
+    if ( (node.left() != null) && (node.right() != null))
+    {
+      _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;
+    }
+    else
     {
-        ycount = 0;
-        _reCount(node);
+      ( (SequenceNode) node).count = 1;
+      ( (SequenceNode) node).ycount = ycount++;
     }
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param node DOCUMENT ME!
-     */
-    public void _reCount(SequenceNode node)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param node DOCUMENT ME!
+   */
+  public void swapNodes(SequenceNode node)
+  {
+    if (node == null)
     {
-        if (node == null)
-        {
-            return;
-        }
+      return;
+    }
 
-        if ((node.left() != null) && (node.right() != null))
-        {
-            _reCount((SequenceNode) node.left());
-            _reCount((SequenceNode) node.right());
+    SequenceNode tmp = (SequenceNode) node.left();
 
-            SequenceNode l = (SequenceNode) node.left();
-            SequenceNode r = (SequenceNode) node.right();
+    node.setLeft(node.right());
+    node.setRight(tmp);
+  }
 
-            ((SequenceNode) node).count = l.count + r.count;
-            ((SequenceNode) node).ycount = (l.ycount + r.ycount) / 2;
-        }
-        else
-        {
-            ((SequenceNode) node).count = 1;
-            ((SequenceNode) node).ycount = ycount++;
-        }
+  /**
+   * DOCUMENT ME!
+   *
+   * @param node DOCUMENT ME!
+   * @param dir DOCUMENT ME!
+   */
+  public void changeDirection(SequenceNode node, SequenceNode dir)
+  {
+    if (node == null)
+    {
+      return;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param node DOCUMENT ME!
-     */
-    public void swapNodes(SequenceNode node)
+    if (node.parent() != top)
     {
-        if (node == null)
-        {
-            return;
-        }
+      changeDirection( (SequenceNode) node.parent(), node);
 
-        SequenceNode tmp = (SequenceNode) node.left();
+      SequenceNode tmp = (SequenceNode) node.parent();
 
-        node.setLeft(node.right());
+      if (dir == node.left())
+      {
+        node.setParent(dir);
+        node.setLeft(tmp);
+      }
+      else if (dir == node.right())
+      {
+        node.setParent(dir);
         node.setRight(tmp);
+      }
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param node DOCUMENT ME!
-     * @param dir DOCUMENT ME!
-     */
-    public void changeDirection(SequenceNode node, SequenceNode dir)
+    else
     {
-        if (node == null)
+      if (dir == node.left())
+      {
+        node.setParent(node.left());
+
+        if (top.left() == node)
         {
-            return;
+          node.setRight(top.right());
         }
-
-        if (node.parent() != top)
+        else
         {
-            changeDirection((SequenceNode) node.parent(), node);
-
-            SequenceNode tmp = (SequenceNode) node.parent();
+          node.setRight(top.left());
+        }
+      }
+      else
+      {
+        node.setParent(node.right());
 
-            if (dir == node.left())
-            {
-                node.setParent(dir);
-                node.setLeft(tmp);
-            }
-            else if (dir == node.right())
-            {
-                node.setParent(dir);
-                node.setRight(tmp);
-            }
+        if (top.left() == node)
+        {
+          node.setLeft(top.right());
         }
         else
         {
-            if (dir == node.left())
-            {
-                node.setParent(node.left());
-
-                if (top.left() == node)
-                {
-                    node.setRight(top.right());
-                }
-                else
-                {
-                    node.setRight(top.left());
-                }
-            }
-            else
-            {
-                node.setParent(node.right());
-
-                if (top.left() == node)
-                {
-                    node.setLeft(top.right());
-                }
-                else
-                {
-                    node.setLeft(top.left());
-                }
-            }
+          node.setLeft(top.left());
         }
+      }
     }
+  }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public SequenceNode getMaxDist()
+  {
+    return maxdist;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public SequenceNode getMaxDist()
-    {
-        return maxdist;
-    }
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public SequenceNode getTopNode()
+  {
+    return top;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public SequenceNode getTopNode()
-    {
-        return top;
-    }
-    /**
-     *
-     * @return true if tree has real distances
-     */
-    public boolean isHasDistances() {
-      return hasDistances;
-    }
+  /**
+   *
+   * @return true if tree has real distances
+   */
+  public boolean isHasDistances()
+  {
+    return hasDistances;
+  }
 
-    /**
-     *
-     * @return true if tree has real bootstrap values
-     */
-    public boolean isHasBootstrap() {
-      return hasBootstrap;
-    }
+  /**
+   *
+   * @return true if tree has real bootstrap values
+   */
+  public boolean isHasBootstrap()
+  {
+    return hasBootstrap;
+  }
 
   public boolean isHasRootDistance()
   {
@@ -1253,7 +1274,6 @@ public class NJTree
 
 }
 
-
 /**
  * DOCUMENT ME!
  *
@@ -1262,16 +1282,15 @@ public class NJTree
  */
 class Cluster
 {
-    int[] value;
-
-    /**
-     * Creates a new Cluster object.
-     *
-     * @param value DOCUMENT ME!
-     */
-    public Cluster(int[] value)
-    {
-        this.value = value;
-    }
+  int[] value;
+
+  /**
+   * Creates a new Cluster object.
+   *
+   * @param value DOCUMENT ME!
+   */
+  public Cluster(int[] value)
+  {
+    this.value = value;
+  }
 }
-
diff --git a/src/jalview/analysis/PCA.java b/src/jalview/analysis/PCA.java
index 5005732..c11610a 100755
--- a/src/jalview/analysis/PCA.java
+++ b/src/jalview/analysis/PCA.java
@@ -1,241 +1,239 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 jalview.analysis;
 
-import jalview.datamodel.*;
+import java.io.*;
 
+import jalview.datamodel.*;
 import jalview.math.*;
 
-import java.io.*;
-
 /**
  * Performs Principal Component Analysis on given sequences
  *
  * @author $author$
  * @version $Revision$
  */
-public class PCA implements Runnable
+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)
+  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[] 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
-       */
+    BinarySequence[] bs2 = new BinarySequence[s.length];
+    ii = 0;
 
-      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)
+    while ( (ii < s.length) && (s[ii] != null))
     {
-        return eigenvector.d[i];
+      bs2[ii] = new BinarySequence(s[ii]);
+      bs2[ii].blosumEncode();
+      ii++;
     }
 
-     /**
-     * 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;
-        }
+    //System.out.println("Created binary encoding");
+    //printMemory(rt);
+    int count = 0;
 
-        return out;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param n DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public double[] component(int n)
+    while ( (count < bs.length) && (bs[count] != null))
     {
-        // n = index of eigenvector
-        double[] out = new double[m.rows];
+      count++;
+    }
 
-        for (int i = 0; i < m.rows; i++)
-        {
-            out[i] = component(i, n);
-        }
+    double[][] seqmat = new double[count][bs[0].getDBinary().length];
+    double[][] seqmat2 = new double[count][bs2[0].getDBinary().length];
+    int i = 0;
 
-        return out;
+    while (i < count)
+    {
+      seqmat[i] = bs[i].getDBinary();
+      seqmat2[i] = bs2[i].getDBinary();
+      i++;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param row DOCUMENT ME!
-     * @param n DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    double component(int row, int n)
+    //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++)
     {
-        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];
+      out[i][0] = (float) component(i, l) * factor;
+      out[i][1] = (float) component(i, n) * factor;
+      out[i][2] = (float) component(i, mm) * factor;
     }
 
-    public String getDetails()
+    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++)
     {
-      return details.toString();
+      out[i] = component(i, n);
     }
 
-
-    /**
-     * DOCUMENT ME!
-     */
-    public void run()
+    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++)
     {
-        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 );
+      out += (symm.value[row][i] * eigenvector.value[i][n]);
+    }
 
-        symm = eigenvector.copy();
+    return out / eigenvector.d[n];
+  }
 
-        eigenvector.tred();
+  public String getDetails()
+  {
+    return details.toString();
+  }
 
-        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();
+  /**
+   * DOCUMENT ME!
+   */
+  public void run()
+  {
+    Matrix mt = m.transpose();
 
-        // Now produce the diagonalization matrix
-        eigenvector.tqli();
+    details.append(" --- OrigT * Orig ---- \n");
+    eigenvector = mt.preMultiply(m2);
 
+    PrintStream ps = new PrintStream(System.out)
+    {
+      public void print(String x)
+      {
+        details.append(x);
+      }
 
-        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);
-    }
+      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/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java
index 00fbad5..f5ca651 100755
--- a/src/jalview/analysis/SeqsetUtils.java
+++ b/src/jalview/analysis/SeqsetUtils.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -49,18 +49,25 @@ public class SeqsetUtils
     sqinfo.put("Name", seq.getName());
     sqinfo.put("Start", new Integer(seq.getStart()));
     sqinfo.put("End", new Integer(seq.getEnd()));
-    if (seq.getDescription()!=null)
+    if (seq.getDescription() != null)
+    {
       sqinfo.put("Description", seq.getDescription());
+    }
     Vector sfeat = new Vector();
-    jalview.datamodel.SequenceFeature[] sfarray=seq.getSequenceFeatures();
-    if (sfarray!=null && sfarray.length>0) {
-      for (int i=0;i<sfarray.length;i++)
+    jalview.datamodel.SequenceFeature[] sfarray = seq.getSequenceFeatures();
+    if (sfarray != null && sfarray.length > 0)
+    {
+      for (int i = 0; i < sfarray.length; i++)
+      {
         sfeat.add(sfarray[i]);
+      }
     }
     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("datasetSequence",
+               (seq.getDatasetSequence() != null) ? seq.getDatasetSequence() :
+               new Sequence("THISISAPLACEHOLDER", ""));
     return sqinfo;
   }
 
@@ -74,15 +81,17 @@ public class SeqsetUtils
   public static boolean SeqCharacterUnhash(SequenceI sq, Hashtable sqinfo)
   {
     boolean namePresent = true;
-    if (sqinfo==null)
+    if (sqinfo == null)
+    {
       return false;
+    }
     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 pdbid = (Vector) sqinfo.get("PdbId");
-    String description=(String) sqinfo.get("Description");
+    String description = (String) sqinfo.get("Description");
     Sequence seqds = (Sequence) sqinfo.get("datasetSequence");
     if (oldname == null)
     {
@@ -92,7 +101,7 @@ public class SeqsetUtils
     {
       sq.setName(oldname);
     }
-    if (pdbid!=null && pdbid.size()>0)
+    if (pdbid != null && pdbid.size() > 0)
     {
       sq.setPDBId(pdbid);
     }
@@ -103,14 +112,19 @@ public class SeqsetUtils
       sq.setEnd(end.intValue());
     }
 
-    if ((sfeatures != null) && (sfeatures.size()>0))
+    if ( (sfeatures != null) && (sfeatures.size() > 0))
     {
       SequenceFeature[] sfarray = (SequenceFeature[]) sfeatures.toArray();
       sq.setSequenceFeatures(sfarray);
     }
-    if (description!=null)
+    if (description != null)
+    {
       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);
     }
 
@@ -152,9 +166,9 @@ public class SeqsetUtils
       }
     }
 
-
     return map;
   }
+
   /**
    * recover unsafe sequence names and original properties for a sequence
    * set using a map generated by @see uniquify(sequences,true)
@@ -164,66 +178,88 @@ public class SeqsetUtils
    */
   public static boolean deuniquify(Hashtable map, SequenceI[] sequences)
   {
-    jalview.analysis.SequenceIdMatcher matcher = new SequenceIdMatcher(sequences);
+    jalview.analysis.SequenceIdMatcher matcher = new SequenceIdMatcher(
+        sequences);
     SequenceI msq = null;
     Enumeration keys = map.keys();
     Vector unmatched = new Vector();
-    for (int i=0, j=sequences.length; i<j; i++)
+    for (int i = 0, j = sequences.length; i < j; i++)
+    {
       unmatched.add(sequences[i]);
-    while (keys.hasMoreElements()) {
+    }
+    while (keys.hasMoreElements())
+    {
       Object key = keys.nextElement();
-      if (key instanceof String) {
-        if ((msq = matcher.findIdMatch((String) key))!=null) {
+      if (key instanceof String)
+      {
+        if ( (msq = matcher.findIdMatch( (String) key)) != null)
+        {
           Hashtable sqinfo = (Hashtable) map.get(key);
           unmatched.remove(msq);
           SeqCharacterUnhash(msq, sqinfo);
         }
         else
         {
-          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) {
+    if (unmatched.size() > 0)
+    {
       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()))
+      {
+        ;
+      }
       return false;
     }
 
     return true;
   }
+
   /**
    * 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) {
-      // Identify first row of alignment with residues for prediction
-      boolean ungapped[] = new boolean[sequences.length];
-      int msflen=0;
-      for (int i=0,j=sequences.length; i<j;i++) {
-        String tempseq = jalview.analysis.AlignSeq.extractGaps(
-            jalview.util.Comparison.GapChars,
-            sequences[i].getSequenceAsString());
-
-        if (tempseq.length()==0)
-          ungapped[i]=false;
-        else {
-          ungapped[i]=true;
-          msflen++;
-        }
+  public static SequenceI[] getNonEmptySequenceSet(SequenceI[] sequences)
+  {
+    // Identify first row of alignment with residues for prediction
+    boolean ungapped[] = new boolean[sequences.length];
+    int msflen = 0;
+    for (int i = 0, j = sequences.length; i < j; i++)
+    {
+      String tempseq = jalview.analysis.AlignSeq.extractGaps(
+          jalview.util.Comparison.GapChars,
+          sequences[i].getSequenceAsString());
+
+      if (tempseq.length() == 0)
+      {
+        ungapped[i] = false;
       }
-      if (msflen==0)
-        return null; // no minimal set
-      // compose minimal set
-      SequenceI[] mset = new SequenceI[msflen];
-      for (int i=0,j=sequences.length,k=0; i<j;i++) {
-        if (ungapped[i])
-          mset[k++] = sequences[i];
+      else
+      {
+        ungapped[i] = true;
+        msflen++;
+      }
+    }
+    if (msflen == 0)
+    {
+      return null; // no minimal set
+    }
+    // compose minimal set
+    SequenceI[] mset = new SequenceI[msflen];
+    for (int i = 0, j = sequences.length, k = 0; i < j; i++)
+    {
+      if (ungapped[i])
+      {
+        mset[k++] = sequences[i];
       }
-      ungapped = null;
-      return mset;
+    }
+    ungapped = null;
+    return mset;
   }
 }
diff --git a/src/jalview/analysis/SequenceIdMatcher.java b/src/jalview/analysis/SequenceIdMatcher.java
index 7c974e2..0744937 100755
--- a/src/jalview/analysis/SequenceIdMatcher.java
+++ b/src/jalview/analysis/SequenceIdMatcher.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -49,6 +49,7 @@ public class SequenceIdMatcher
       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.
@@ -56,22 +57,28 @@ public class SequenceIdMatcher
    * @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)
+  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);
+    }
+    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) {
+    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);
+      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) {
+      if (Math.abs(matchlen - namlen) > Math.abs(candlen - namlen) &&
+          candlen > matchlen)
+      {
         match = cand;
         matchlen = candlen;
       }
@@ -91,10 +98,11 @@ public class SequenceIdMatcher
   }
 
   SequenceI findIdMatch(String seqnam)
-    {
-      SeqIdName nam = new SeqIdName(seqnam);
-      return findIdMatch(nam);
+  {
+    SeqIdName nam = new SeqIdName(seqnam);
+    return findIdMatch(nam);
   }
+
   /**
    * findIdMatch
    *
@@ -140,7 +148,7 @@ public class SequenceIdMatcher
   private SequenceI findIdMatch(jalview.analysis.SequenceIdMatcher.SeqIdName
                                 nam)
   {
-    Vector matches=new Vector();
+    Vector matches = new Vector();
     while (names.containsKey(nam))
     {
       matches.addElement(names.remove(nam));
@@ -154,15 +162,19 @@ public class SequenceIdMatcher
 
     SeqIdName(String s)
     {
-      if (s!=null)
+      if (s != null)
+      {
         id = new String(s);
+      }
       else
+      {
         id = "";
+      }
     }
 
     public int hashCode()
     {
-      return ((id.length()>=4) ? id.substring(0, 4).hashCode() : id.hashCode());
+      return ( (id.length() >= 4) ? id.substring(0, 4).hashCode() : id.hashCode());
     }
 
     public boolean equals(Object s)
@@ -188,39 +200,47 @@ public class SequenceIdMatcher
      * 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="~. |#\\/<>!\"£$%^*)}[@',?_";
-
-   /**
-    * matches if one ID properly contains another at a whitespace boundary.
-    * TODO: (JBPNote) These are not efficient. should use char[] for speed
-    * todo: (JBPNote) Set separator characters appropriately
-    * @param s SeqIdName
-    * @return boolean
-    */
+    private String WORD_SEP = "~. |#\\/<>!\"£$%^*)}[@',?_";
+
+    /**
+     * 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()) {
+      if (id.length() > s.id.length())
+      {
         return id.startsWith(s.id) ?
-            (WORD_SEP.indexOf(id.charAt(s.id.length()))>-1)
+            (WORD_SEP.indexOf(id.charAt(s.id.length())) > -1)
             : false;
-      } else
+      }
+      else
+      {
         return s.id.startsWith(id) ?
             (s.id.equals(id) ? true :
-             (WORD_SEP.indexOf(s.id.charAt(id.length()))>-1))
+             (WORD_SEP.indexOf(s.id.charAt(id.length())) > -1))
             : false;
+      }
     }
 
     public boolean equals(String s)
     {
-      if (id.length()>s.length()) {
+      if (id.length() > s.length())
+      {
         return id.startsWith(s) ?
-            (WORD_SEP.indexOf(id.charAt(s.length()))>-1)
+            (WORD_SEP.indexOf(id.charAt(s.length())) > -1)
             : false;
-      } else
+      }
+      else
+      {
         return s.startsWith(id) ?
             (s.equals(id) ? true :
-             (WORD_SEP.indexOf(s.charAt(id.length()))>-1))
+             (WORD_SEP.indexOf(s.charAt(id.length())) > -1))
             : false;
+      }
     }
   }
 }
diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 5f73fbf..fde6bb8 100755
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -19,14 +19,15 @@
 
 package jalview.appletgui;
 
+import java.util.*;
+
 import java.awt.*;
 import java.awt.event.*;
-import java.util.Vector;
 
 import jalview.analysis.*;
+import jalview.commands.*;
 import jalview.datamodel.*;
 import jalview.schemes.*;
-import jalview.commands.ChangeCaseCommand;
 
 public class APopupMenu
     extends java.awt.PopupMenu implements ActionListener, ItemListener
@@ -93,9 +94,11 @@ public class APopupMenu
       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);
@@ -103,7 +106,7 @@ public class APopupMenu
 
     SequenceGroup sg = ap.av.getSelectionGroup();
 
-    if (sg != null && sg.getSize()>0)
+    if (sg != null && sg.getSize() > 0)
     {
       editGroupName.setLabel(sg.getName());
       showText.setState(sg.getDisplayText());
@@ -121,12 +124,12 @@ public class APopupMenu
       remove(groupMenu);
     }
 
-    if (links!=null)
+    if (links != null)
     {
       Menu linkMenu = new Menu("Link");
       MenuItem item;
       String link;
-      for(int i=0; i<links.size(); i++)
+      for (int i = 0; i < links.size(); i++)
       {
         link = links.elementAt(i).toString();
         final String target = link.substring(0, link.indexOf("|"));
@@ -138,7 +141,9 @@ public class APopupMenu
         {
           String id = seq.getName();
           if (id.indexOf("|") > -1)
+          {
             id = id.substring(id.lastIndexOf("|") + 1);
+          }
 
           url = link.substring(link.indexOf("|") + 1,
                                link.indexOf("$SEQUENCE_ID$"))
@@ -146,95 +151,151 @@ public class APopupMenu
               link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
         }
         else
-          url = link.substring(link.lastIndexOf("|")+1);
-
-           item.addActionListener(new java.awt.event.ActionListener()
-           {
-               public void actionPerformed(ActionEvent e)
-               {
-                  ap.alignFrame.showURL(url, target);
-               }
-           });
-          linkMenu.add(item);
+        {
+          url = link.substring(link.lastIndexOf("|") + 1);
+        }
+
+        item.addActionListener(new java.awt.event.ActionListener()
+        {
+          public void actionPerformed(ActionEvent e)
+          {
+            ap.alignFrame.showURL(url, target);
+          }
+        });
+        linkMenu.add(item);
       }
-      if(seq!=null)
+      if (seq != null)
+      {
         seqMenu.add(linkMenu);
+      }
       else
+      {
         add(linkMenu);
+      }
     }
-    if(seq!=null)
+    if (seq != null)
     {
       seqMenu.setLabel(seq.getName());
       repGroup.setLabel("Represent Group with " + seq.getName());
     }
     else
+    {
       remove(seqMenu);
+    }
 
-    if(!ap.av.hasHiddenRows)
+    if (!ap.av.hasHiddenRows)
+    {
       remove(revealAll);
+    }
   }
 
   public void itemStateChanged(ItemEvent evt)
   {
-    if(evt.getSource()==abovePIDColour)
+    if (evt.getSource() == abovePIDColour)
+    {
       abovePIDColour_itemStateChanged();
-    else if(evt.getSource()==showColourText)
+    }
+    else if (evt.getSource() == showColourText)
+    {
       showColourText_itemStateChanged();
-    else if(evt.getSource()==showText)
+    }
+    else if (evt.getSource() == showText)
+    {
       showText_itemStateChanged();
-    else if(evt.getSource()==showBoxes)
-       showBoxes_itemStateChanged()   ;
+    }
+    else if (evt.getSource() == showBoxes)
+    {
+      showBoxes_itemStateChanged();
+    }
   }
 
   public void actionPerformed(ActionEvent evt)
   {
     Object source = evt.getSource();
-    if(source==clustalColour)
+    if (source == clustalColour)
+    {
       clustalColour_actionPerformed();
-    else if(source==zappoColour)
+    }
+    else if (source == zappoColour)
+    {
       zappoColour_actionPerformed();
-    else if(source==taylorColour)
+    }
+    else if (source == taylorColour)
+    {
       taylorColour_actionPerformed();
-    else if(source==hydrophobicityColour)
+    }
+    else if (source == hydrophobicityColour)
+    {
       hydrophobicityColour_actionPerformed();
-    else if(source==helixColour)
+    }
+    else if (source == helixColour)
+    {
       helixColour_actionPerformed();
-    else if(source==strandColour)
+    }
+    else if (source == strandColour)
+    {
       strandColour_actionPerformed();
-    else if(source==turnColour)
+    }
+    else if (source == turnColour)
+    {
       turnColour_actionPerformed();
-    else if(source==buriedColour)
+    }
+    else if (source == buriedColour)
+    {
       buriedColour_actionPerformed();
-    else if(source==nucleotideMenuItem)
+    }
+    else if (source == nucleotideMenuItem)
+    {
       nucleotideMenuItem_actionPerformed();
+    }
 
     else if (source == userDefinedColour)
+    {
       userDefinedColour_actionPerformed();
+    }
     else if (source == PIDColour)
+    {
       PIDColour_actionPerformed();
+    }
     else if (source == BLOSUM62Colour)
+    {
       BLOSUM62Colour_actionPerformed();
+    }
     else if (source == noColourmenuItem)
+    {
       noColourmenuItem_actionPerformed();
+    }
     else if (source == conservationMenuItem)
+    {
       conservationMenuItem_itemStateChanged();
+    }
     else if (source == unGroupMenuItem)
+    {
       unGroupMenuItem_actionPerformed();
+    }
 
-    else if(source == sequenceName)
+    else if (source == sequenceName)
+    {
       editName();
-    else if(source == pdb)
+    }
+    else if (source == pdb)
+    {
       addPDB();
-    else if(source == hideSeqs)
+    }
+    else if (source == hideSeqs)
+    {
       hideSequences(false);
-    else if(source == repGroup)
+    }
+    else if (source == repGroup)
+    {
       hideSequences(true);
-    else if(source == revealAll)
+    }
+    else if (source == revealAll)
     {
-        ap.av.showAllHiddenSeqs();
+      ap.av.showAllHiddenSeqs();
     }
 
-    else if(source==editGroupName)
+    else if (source == editGroupName)
     {
       EditNameDialog dialog = new EditNameDialog(
           getGroup().getName(),
@@ -252,84 +313,95 @@ public class APopupMenu
       }
 
     }
-    else if(source==copy)
+    else if (source == copy)
+    {
       ap.alignFrame.copy_actionPerformed();
-    else if(source==cut)
-      ap.alignFrame.cut_actionPerformed();
-    else if(source==toUpper || source==toLower || source==toggleCase)
+    }
+    else if (source == cut)
     {
-    SequenceGroup sg = ap.av.getSelectionGroup();
-    Vector regions = new Vector();
-    if (sg != null)
+      ap.alignFrame.cut_actionPerformed();
+    }
+    else if (source == toUpper || source == toLower || source == toggleCase)
     {
-      int start = sg.getStartRes();
-      int end = sg.getEndRes() + 1;
-
-      do
+      SequenceGroup sg = ap.av.getSelectionGroup();
+      Vector regions = new Vector();
+      if (sg != null)
       {
-        if (ap.av.hasHiddenColumns)
+        int start = sg.getStartRes();
+        int end = sg.getEndRes() + 1;
+
+        do
         {
-          if(start==0)
-            start = ap.av.colSel.adjustForHiddenColumns(start);
-
-          end = ap.av.colSel.getHiddenBoundaryRight(start);
-          if (start == end)
-            end = sg.getEndRes() + 1;
-          if (end > sg.getEndRes())
-            end = sg.getEndRes() + 1;
+          if (ap.av.hasHiddenColumns)
+          {
+            if (start == 0)
+            {
+              start = ap.av.colSel.adjustForHiddenColumns(start);
+            }
+
+            end = ap.av.colSel.getHiddenBoundaryRight(start);
+            if (start == end)
+            {
+              end = sg.getEndRes() + 1;
+            }
+            if (end > sg.getEndRes())
+            {
+              end = sg.getEndRes() + 1;
+            }
+          }
+
+          regions.addElement(new int[]
+                             {start, end});
+
+          if (ap.av.hasHiddenColumns)
+          {
+            start = ap.av.colSel.adjustForHiddenColumns(end);
+            start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;
+          }
         }
+        while (end < sg.getEndRes());
 
-        regions.addElement(new int[]
-                           {start, end});
-
-        if (ap.av.hasHiddenColumns)
+        int[][] startEnd = new int[regions.size()][2];
+        for (int i = 0; i < regions.size(); i++)
         {
-          start = ap.av.colSel.adjustForHiddenColumns(end);
-          start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;
+          startEnd[i] = (int[]) regions.elementAt(i);
         }
-      }
-      while (end < sg.getEndRes());
 
-      int[][] startEnd = new int[regions.size()][2];
-      for (int i = 0; i < regions.size(); i++)
-      {
-        startEnd[i] = (int[]) regions.elementAt(i);
-      }
+        String description;
+        int caseChange;
 
+        if (source == toggleCase)
+        {
+          description = "Toggle Case";
+          caseChange = ChangeCaseCommand.TOGGLE_CASE;
+        }
+        else if (source == toUpper)
+        {
+          description = "To Upper Case";
+          caseChange = ChangeCaseCommand.TO_UPPER;
+        }
+        else
+        {
+          description = "To Lower Case";
+          caseChange = ChangeCaseCommand.TO_LOWER;
+        }
 
-      String description;
-      int caseChange;
-
-      if(source==toggleCase)
-      {
-        description = "Toggle Case";
-        caseChange = ChangeCaseCommand.TOGGLE_CASE;
-      }
-      else if(source==toUpper)
-      {
-        description = "To Upper Case";
-        caseChange = ChangeCaseCommand.TO_UPPER;
-      }
-      else
-      {
-        description = "To Lower Case";
-        caseChange = ChangeCaseCommand.TO_LOWER;
-      }
-
-      ChangeCaseCommand caseCommand = new ChangeCaseCommand(
-          description, sg.getSequencesAsArray(ap.av.hiddenRepSequences), startEnd, caseChange
-          );
-
-      ap.alignFrame.addHistoryItem(caseCommand);
+        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
+    {
       outputText(evt);
+    }
 
   }
 
@@ -345,7 +417,7 @@ public class APopupMenu
 
     cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(
         e.getActionCommand(),
-      new Alignment( ap.av.getSelectionAsNewSequence() ),
+        new Alignment(ap.av.getSelectionAsNewSequence()),
         ap.av.showJVSuffix));
 
   }
@@ -490,8 +562,10 @@ public class APopupMenu
   void refresh()
   {
     ap.seqPanel.seqCanvas.repaint();
-    if(ap.overviewPanel!=null)
+    if (ap.overviewPanel != null)
+    {
       ap.overviewPanel.updateOverviewImage();
+    }
   }
 
   protected void clustalColour_actionPerformed()
@@ -553,12 +627,15 @@ public class APopupMenu
   protected void abovePIDColour_itemStateChanged()
   {
     SequenceGroup sg = getGroup();
-    if(sg.cs==null)
-          return;
+    if (sg.cs == null)
+    {
+      return;
+    }
 
     if (abovePIDColour.getState())
     {
-      sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.hiddenRepSequences), 0,
+      sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
+          hiddenRepSequences), 0,
                                                ap.av.alignment.getWidth()));
       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
           getGroup().getName());
@@ -586,7 +663,8 @@ public class APopupMenu
   {
     SequenceGroup sg = getGroup();
     sg.cs = new PIDColourScheme();
-    sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.hiddenRepSequences), 0,
+    sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
+        hiddenRepSequences), 0,
                                              ap.av.alignment.getWidth()));
     refresh();
   }
@@ -597,7 +675,8 @@ public class APopupMenu
 
     sg.cs = new Blosum62ColourScheme();
 
-    sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.hiddenRepSequences), 0,
+    sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
+        hiddenRepSequences), 0,
                                              ap.av.alignment.getWidth()));
 
     refresh();
@@ -612,15 +691,18 @@ public class APopupMenu
   protected void conservationMenuItem_itemStateChanged()
   {
     SequenceGroup sg = getGroup();
-    if(sg.cs==null)
-          return;
+    if (sg.cs == null)
+    {
+      return;
+    }
 
     if (conservationMenuItem.getState())
     {
 
       Conservation c = new Conservation("Group",
                                         ResidueProperties.propHash, 3,
-                                        sg.getSequences(ap.av.hiddenRepSequences), 0,
+                                        sg.getSequences(ap.av.
+          hiddenRepSequences), 0,
                                         ap.av.alignment.getWidth());
 
       c.calculate();
@@ -639,14 +721,15 @@ public class APopupMenu
     refresh();
   }
 
-
   SequenceGroup getGroup()
   {
     SequenceGroup sg = ap.av.getSelectionGroup();
 
     // this method won't add a new group if it already exists
-    if(sg!=null)
+    if (sg != null)
+    {
       ap.av.alignment.addGroup(sg);
+    }
 
     return sg;
   }
@@ -680,9 +763,10 @@ public class APopupMenu
   void hideSequences(boolean representGroup)
   {
     SequenceGroup sg = ap.av.getSelectionGroup();
-    if(sg==null || sg.getSize()<1)
+    if (sg == null || sg.getSize() < 1)
     {
-      ap.av.hideSequence(new SequenceI[]{seq});
+      ap.av.hideSequence(new SequenceI[]
+                         {seq});
       return;
     }
 
@@ -707,6 +791,6 @@ public class APopupMenu
     }
 
     ap.av.hideSequence(hseqs);
-    }
+  }
 
 }
diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index de9da9f..a076345 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -19,20 +19,21 @@
 
 package jalview.appletgui;
 
-import jalview.schemes.*;
-import jalview.datamodel.*;
-import jalview.analysis.*;
-import jalview.io.*;
-import jalview.commands.*;
+import java.io.*;
+import java.net.*;
+import java.util.*;
+
 import java.awt.*;
 import java.awt.event.*;
-import java.util.*;
-import java.io.InputStreamReader;
-import java.io.BufferedReader;
-import java.net.URL;
 
+import jalview.analysis.*;
+import jalview.commands.*;
+import jalview.datamodel.*;
+import jalview.io.*;
+import jalview.schemes.*;
 
-public class AlignFrame extends Frame implements ActionListener,
+public class AlignFrame
+    extends Frame implements ActionListener,
     ItemListener, KeyListener, MouseListener
 {
   public AlignmentPanel alignPanel;
@@ -42,19 +43,22 @@ public class AlignFrame extends Frame implements ActionListener,
 
   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)
+    {
       jalviewServletURL = applet.getParameter("APPLICATION_URL");
+    }
 
-    try{
+    try
+    {
       jbInit();
-    }catch(Exception ex)
+    }
+    catch (Exception ex)
     {
       ex.printStackTrace();
     }
@@ -69,15 +73,19 @@ public class AlignFrame extends Frame implements ActionListener,
 
     seqLimits.setState(viewport.showJVSuffix);
 
-    if(applet!=null)
+    if (applet != null)
     {
       String param = applet.getParameter("sortBy");
       if (param != null)
       {
         if (param.equalsIgnoreCase("Id"))
+        {
           sortIDMenuItem_actionPerformed();
+        }
         else if (param.equalsIgnoreCase("Pairwise Identity"))
+        {
           sortPairwiseMenuItem_actionPerformed();
+        }
       }
 
       param = applet.getParameter("wrap");
@@ -110,28 +118,28 @@ public class AlignFrame extends Frame implements ActionListener,
 
     }
 
-   //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);
-   alignPanel.scalePanel.addKeyListener(this);
-   alignPanel.annotationPanel.addKeyListener(this);
+    //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);
+    alignPanel.scalePanel.addKeyListener(this);
+    alignPanel.annotationPanel.addKeyListener(this);
 
-
-   if(embedded)
-   {
-     setEmbedded();
-   }
-   else
-   {
-     add(alignPanel, BorderLayout.CENTER);
-     jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
-                                      DEFAULT_HEIGHT);
-   }
-   alignPanel.validate();
-   alignPanel.repaint();
+    if (embedded)
+    {
+      setEmbedded();
+    }
+    else
+    {
+      add(alignPanel, BorderLayout.CENTER);
+      jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
+                                       DEFAULT_HEIGHT);
+    }
+    alignPanel.validate();
+    alignPanel.repaint();
   }
+
   public AlignViewport getAlignViewport()
   {
     return viewport;
@@ -142,7 +150,6 @@ public class AlignFrame extends Frame implements ActionListener,
     return alignPanel.seqPanel.seqCanvas;
   }
 
-
   /**
    * DOCUMENT ME!
    *
@@ -153,23 +160,27 @@ public class AlignFrame extends Frame implements ActionListener,
   {
     Hashtable featureLinks = new Hashtable();
     boolean featuresFile = false;
-    try{
-      featuresFile = new jalview.io.FeaturesFile(file, type).parse(viewport.alignment,
-                                         alignPanel.seqPanel.seqCanvas.
-                                         getFeatureRenderer().featureColours,
-                                         featureLinks,
-                                         true);
+    try
+    {
+      featuresFile = new jalview.io.FeaturesFile(file,
+          type).parse(viewport.alignment,
+                      alignPanel.seqPanel.seqCanvas.
+                      getFeatureRenderer().featureColours,
+                      featureLinks,
+                      true);
     }
-    catch(Exception ex)
+    catch (Exception ex)
     {
       ex.printStackTrace();
     }
 
-    if(featuresFile)
+    if (featuresFile)
     {
-      if(featureLinks.size()>0)
+      if (featureLinks.size() > 0)
+      {
         alignPanel.seqPanel.seqCanvas
             .getFeatureRenderer().featureLinks = featureLinks;
+      }
       viewport.showSequenceFeatures = true;
       sequenceFeatures.setState(true);
       alignPanel.repaint();
@@ -177,7 +188,6 @@ public class AlignFrame extends Frame implements ActionListener,
 
   }
 
-
   public void keyPressed(KeyEvent evt)
   {
     if (viewport.cursorMode
@@ -221,38 +231,42 @@ public class AlignFrame extends Frame implements ActionListener,
         }
         break;
       case KeyEvent.VK_DOWN:
-        if(viewport.cursorMode)
+        if (viewport.cursorMode)
         {
-          alignPanel.seqPanel.moveCursor(0,1);
+          alignPanel.seqPanel.moveCursor(0, 1);
         }
         else
+        {
           moveSelectedSequences(false);
+        }
         break;
 
       case KeyEvent.VK_UP:
         if (viewport.cursorMode)
         {
-          alignPanel.seqPanel.moveCursor(0,-1);
+          alignPanel.seqPanel.moveCursor(0, -1);
         }
         else
+        {
           moveSelectedSequences(true);
+        }
         break;
 
       case KeyEvent.VK_LEFT:
-        if(viewport.cursorMode)
+        if (viewport.cursorMode)
         {
-          alignPanel.seqPanel.moveCursor(-1,0);
+          alignPanel.seqPanel.moveCursor( -1, 0);
         }
         break;
 
       case KeyEvent.VK_RIGHT:
         if (viewport.cursorMode)
         {
-          alignPanel.seqPanel.moveCursor(1,0);
+          alignPanel.seqPanel.moveCursor(1, 0);
         }
         break;
       case KeyEvent.VK_SPACE:
-        if(viewport.cursorMode)
+        if (viewport.cursorMode)
         {
           alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
                                                 || evt.isShiftDown()
@@ -263,13 +277,13 @@ public class AlignFrame extends Frame implements ActionListener,
 
       case KeyEvent.VK_DELETE:
       case KeyEvent.VK_BACK_SPACE:
-        if(viewport.cursorMode)
+        if (viewport.cursorMode)
         {
           alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
                                                 || evt.isShiftDown()
                                                 || evt.isAltDown());
         }
-       else
+        else
         {
           cut_actionPerformed();
           alignPanel.seqPanel.seqCanvas.repaint();
@@ -277,13 +291,13 @@ public class AlignFrame extends Frame implements ActionListener,
         break;
 
       case KeyEvent.VK_S:
-        if(viewport.cursorMode)
+        if (viewport.cursorMode)
         {
           alignPanel.seqPanel.setCursorRow();
         }
         break;
       case KeyEvent.VK_P:
-        if(viewport.cursorMode)
+        if (viewport.cursorMode)
         {
           alignPanel.seqPanel.setCursorPosition();
         }
@@ -291,35 +305,35 @@ public class AlignFrame extends Frame implements ActionListener,
 
       case KeyEvent.VK_ENTER:
       case KeyEvent.VK_COMMA:
-        if(viewport.cursorMode)
+        if (viewport.cursorMode)
         {
           alignPanel.seqPanel.setCursorRowAndColumn();
         }
         break;
 
       case KeyEvent.VK_Q:
-        if(viewport.cursorMode)
+        if (viewport.cursorMode)
         {
           alignPanel.seqPanel.setSelectionAreaAtCursor(true);
         }
         break;
       case KeyEvent.VK_M:
-        if(viewport.cursorMode)
+        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_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())
@@ -335,47 +349,61 @@ public class AlignFrame extends Frame implements ActionListener,
         boolean hide = false;
         SequenceGroup sg = viewport.getSelectionGroup();
 
-        if(toggleSeqs)
+        if (toggleSeqs)
         {
           if (sg != null && sg.getSize() != viewport.alignment.getHeight())
           {
             hide = true;
             viewport.hideAllSelectedSeqs();
           }
-          else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
+          else if (! (toggleCols && viewport.colSel.getSelected().size() > 0))
+          {
             viewport.showAllHiddenSeqs();
+          }
         }
 
-        if(toggleCols)
+        if (toggleCols)
         {
           if (viewport.colSel.getSelected().size() > 0)
           {
             viewport.hideSelectedColumns();
-            if(!toggleSeqs)
-                   viewport.selectionGroup = sg;
+            if (!toggleSeqs)
+            {
+              viewport.selectionGroup = sg;
+            }
           }
           else if (!hide)
+          {
             viewport.showAllHiddenColumns();
+          }
         }
         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_Z:
@@ -410,18 +438,26 @@ public class AlignFrame extends Frame implements ActionListener,
         if (evt.isControlDown())
         {
           if (evt.isShiftDown())
+          {
             this.removeAllGapsMenuItem_actionPerformed();
+          }
           else
+          {
             removeGappedColumnMenuItem_actionPerformed();
+          }
         }
         break;
       case KeyEvent.VK_I:
         if (evt.isControlDown())
         {
           if (evt.isAltDown())
+          {
             viewport.invertColumnSelection();
+          }
           else
+          {
             this.invertSequenceMenuItem_actionPerformed();
+          }
         }
         break;
 
@@ -430,213 +466,364 @@ public class AlignFrame extends Frame implements ActionListener,
         {
           this.deleteGroups_actionPerformed();
         }
-      break;
-
-    case KeyEvent.VK_T:
-      if (evt.isControlDown())
-      {
-       newView();
-      }
-      break;
+        break;
 
+      case KeyEvent.VK_T:
+        if (evt.isControlDown())
+        {
+          newView();
+        }
+        break;
 
-      }
-      alignPanel.repaint();
+    }
+    alignPanel.repaint();
   }
+
   public void keyReleased(KeyEvent evt)
   {}
+
   public void keyTyped(KeyEvent evt)
   {}
 
-public void itemStateChanged(ItemEvent evt)
-  {
-    if(evt.getSource()==colourTextMenuItem)
-            colourTextMenuItem_actionPerformed();
-    else if(evt.getSource()==wrapMenuItem)
-            wrapMenuItem_actionPerformed();
-    else if(evt.getSource()==scaleAbove)
-            viewport.setScaleAboveWrapped(scaleAbove.getState());
-    else if(evt.getSource()==scaleLeft)
-            viewport.setScaleLeftWrapped(scaleLeft.getState());
-    else if(evt.getSource()==scaleRight)
-            viewport.setScaleRightWrapped(scaleRight.getState());
-     else if(evt.getSource()==seqLimits)
+  public void itemStateChanged(ItemEvent evt)
+  {
+    if (evt.getSource() == colourTextMenuItem)
+    {
+      colourTextMenuItem_actionPerformed();
+    }
+    else if (evt.getSource() == wrapMenuItem)
+    {
+      wrapMenuItem_actionPerformed();
+    }
+    else if (evt.getSource() == scaleAbove)
+    {
+      viewport.setScaleAboveWrapped(scaleAbove.getState());
+    }
+    else if (evt.getSource() == scaleLeft)
+    {
+      viewport.setScaleLeftWrapped(scaleLeft.getState());
+    }
+    else if (evt.getSource() == scaleRight)
+    {
+      viewport.setScaleRightWrapped(scaleRight.getState());
+    }
+    else if (evt.getSource() == seqLimits)
+    {
       seqLimits_itemStateChanged();
-    else if(evt.getSource()==viewBoxesMenuItem)
-            viewport.setShowBoxes(viewBoxesMenuItem.getState());
-    else if(evt.getSource()==viewTextMenuItem)
-            viewport.setShowText(viewTextMenuItem.getState());
-    else if(evt.getSource()==renderGapsMenuItem)
-            viewport.setRenderGaps(renderGapsMenuItem.getState());
-    else if(evt.getSource()==annotationPanelMenuItem)
+    }
+    else if (evt.getSource() == viewBoxesMenuItem)
+    {
+      viewport.setShowBoxes(viewBoxesMenuItem.getState());
+    }
+    else if (evt.getSource() == viewTextMenuItem)
+    {
+      viewport.setShowText(viewTextMenuItem.getState());
+    }
+    else if (evt.getSource() == renderGapsMenuItem)
+    {
+      viewport.setRenderGaps(renderGapsMenuItem.getState());
+    }
+    else if (evt.getSource() == annotationPanelMenuItem)
     {
       viewport.setShowAnnotation(annotationPanelMenuItem.getState());
       alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
     }
-      else if(evt.getSource()==sequenceFeatures)
-      {
-           viewport.showSequenceFeatures(sequenceFeatures.getState());
-            alignPanel.seqPanel.seqCanvas.repaint();
-      }
-      else if(evt.getSource()==conservationMenuItem)
-            conservationMenuItem_actionPerformed();
-      else if(evt.getSource()==abovePIDThreshold)
-            abovePIDThreshold_actionPerformed();
-      else if(evt.getSource()==applyToAllGroups)
-            viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
-      else if(evt.getSource()==autoCalculate)
-          viewport.autocalculateConsensus = autoCalculate.getState();
+    else if (evt.getSource() == sequenceFeatures)
+    {
+      viewport.showSequenceFeatures(sequenceFeatures.getState());
+      alignPanel.seqPanel.seqCanvas.repaint();
+    }
+    else if (evt.getSource() == conservationMenuItem)
+    {
+      conservationMenuItem_actionPerformed();
+    }
+    else if (evt.getSource() == abovePIDThreshold)
+    {
+      abovePIDThreshold_actionPerformed();
+    }
+    else if (evt.getSource() == applyToAllGroups)
+    {
+      viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
+    }
+    else if (evt.getSource() == autoCalculate)
+    {
+      viewport.autocalculateConsensus = autoCalculate.getState();
+    }
 
-      alignPanel.repaint();
+    alignPanel.repaint();
   }
- public void actionPerformed(ActionEvent evt)
- {
+
+  public void actionPerformed(ActionEvent evt)
+  {
     Object source = evt.getSource();
 
-    if(source==inputText)
+    if (source == inputText)
+    {
       inputText_actionPerformed();
-    else if(source==loadTree)
+    }
+    else if (source == loadTree)
+    {
       loadTree_actionPerformed();
-    else if(source==loadApplication)
+    }
+    else if (source == loadApplication)
+    {
       launchFullApplication();
+    }
     else if (source == loadAnnotations)
+    {
       loadAnnotations();
+    }
     else if (source == outputAnnotations)
+    {
       outputAnnotations(true);
-    else if(source == outputFeatures)
+    }
+    else if (source == outputFeatures)
+    {
       outputFeatures(true, "Jalview");
-    else if(source==closeMenuItem)
+    }
+    else if (source == closeMenuItem)
+    {
       closeMenuItem_actionPerformed();
-    else if(source==copy)
+    }
+    else if (source == copy)
+    {
       copy_actionPerformed();
-    else if(source==undoMenuItem)
+    }
+    else if (source == undoMenuItem)
+    {
       undoMenuItem_actionPerformed();
-    else if(source==redoMenuItem)
+    }
+    else if (source == redoMenuItem)
+    {
       redoMenuItem_actionPerformed();
-    else if(source==inputText)
-            inputText_actionPerformed();
-    else if(source==closeMenuItem)
-            closeMenuItem_actionPerformed();
-    else if(source==undoMenuItem)
-            undoMenuItem_actionPerformed();
-    else if(source==redoMenuItem)
-            redoMenuItem_actionPerformed();
-    else if(source==copy)
-            copy_actionPerformed();
-    else if(source==pasteNew)
-            pasteNew_actionPerformed();
-    else if(source==pasteThis)
-            pasteThis_actionPerformed();
-    else if(source==cut)
-            cut_actionPerformed();
-    else if(source==delete)
-            delete_actionPerformed();
-    else if(source==deleteGroups)
-            deleteGroups_actionPerformed();
-    else if(source==selectAllSequenceMenuItem)
-            selectAllSequenceMenuItem_actionPerformed();
-    else if(source==deselectAllSequenceMenuItem)
-            deselectAllSequenceMenuItem_actionPerformed();
-    else if(source==invertSequenceMenuItem)
-            invertSequenceMenuItem_actionPerformed();
-    else if(source==invertColSel)
-    { viewport.invertColumnSelection(); alignPanel.repaint(); }
-    else if(source==remove2LeftMenuItem)
-            trimAlignment(true);
-    else if(source==remove2RightMenuItem)
-            trimAlignment(false);
-    else if(source==removeGappedColumnMenuItem)
-            removeGappedColumnMenuItem_actionPerformed();
-    else if(source==removeAllGapsMenuItem)
-            removeAllGapsMenuItem_actionPerformed();
-    else if(source==findMenuItem)
-            findMenuItem_actionPerformed();
-    else if(source==font)
-            new FontChooser(alignPanel);
+    }
+    else if (source == inputText)
+    {
+      inputText_actionPerformed();
+    }
+    else if (source == closeMenuItem)
+    {
+      closeMenuItem_actionPerformed();
+    }
+    else if (source == undoMenuItem)
+    {
+      undoMenuItem_actionPerformed();
+    }
+    else if (source == redoMenuItem)
+    {
+      redoMenuItem_actionPerformed();
+    }
+    else if (source == copy)
+    {
+      copy_actionPerformed();
+    }
+    else if (source == pasteNew)
+    {
+      pasteNew_actionPerformed();
+    }
+    else if (source == pasteThis)
+    {
+      pasteThis_actionPerformed();
+    }
+    else if (source == cut)
+    {
+      cut_actionPerformed();
+    }
+    else if (source == delete)
+    {
+      delete_actionPerformed();
+    }
+    else if (source == deleteGroups)
+    {
+      deleteGroups_actionPerformed();
+    }
+    else if (source == selectAllSequenceMenuItem)
+    {
+      selectAllSequenceMenuItem_actionPerformed();
+    }
+    else if (source == deselectAllSequenceMenuItem)
+    {
+      deselectAllSequenceMenuItem_actionPerformed();
+    }
+    else if (source == invertSequenceMenuItem)
+    {
+      invertSequenceMenuItem_actionPerformed();
+    }
+    else if (source == invertColSel)
+    {
+      viewport.invertColumnSelection();
+      alignPanel.repaint();
+    }
+    else if (source == remove2LeftMenuItem)
+    {
+      trimAlignment(true);
+    }
+    else if (source == remove2RightMenuItem)
+    {
+      trimAlignment(false);
+    }
+    else if (source == removeGappedColumnMenuItem)
+    {
+      removeGappedColumnMenuItem_actionPerformed();
+    }
+    else if (source == removeAllGapsMenuItem)
+    {
+      removeAllGapsMenuItem_actionPerformed();
+    }
+    else if (source == findMenuItem)
+    {
+      findMenuItem_actionPerformed();
+    }
+    else if (source == font)
+    {
+      new FontChooser(alignPanel);
+    }
     else if (source == newView)
+    {
       newView();
-    else if(source==showColumns)
+    }
+    else if (source == showColumns)
     {
-      viewport.showAllHiddenColumns(); alignPanel.repaint();
+      viewport.showAllHiddenColumns();
+      alignPanel.repaint();
     }
-    else if(source==showSeqs)
+    else if (source == showSeqs)
     {
       viewport.showAllHiddenSeqs();
     }
-    else if(source == hideColumns)
+    else if (source == hideColumns)
     {
-      viewport.hideSelectedColumns(); alignPanel.repaint();
+      viewport.hideSelectedColumns();
+      alignPanel.repaint();
     }
-    else if(source == hideSequences && viewport.getSelectionGroup()!=null)
+    else if (source == hideSequences && viewport.getSelectionGroup() != null)
     {
       viewport.hideAllSelectedSeqs();
     }
-    else if(source==featureSettings)
-            new FeatureSettings(alignPanel);
-    else if(source==overviewMenuItem)
-            overviewMenuItem_actionPerformed();
-    else if(source==noColourmenuItem)
-            changeColour(null);
-    else if(source==clustalColour)
+    else if (source == featureSettings)
+    {
+      new FeatureSettings(alignPanel);
+    }
+    else if (source == overviewMenuItem)
+    {
+      overviewMenuItem_actionPerformed();
+    }
+    else if (source == noColourmenuItem)
+    {
+      changeColour(null);
+    }
+    else if (source == clustalColour)
     {
       abovePIDThreshold.setState(false);
       changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),
                                             viewport.alignment.getWidth()));
+    }
+    else if (source == zappoColour)
+    {
+      changeColour(new ZappoColourScheme());
+    }
+    else if (source == taylorColour)
+    {
+      changeColour(new TaylorColourScheme());
+    }
+    else if (source == hydrophobicityColour)
+    {
+      changeColour(new HydrophobicColourScheme());
+    }
+    else if (source == helixColour)
+    {
+      changeColour(new HelixColourScheme());
+    }
+    else if (source == strandColour)
+    {
+      changeColour(new StrandColourScheme());
+    }
+    else if (source == turnColour)
+    {
+      changeColour(new TurnColourScheme());
+    }
+    else if (source == buriedColour)
+    {
+      changeColour(new BuriedColourScheme());
+    }
+    else if (source == nucleotideColour)
+    {
+      changeColour(new NucleotideColourScheme());
+    }
+    else if (source == modifyPID)
+    {
+      modifyPID_actionPerformed();
+    }
+    else if (source == modifyConservation)
+    {
+      modifyConservation_actionPerformed();
+    }
+    else if (source == userDefinedColour)
+    {
+      new UserDefinedColours(alignPanel, null);
+    }
+    else if (source == PIDColour)
+    {
+      changeColour(new PIDColourScheme());
+    }
+    else if (source == BLOSUM62Colour)
+    {
+      changeColour(new Blosum62ColourScheme());
+    }
+    else if (source == annotationColour)
+    {
+      new AnnotationColourChooser(viewport, alignPanel);
+    }
+    else if (source == sortPairwiseMenuItem)
+    {
+      sortPairwiseMenuItem_actionPerformed();
+    }
+    else if (source == sortIDMenuItem)
+    {
+      sortIDMenuItem_actionPerformed();
+    }
+    else if (source == sortGroupMenuItem)
+    {
+      sortGroupMenuItem_actionPerformed();
+    }
+    else if (source == removeRedundancyMenuItem)
+    {
+      removeRedundancyMenuItem_actionPerformed();
+    }
+    else if (source == pairwiseAlignmentMenuItem)
+    {
+      pairwiseAlignmentMenuItem_actionPerformed();
+    }
+    else if (source == PCAMenuItem)
+    {
+      PCAMenuItem_actionPerformed();
+    }
+    else if (source == averageDistanceTreeMenuItem)
+    {
+      averageDistanceTreeMenuItem_actionPerformed();
+    }
+    else if (source == neighbourTreeMenuItem)
+    {
+      neighbourTreeMenuItem_actionPerformed();
+    }
+    else if (source == njTreeBlosumMenuItem)
+    {
+      njTreeBlosumMenuItem_actionPerformed();
+    }
+    else if (source == avDistanceTreeBlosumMenuItem)
+    {
+      avTreeBlosumMenuItem_actionPerformed();
+    }
+    else if (source == documentation)
+    {
+      documentation_actionPerformed();
+    }
+    else if (source == about)
+    {
+      about_actionPerformed();
+    }
+
   }
-    else if(source==zappoColour)
-            changeColour(new ZappoColourScheme());
-    else if(source==taylorColour)
-            changeColour(new TaylorColourScheme());
-    else if(source==hydrophobicityColour)
-            changeColour(new HydrophobicColourScheme());
-    else if(source==helixColour)
-            changeColour(new HelixColourScheme());
-    else if(source==strandColour)
-            changeColour(new StrandColourScheme());
-    else if(source==turnColour)
-            changeColour(new TurnColourScheme());
-    else if(source==buriedColour)
-            changeColour(new BuriedColourScheme());
-    else if(source==nucleotideColour)
-            changeColour(new NucleotideColourScheme());
-    else if(source==modifyPID)
-            modifyPID_actionPerformed();
-    else if(source==modifyConservation)
-            modifyConservation_actionPerformed();
-    else if(source==userDefinedColour)
-            new UserDefinedColours(alignPanel, null);
-    else if(source==PIDColour)
-            changeColour(new PIDColourScheme());
-    else if(source==BLOSUM62Colour)
-            changeColour(new Blosum62ColourScheme());
-    else if(source==annotationColour)
-           new AnnotationColourChooser(viewport, alignPanel);
-    else if(source==sortPairwiseMenuItem)
-            sortPairwiseMenuItem_actionPerformed();
-    else if(source==sortIDMenuItem)
-            sortIDMenuItem_actionPerformed();
-    else if(source==sortGroupMenuItem)
-            sortGroupMenuItem_actionPerformed();
-    else if(source==removeRedundancyMenuItem)
-            removeRedundancyMenuItem_actionPerformed();
-    else if(source==pairwiseAlignmentMenuItem)
-            pairwiseAlignmentMenuItem_actionPerformed();
-    else if(source==PCAMenuItem)
-            PCAMenuItem_actionPerformed();
-    else if(source==averageDistanceTreeMenuItem)
-            averageDistanceTreeMenuItem_actionPerformed();
-    else if(source==neighbourTreeMenuItem)
-            neighbourTreeMenuItem_actionPerformed();
-    else if(source==njTreeBlosumMenuItem)
-            njTreeBlosumMenuItem_actionPerformed();
-    else if(source==avDistanceTreeBlosumMenuItem)
-            avTreeBlosumMenuItem_actionPerformed();
-    else if(source==documentation)
-            documentation_actionPerformed();
-    else if(source==about)
-            about_actionPerformed();
-
- }
 
   public void inputText_actionPerformed()
   {
@@ -655,8 +842,8 @@ public void itemStateChanged(ItemEvent evt)
                                      "Alignment output - " + e.getActionCommand(),
                                      600, 500);
     cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),
-                                              viewport.getAlignment(),
-                                                      viewport.showJVSuffix));
+        viewport.getAlignment(),
+        viewport.showJVSuffix));
   }
 
   public void loadAnnotations()
@@ -666,7 +853,7 @@ public void itemStateChanged(ItemEvent evt)
     cap.setAnnotationImport();
     Frame frame = new Frame();
     frame.add(cap);
-      jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);
+    jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);
 
   }
 
@@ -676,7 +863,7 @@ public void itemStateChanged(ItemEvent evt)
         viewport.showAnnotation ? viewport.alignment.getAlignmentAnnotation() : null,
         viewport.alignment.getGroups());
 
-    if(displayTextbox)
+    if (displayTextbox)
     {
       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
       Frame frame = new Frame();
@@ -694,16 +881,19 @@ public void itemStateChanged(ItemEvent evt)
   {
     String features;
     if (format.equalsIgnoreCase("Jalview"))
+    {
       features = new FeaturesFile().printJalviewFormat(
-              viewport.alignment.getSequencesArray(),
-              viewport.featuresDisplayed);
+          viewport.alignment.getSequencesArray(),
+          viewport.featuresDisplayed);
+    }
     else
+    {
       features = new FeaturesFile().printGFFFormat(
-             viewport.alignment.getSequencesArray(),
-             viewport.featuresDisplayed);
-
+          viewport.alignment.getSequencesArray(),
+          viewport.featuresDisplayed);
+    }
 
-    if(displayTextbox)
+    if (displayTextbox)
     {
       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
       Frame frame = new Frame();
@@ -722,67 +912,72 @@ public void itemStateChanged(ItemEvent evt)
   {
     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)
+    if (viewport.applet.getParameter("features") != null)
     {
-      url.append( "&features=" );
-      url.append( appendProtocol( viewport.applet.getParameter("features") ) );
+      url.append("&features=");
+      url.append(appendProtocol(viewport.applet.getParameter("features")));
     }
 
-    if(viewport.applet.getParameter("annotations")!=null)
+    if (viewport.applet.getParameter("annotations") != null)
     {
-      url.append( "&annotations=" );
-      url.append( appendProtocol( viewport.applet.getParameter("annotations") ) );
+      url.append("&annotations=");
+      url.append(appendProtocol(viewport.applet.getParameter("annotations")));
     }
 
-    if(viewport.applet.getParameter("jnetfile")!=null)
+    if (viewport.applet.getParameter("jnetfile") != null)
     {
-      url.append( "&annotations=" );
-      url.append( appendProtocol( viewport.applet.getParameter("jnetfile") ) );
+      url.append("&annotations=");
+      url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
     }
 
-    if(viewport.applet.getParameter("defaultColour")!=null)
+    if (viewport.applet.getParameter("defaultColour") != null)
     {
       url.append("&colour=" +
                  removeWhiteSpace(viewport.applet.getParameter("defaultColour"))
           );
     }
 
-    if(viewport.applet.getParameter("userDefinedColour")!=null)
+    if (viewport.applet.getParameter("userDefinedColour") != null)
     {
-      url.append( "&colour=" +
-                 removeWhiteSpace( viewport.applet.getParameter("userDefinedColour") )
-         );
+      url.append("&colour=" +
+                 removeWhiteSpace(viewport.applet.getParameter(
+          "userDefinedColour"))
+          );
     }
 
     showURL(url.toString(), "FULL_APP");
   }
 
-
   String removeWhiteSpace(String colour)
   {
     StringBuffer sb = new StringBuffer();
     for (int i = 0; i < colour.length(); i++)
     {
       if (Character.isWhitespace(colour.charAt(i)))
+      {
         sb.append("%20");
+      }
       else
+      {
         sb.append(colour.charAt(i));
+      }
     }
 
     return sb.toString();
   }
 
-
   String appendProtocol(String url)
   {
-    try{
-       new URL(url);
-    }catch(java.net.MalformedURLException ex)
+    try
+    {
+      new URL(url);
+    }
+    catch (java.net.MalformedURLException ex)
     {
-      url = viewport.applet.getCodeBase()+url;
+      url = viewport.applet.getCodeBase() + url;
     }
     return url;
   }
@@ -793,13 +988,14 @@ public void itemStateChanged(ItemEvent evt)
     PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
     PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
 
-    if(PaintRefresher.components.size()==0 && viewport.applet==null)
+    if (PaintRefresher.components.size() == 0 && viewport.applet == null)
+    {
       System.exit(0);
+    }
 
     this.dispose();
   }
 
-
   /**
    * DOCUMENT ME!
    */
@@ -834,7 +1030,7 @@ public void itemStateChanged(ItemEvent evt)
 
   public void addHistoryItem(CommandI command)
   {
-    if(command.getSize()>0)
+    if (command.getSize() > 0)
     {
       viewport.historyList.push(command);
       viewport.redoList.removeAllElements();
@@ -850,10 +1046,12 @@ public void itemStateChanged(ItemEvent evt)
    */
   protected void undoMenuItem_actionPerformed()
   {
-    if(viewport.historyList.size()<1)
+    if (viewport.historyList.size() < 1)
+    {
       return;
+    }
 
-    CommandI command = (CommandI)viewport.historyList.pop();
+    CommandI command = (CommandI) viewport.historyList.pop();
     viewport.redoList.push(command);
     command.undoCommand();
 
@@ -861,7 +1059,8 @@ public void itemStateChanged(ItemEvent evt)
 
     originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
     updateEditMenuBar();
-    originalSource.firePropertyChange("alignment", null,originalSource.alignment.getSequences());
+    originalSource.firePropertyChange("alignment", null,
+                                      originalSource.alignment.getSequences());
   }
 
   /**
@@ -871,27 +1070,30 @@ public void itemStateChanged(ItemEvent evt)
    */
   protected void redoMenuItem_actionPerformed()
   {
-    if(viewport.redoList.size()<1)
+    if (viewport.redoList.size() < 1)
+    {
       return;
+    }
 
     CommandI command = (CommandI) viewport.redoList.pop();
     viewport.historyList.push(command);
     command.doCommand();
 
     AlignViewport originalSource = getOriginatingSource(command);
-    originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns()!=null;
+    originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
 
     updateEditMenuBar();
-    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;
+    //the property change event FROM the viewport where the
+    //original alignment was altered
+    AlignmentI al = null;
     if (command instanceof EditCommand)
     {
       EditCommand editCommand = (EditCommand) command;
@@ -916,12 +1118,13 @@ public void itemStateChanged(ItemEvent evt)
       //The original view is closed, we must validate
       //the current view against the closed view first
       if (al != null)
+      {
         PaintRefresher.validateSequences(al, viewport.alignment);
+      }
 
       originalSource = viewport;
     }
 
-
     return originalSource;
   }
 
@@ -1010,60 +1213,61 @@ public void itemStateChanged(ItemEvent evt)
             viewport.getColumnSelection().getHiddenColumns().elementAt(i);
 
         copiedHiddenColumns.addElement(new int[]
-                                 {region[0] - hiddenOffset,
-                                 region[1] - hiddenOffset});
+                                       {region[0] - hiddenOffset,
+                                       region[1] - hiddenOffset});
       }
     }
     else
+    {
       copiedHiddenColumns = null;
-
+    }
 
     for (int i = 0; i < sg.getSize(); i++)
     {
-        SequenceI seq = null;
+      SequenceI seq = null;
 
-        while (seq == null)
+      while (seq == null)
+      {
+        if (orderedSeqs.containsKey(index + ""))
         {
-            if (orderedSeqs.containsKey(index + ""))
-            {
-                seq = (SequenceI) orderedSeqs.get(index + "");
-                index++;
+          seq = (SequenceI) orderedSeqs.get(index + "");
+          index++;
 
-                break;
-            }
-            else
-            {
-                index++;
-            }
+          break;
+        }
+        else
+        {
+          index++;
         }
+      }
 
-        //FIND START RES
-        //Returns residue following index if gap
-        startRes = seq.findPosition(sg.getStartRes());
+      //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
-        endRes = 0;
+      //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++)
+      for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
+      {
+        ch = seq.getCharAt(j);
+        if (!jalview.util.Comparison.isGap( (ch)))
         {
-          ch = seq.getCharAt(j);
-          if (!jalview.util.Comparison.isGap( (ch)))
-          {
-            endRes++;
-          }
+          endRes++;
         }
+      }
 
-        if(endRes>0)
-        {
-          endRes += seq.getStart() -1;
-        }
+      if (endRes > 0)
+      {
+        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");
     }
 
   }
@@ -1127,7 +1331,6 @@ public void itemStateChanged(ItemEvent evt)
           }
         }
 
-
         jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
                                          DEFAULT_HEIGHT);
       }
@@ -1189,47 +1392,45 @@ public void itemStateChanged(ItemEvent evt)
       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);
+    }
 
-   // 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++)
-      cut[i] = (SequenceI)seqs.elementAt(i);
-
+    SequenceI[] cut = new SequenceI[seqs.size()];
+    for (int i = 0; i < seqs.size(); i++)
+    {
+      cut[i] = (SequenceI) seqs.elementAt(i);
+    }
 
     /*
-    //ADD HISTORY ITEM
-    */
+         //ADD HISTORY ITEM
+     */
     addHistoryItem(new EditCommand("Cut Sequences",
-                                      EditCommand.CUT,
-                                      cut,
-                                      sg.getStartRes(),
-                                      sg.getEndRes()-sg.getStartRes()+1,
-                                      viewport.alignment));
-
+                                   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.getAlignment().getSequences());
 
     if (viewport.getAlignment().getHeight() < 1)
     {
-        this.setVisible(false);
+      this.setVisible(false);
     }
   }
 
   protected void deleteGroups_actionPerformed()
   {
     viewport.alignment.deleteAllGroups();
-    viewport.sequenceColours=null;
+    viewport.sequenceColours = null;
     viewport.setSelectionGroup(null);
 
     alignPanel.repaint();
@@ -1242,7 +1443,7 @@ public void itemStateChanged(ItemEvent evt)
     {
       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
     }
-    sg.setEndRes(viewport.alignment.getWidth()-1);
+    sg.setEndRes(viewport.alignment.getWidth() - 1);
     viewport.setSelectionGroup(sg);
     alignPanel.repaint();
     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
@@ -1250,10 +1451,10 @@ public void itemStateChanged(ItemEvent evt)
 
   public void deselectAllSequenceMenuItem_actionPerformed()
   {
-    if(viewport.cursorMode)
+    if (viewport.cursorMode)
     {
-      alignPanel.seqPanel.keyboardNo1=null;
-      alignPanel.seqPanel.keyboardNo2=null;
+      alignPanel.seqPanel.keyboardNo1 = null;
+      alignPanel.seqPanel.keyboardNo2 = null;
     }
     viewport.setSelectionGroup(null);
     viewport.getColumnSelection().clear();
@@ -1282,43 +1483,50 @@ public void itemStateChanged(ItemEvent evt)
 
     if (colSel.size() > 0)
     {
-      if(trimLeft)
+      if (trimLeft)
+      {
         column = colSel.getMin();
+      }
       else
+      {
         column = colSel.getMax();
+      }
 
-      SequenceI [] seqs;
-      if(viewport.getSelectionGroup()!=null)
-        seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences);
+      SequenceI[] seqs;
+      if (viewport.getSelectionGroup() != null)
+      {
+        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);
+                                           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);
-     }
-
-     statusBar.setText("Removed "+trimRegion.getSize()+" columns.");
+      else
+      {
+        trimRegion = new TrimRegionCommand("Remove Right",
+                                           TrimRegionCommand.TRIM_RIGHT,
+                                           seqs,
+                                           column,
+                                           viewport.alignment,
+                                           viewport.colSel,
+                                           viewport.selectionGroup);
+      }
 
+      statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
 
       addHistoryItem(trimRegion);
 
@@ -1340,21 +1548,22 @@ public void itemStateChanged(ItemEvent evt)
     }
   }
 
-
   public void removeGappedColumnMenuItem_actionPerformed()
   {
-    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();
     }
     else
+    {
       seqs = viewport.alignment.getSequencesArray();
-
+    }
 
     RemoveGapColCommand removeGapCols =
         new RemoveGapColCommand("Remove Gapped Columns",
@@ -1364,35 +1573,39 @@ public void itemStateChanged(ItemEvent evt)
 
     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
     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());
 
   }
 
   public void removeAllGapsMenuItem_actionPerformed()
   {
-    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();
     }
     else
+    {
       seqs = viewport.alignment.getSequencesArray();
+    }
 
     //This is to maintain viewport position on first residue
     //of first sequence
@@ -1400,13 +1613,14 @@ public void itemStateChanged(ItemEvent evt)
     int startRes = seq.findPosition(viewport.startRes);
 
     addHistoryItem(new RemoveGapsCommand("Remove Gaps",
-                                           seqs,
-                                           start, end,
-                     viewport.alignment));
+                                         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());
 
   }
 
@@ -1419,18 +1633,22 @@ public void itemStateChanged(ItemEvent evt)
   {
     AlignmentI newal;
     if (viewport.hasHiddenRows)
+    {
       newal = new Alignment(viewport.getAlignment().
                             getHiddenSequences()
                             .getFullAlignment().
                             getSequencesArray());
+    }
     else
+    {
       newal = new Alignment(viewport.alignment.getSequencesArray());
+    }
 
-    if(viewport.alignment.getAlignmentAnnotation()!=null)
+    if (viewport.alignment.getAlignmentAnnotation() != null)
     {
-      for(int i=0; i<viewport.alignment.getAlignmentAnnotation().length; i++)
+      for (int i = 0; i < viewport.alignment.getAlignmentAnnotation().length; i++)
       {
-        if(!viewport.alignment.getAlignmentAnnotation()[i].autoCalculated)
+        if (!viewport.alignment.getAlignmentAnnotation()[i].autoCalculated)
         {
           newal.addAnnotation(viewport.alignment.getAlignmentAnnotation()[i]);
         }
@@ -1452,28 +1670,31 @@ public void itemStateChanged(ItemEvent evt)
     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
                             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++)
     {
       if (comps.elementAt(i) instanceof AlignmentPanel)
+      {
         viewSize++;
+      }
     }
 
     String title = new String(this.getTitle());
     if (title.indexOf("(View") > -1)
+    {
       title = title.substring(0, title.indexOf("(View"));
+    }
 
-    title+= "(View "+viewSize+")";
+    title += "(View " + viewSize + ")";
 
     newaf.setTitle(title.toString());
 
-
     newaf.viewport.historyList = viewport.historyList;
     newaf.viewport.redoList = viewport.redoList;
 
-   }
-
+  }
 
   public void seqLimits_itemStateChanged()
   {
@@ -1482,7 +1703,6 @@ public void itemStateChanged(ItemEvent evt)
     alignPanel.repaint();
   }
 
-
   protected void colourTextMenuItem_actionPerformed()
   {
     viewport.setColourText(colourTextMenuItem.getState());
@@ -1499,7 +1719,6 @@ public void itemStateChanged(ItemEvent evt)
     alignPanel.repaint();
   }
 
-
   public void overviewMenuItem_actionPerformed()
   {
     if (alignPanel.overviewPanel != null)
@@ -1528,12 +1747,11 @@ public void itemStateChanged(ItemEvent evt)
 
   }
 
-
   void changeColour(ColourSchemeI cs)
   {
     int threshold = 0;
 
-    if(cs!=null)
+    if (cs != null)
     {
       if (viewport.getAbovePIDThreshold())
       {
@@ -1583,7 +1801,7 @@ public void itemStateChanged(ItemEvent evt)
       {
         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
 
-        if(cs==null)
+        if (cs == null)
         {
           sg.cs = null;
           continue;
@@ -1616,13 +1834,16 @@ public void itemStateChanged(ItemEvent evt)
               sg.getSequences(viewport.hiddenRepSequences), 0, sg.getWidth()));
         }
         else
+        {
           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
+        }
 
         if (viewport.getConservationSelected())
         {
           Conservation c = new Conservation("Group",
                                             ResidueProperties.propHash, 3,
-                                            sg.getSequences(viewport.hiddenRepSequences), 0,
+                                            sg.getSequences(viewport.
+              hiddenRepSequences), 0,
                                             viewport.alignment.getWidth() - 1);
           c.calculate();
           c.verdict(false, viewport.ConsPercGaps);
@@ -1637,7 +1858,6 @@ public void itemStateChanged(ItemEvent evt)
       }
     }
 
-
     if (alignPanel.getOverviewPanel() != null)
     {
       alignPanel.getOverviewPanel().updateOverviewImage();
@@ -1646,11 +1866,9 @@ public void itemStateChanged(ItemEvent evt)
     alignPanel.repaint();
   }
 
-
-
   protected void modifyPID_actionPerformed()
   {
-    if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
+    if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme != null)
     {
       SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
                                      "Background");
@@ -1660,7 +1878,7 @@ public void itemStateChanged(ItemEvent evt)
 
   protected void modifyConservation_actionPerformed()
   {
-    if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
+    if (viewport.getConservationSelected() && viewport.globalColourScheme != null)
     {
       SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
                                         "Background");
@@ -1692,29 +1910,28 @@ public void itemStateChanged(ItemEvent evt)
     modifyPID_actionPerformed();
   }
 
-
-
   public void sortPairwiseMenuItem_actionPerformed()
   {
-    SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
+    SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
     AlignmentSorter.sortByPID(viewport.getAlignment(),
                               viewport.getAlignment().getSequenceAt(0));
-    addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, viewport.alignment));
+    addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
+                                    viewport.alignment));
     alignPanel.repaint();
   }
 
   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.repaint();
   }
 
   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.repaint();
 
@@ -1722,12 +1939,12 @@ public void itemStateChanged(ItemEvent evt)
 
   public void removeRedundancyMenuItem_actionPerformed()
   {
-     new RedundancyPanel(alignPanel);
+    new RedundancyPanel(alignPanel);
   }
 
   public void pairwiseAlignmentMenuItem_actionPerformed()
   {
-    if (viewport.getSelectionGroup()!=null
+    if (viewport.getSelectionGroup() != null
         && viewport.getSelectionGroup().getSize() > 1)
     {
       Frame frame = new Frame();
@@ -1819,8 +2036,8 @@ public void itemStateChanged(ItemEvent evt)
 
     if ( (viewport.getSelectionGroup() != null &&
           viewport.getSelectionGroup().getSize() > 1)
-      || (viewport.getSelectionGroup() == null
-          && viewport.alignment.getHeight() > 1))
+        || (viewport.getSelectionGroup() == null
+            && viewport.alignment.getHeight() > 1))
     {
       final TreePanel tp = new TreePanel(viewport,
                                          type,
@@ -1834,12 +2051,12 @@ public void itemStateChanged(ItemEvent evt)
 
   void loadTree_actionPerformed()
   {
-      CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
-      cap.setText("Paste your Newick tree file here.");
-      cap.setTreeImport();
-      Frame frame = new Frame();
-      frame.add(cap);
-      jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
+    cap.setText("Paste your Newick tree file here.");
+    cap.setTreeImport();
+    Frame frame = new Frame();
+    frame.add(cap);
+    jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
   }
 
   public void loadTree(jalview.io.NewickFile tree, String treeFile)
@@ -1860,8 +2077,8 @@ public void itemStateChanged(ItemEvent evt)
     {
       public void actionPerformed(ActionEvent evt)
       {
-      //  addHistoryItem(new HistoryItem("Sort", viewport.alignment,
-      //                                 HistoryItem.SORT));
+        //  addHistoryItem(new HistoryItem("Sort", viewport.alignment,
+        //                                 HistoryItem.SORT));
         AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
         alignPanel.repaint();
       }
@@ -1884,11 +2101,14 @@ public void itemStateChanged(ItemEvent evt)
   protected void about_actionPerformed()
   {
 
-    class AboutPanel extends Canvas
+    class AboutPanel
+        extends Canvas
     {
       String version;
       public AboutPanel(String version)
-      { this.version = version; }
+      {
+        this.version = version;
+      }
 
       public void paint(Graphics g)
       {
@@ -1900,7 +2120,7 @@ public void itemStateChanged(ItemEvent evt)
         int y = 5, x = 7;
         g.setColor(Color.black);
         g.setFont(new Font("Helvetica", Font.BOLD, 14));
-        g.drawString("Jalview - Release "+version, 200, y += fh);
+        g.drawString("Jalview - Release " + version, 200, 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);
@@ -1939,7 +2159,6 @@ public void itemStateChanged(ItemEvent evt)
       }
     }
 
-
     Frame frame = new Frame();
     frame.add(new AboutPanel(version));
     jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);
@@ -1956,9 +2175,9 @@ public void itemStateChanged(ItemEvent evt)
     {
       try
       {
-        System.out.println("Show url: "+url);
+        System.out.println("Show url: " + url);
         viewport.applet.getAppletContext().showDocument(new java.net.URL(url),
-                                               target);
+            target);
       }
       catch (Exception ex)
       {
@@ -1967,92 +2186,92 @@ public void itemStateChanged(ItemEvent evt)
     }
   }
 
-
   //////////////////////////////////////////////////////////////////////////////////
   //JBuilder Graphics here
 
-    protected MenuBar alignFrameMenuBar = new MenuBar();
-    protected Menu fileMenu = new Menu("File");
-    protected MenuItem loadApplication = new MenuItem("View in Full Application");
-    protected MenuItem loadTree = new MenuItem("Load Associated Tree ...");
-    protected MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");
-    protected MenuItem outputFeatures = new MenuItem("Export Features ...");
-    protected MenuItem outputAnnotations = new MenuItem("Export Annotations ...");
-
-    protected MenuItem closeMenuItem = new MenuItem("Close");
-    protected Menu editMenu = new Menu("Edit");
-    protected Menu viewMenu = new Menu("View");
-    protected Menu colourMenu = new Menu("Colour");
-    protected Menu calculateMenu = new Menu("Calculate");
-    protected MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
-    protected MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
-    protected MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
-    protected MenuItem remove2LeftMenuItem = new MenuItem();
-    protected MenuItem remove2RightMenuItem = new MenuItem();
-    protected MenuItem removeGappedColumnMenuItem = new MenuItem();
-    protected MenuItem removeAllGapsMenuItem = new MenuItem();
-    protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
-    protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
-    protected MenuItem sortPairwiseMenuItem = new MenuItem();
-    protected MenuItem sortIDMenuItem = new MenuItem();
-    protected MenuItem sortGroupMenuItem = new MenuItem();
-    protected MenuItem removeRedundancyMenuItem = new MenuItem();
-    protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();
-    protected MenuItem PCAMenuItem = new MenuItem();
-    protected MenuItem averageDistanceTreeMenuItem = new MenuItem();
-    protected MenuItem neighbourTreeMenuItem = new MenuItem();
-    BorderLayout borderLayout1 = new BorderLayout();
-    public Label statusBar = new Label();
-    protected Menu outputTextboxMenu = new Menu();
-    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 MenuItem userDefinedColour = new MenuItem();
-    protected MenuItem PIDColour = new MenuItem();
-    protected MenuItem BLOSUM62Colour = new MenuItem();
-    MenuItem njTreeBlosumMenuItem = new MenuItem();
-    MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
-    protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
-    protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
-    MenuItem overviewMenuItem = new MenuItem();
-    protected MenuItem undoMenuItem = new MenuItem();
-    protected MenuItem redoMenuItem = new MenuItem();
-    protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
-    MenuItem noColourmenuItem = new MenuItem();
-    protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
-    protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
-    MenuItem findMenuItem = new MenuItem();
+  protected MenuBar alignFrameMenuBar = new MenuBar();
+  protected Menu fileMenu = new Menu("File");
+  protected MenuItem loadApplication = new MenuItem("View in Full Application");
+  protected MenuItem loadTree = new MenuItem("Load Associated Tree ...");
+  protected MenuItem loadAnnotations = new MenuItem(
+      "Load Features/Annotations ...");
+  protected MenuItem outputFeatures = new MenuItem("Export Features ...");
+  protected MenuItem outputAnnotations = new MenuItem("Export Annotations ...");
+
+  protected MenuItem closeMenuItem = new MenuItem("Close");
+  protected Menu editMenu = new Menu("Edit");
+  protected Menu viewMenu = new Menu("View");
+  protected Menu colourMenu = new Menu("Colour");
+  protected Menu calculateMenu = new Menu("Calculate");
+  protected MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
+  protected MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
+  protected MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
+  protected MenuItem remove2LeftMenuItem = new MenuItem();
+  protected MenuItem remove2RightMenuItem = new MenuItem();
+  protected MenuItem removeGappedColumnMenuItem = new MenuItem();
+  protected MenuItem removeAllGapsMenuItem = new MenuItem();
+  protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
+  protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
+  protected MenuItem sortPairwiseMenuItem = new MenuItem();
+  protected MenuItem sortIDMenuItem = new MenuItem();
+  protected MenuItem sortGroupMenuItem = new MenuItem();
+  protected MenuItem removeRedundancyMenuItem = new MenuItem();
+  protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();
+  protected MenuItem PCAMenuItem = new MenuItem();
+  protected MenuItem averageDistanceTreeMenuItem = new MenuItem();
+  protected MenuItem neighbourTreeMenuItem = new MenuItem();
+  BorderLayout borderLayout1 = new BorderLayout();
+  public Label statusBar = new Label();
+  protected Menu outputTextboxMenu = new Menu();
+  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 MenuItem userDefinedColour = new MenuItem();
+  protected MenuItem PIDColour = new MenuItem();
+  protected MenuItem BLOSUM62Colour = new MenuItem();
+  MenuItem njTreeBlosumMenuItem = new MenuItem();
+  MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
+  protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
+  protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
+  MenuItem overviewMenuItem = new MenuItem();
+  protected MenuItem undoMenuItem = new MenuItem();
+  protected MenuItem redoMenuItem = new MenuItem();
+  protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
+  MenuItem noColourmenuItem = new MenuItem();
+  protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
+  protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
+  MenuItem findMenuItem = new MenuItem();
   protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
-    protected 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();
-    protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
-    protected MenuItem font = new MenuItem();
-    protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
-    protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
-    protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();
-    MenuItem modifyPID = new MenuItem();
-    MenuItem modifyConservation = new MenuItem();
-    protected CheckboxMenuItem autoCalculate
-        = new CheckboxMenuItem("Autocalculate Consensus", true);
-    protected 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();
-    protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();
+  protected 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();
+  protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
+  protected MenuItem font = new MenuItem();
+  protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
+  protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
+  protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();
+  MenuItem modifyPID = new MenuItem();
+  MenuItem modifyConservation = new MenuItem();
+  protected CheckboxMenuItem autoCalculate
+      = new CheckboxMenuItem("Autocalculate Consensus", true);
+  protected 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();
+  protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();
   Panel embeddedMenu;
   Label embeddedEdit;
   Label embeddedSelect;
@@ -2064,176 +2283,179 @@ public void itemStateChanged(ItemEvent evt)
   Label embeddedCalculate;
   FlowLayout flowLayout1;
 
-  private void jbInit() throws Exception {
+  private void jbInit()
+      throws Exception
+  {
 
-      setMenuBar(alignFrameMenuBar);
+    setMenuBar(alignFrameMenuBar);
 
-      MenuItem item;
+    MenuItem item;
 
-      // dynamically fill save as menu with available formats
-      for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
-      {
+    // dynamically fill save as menu with available formats
+    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()
+      item.addActionListener(new java.awt.event.ActionListener()
+      {
+        public void actionPerformed(ActionEvent e)
         {
-          public void actionPerformed(ActionEvent e)
-          {
-            outputText_actionPerformed(e);
-          }
-        });
-
-        outputTextboxMenu.add(item);
-      }
-        closeMenuItem.addActionListener(this);
-        loadApplication.addActionListener(this);
-
-        loadTree.addActionListener(this);
-        loadAnnotations.addActionListener(this);
-        outputFeatures.addActionListener(this);
-        outputAnnotations.addActionListener(this);
-        selectAllSequenceMenuItem.addActionListener(this);
-        deselectAllSequenceMenuItem.addActionListener(this);
-        invertSequenceMenuItem.addActionListener(this);
-        remove2LeftMenuItem.setLabel("Remove Left");
-        remove2LeftMenuItem.addActionListener(this);
-        remove2RightMenuItem.setLabel("Remove Right");
-        remove2RightMenuItem.addActionListener(this);
-        removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
-        removeGappedColumnMenuItem.addActionListener(this);
-        removeAllGapsMenuItem.setLabel("Remove All Gaps");
-        removeAllGapsMenuItem.addActionListener(this);
-        viewBoxesMenuItem.setLabel("Boxes");
-        viewBoxesMenuItem.setState(true);
-        viewBoxesMenuItem.addItemListener(this);
-        viewTextMenuItem.setLabel("Text");
-        viewTextMenuItem.setState(true);
-        viewTextMenuItem.addItemListener(this);
-        sortPairwiseMenuItem.setLabel("by Pairwise Identity");
-        sortPairwiseMenuItem.addActionListener(this);
-        sortIDMenuItem.setLabel("by ID");
-        sortIDMenuItem.addActionListener(this);
-        sortGroupMenuItem.setLabel("by Group");
-        sortGroupMenuItem.addActionListener(this);
-        removeRedundancyMenuItem.setLabel("Remove Redundancy...");
-        removeRedundancyMenuItem.addActionListener(this);
-        pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
-        pairwiseAlignmentMenuItem.addActionListener(this);
-        PCAMenuItem.setLabel("Principal Component Analysis");
-        PCAMenuItem.addActionListener(this);
-        averageDistanceTreeMenuItem.setLabel(
-            "Average Distance Using % Identity");
-        averageDistanceTreeMenuItem.addActionListener(this);
-        neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
-        neighbourTreeMenuItem.addActionListener(this);
-        statusBar.setBackground(Color.white);
-        statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
-        statusBar.setText("Status bar");
-        outputTextboxMenu.setLabel("Output to Textbox");
-        clustalColour.setLabel("Clustalx");
-
-        clustalColour.addActionListener(this);
-        zappoColour.setLabel("Zappo");
-        zappoColour.addActionListener(this);
-        taylorColour.setLabel("Taylor");
-        taylorColour.addActionListener(this);
-        hydrophobicityColour.setLabel("Hydrophobicity");
-        hydrophobicityColour.addActionListener(this);
-        helixColour.setLabel("Helix Propensity");
-        helixColour.addActionListener(this);
-        strandColour.setLabel("Strand Propensity");
-        strandColour.addActionListener(this);
-        turnColour.setLabel("Turn Propensity");
-        turnColour.addActionListener(this);
-        buriedColour.setLabel("Buried Index");
-        buriedColour.addActionListener(this);
-        userDefinedColour.setLabel("User Defined...");
-        userDefinedColour.addActionListener(this);
-        PIDColour.setLabel("Percentage Identity");
-        PIDColour.addActionListener(this);
-        BLOSUM62Colour.setLabel("BLOSUM62 Score");
-        BLOSUM62Colour.addActionListener(this);
-        avDistanceTreeBlosumMenuItem.setLabel(
-            "Average Distance Using BLOSUM62");
-        avDistanceTreeBlosumMenuItem.addActionListener(this);
-        njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
-        njTreeBlosumMenuItem.addActionListener(this);
-        annotationPanelMenuItem.setLabel("Show Annotations");
-        annotationPanelMenuItem.addItemListener(this);
-        colourTextMenuItem.setLabel("Colour Text");
-        colourTextMenuItem.addItemListener(this);
-        overviewMenuItem.setLabel("Overview Window");
-        overviewMenuItem.addActionListener(this);
-        undoMenuItem.setEnabled(false);
-        undoMenuItem.setLabel("Undo");
-        undoMenuItem.addActionListener(this);
-        redoMenuItem.setEnabled(false);
-        redoMenuItem.setLabel("Redo");
-        redoMenuItem.addActionListener(this);
-        conservationMenuItem.setLabel("by Conservation");
-        conservationMenuItem.addItemListener(this);
-        noColourmenuItem.setLabel("None");
-        noColourmenuItem.addActionListener(this);
-        wrapMenuItem.setLabel("Wrap");
-        wrapMenuItem.addItemListener(this);
-        renderGapsMenuItem.setLabel("Show Gaps");
-        renderGapsMenuItem.setState(true);
-        renderGapsMenuItem.addItemListener(this);
-        findMenuItem.setLabel("Find...");
-        findMenuItem.addActionListener(this);
+          outputText_actionPerformed(e);
+        }
+      });
+
+      outputTextboxMenu.add(item);
+    }
+    closeMenuItem.addActionListener(this);
+    loadApplication.addActionListener(this);
+
+    loadTree.addActionListener(this);
+    loadAnnotations.addActionListener(this);
+    outputFeatures.addActionListener(this);
+    outputAnnotations.addActionListener(this);
+    selectAllSequenceMenuItem.addActionListener(this);
+    deselectAllSequenceMenuItem.addActionListener(this);
+    invertSequenceMenuItem.addActionListener(this);
+    remove2LeftMenuItem.setLabel("Remove Left");
+    remove2LeftMenuItem.addActionListener(this);
+    remove2RightMenuItem.setLabel("Remove Right");
+    remove2RightMenuItem.addActionListener(this);
+    removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
+    removeGappedColumnMenuItem.addActionListener(this);
+    removeAllGapsMenuItem.setLabel("Remove All Gaps");
+    removeAllGapsMenuItem.addActionListener(this);
+    viewBoxesMenuItem.setLabel("Boxes");
+    viewBoxesMenuItem.setState(true);
+    viewBoxesMenuItem.addItemListener(this);
+    viewTextMenuItem.setLabel("Text");
+    viewTextMenuItem.setState(true);
+    viewTextMenuItem.addItemListener(this);
+    sortPairwiseMenuItem.setLabel("by Pairwise Identity");
+    sortPairwiseMenuItem.addActionListener(this);
+    sortIDMenuItem.setLabel("by ID");
+    sortIDMenuItem.addActionListener(this);
+    sortGroupMenuItem.setLabel("by Group");
+    sortGroupMenuItem.addActionListener(this);
+    removeRedundancyMenuItem.setLabel("Remove Redundancy...");
+    removeRedundancyMenuItem.addActionListener(this);
+    pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
+    pairwiseAlignmentMenuItem.addActionListener(this);
+    PCAMenuItem.setLabel("Principal Component Analysis");
+    PCAMenuItem.addActionListener(this);
+    averageDistanceTreeMenuItem.setLabel(
+        "Average Distance Using % Identity");
+    averageDistanceTreeMenuItem.addActionListener(this);
+    neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
+    neighbourTreeMenuItem.addActionListener(this);
+    statusBar.setBackground(Color.white);
+    statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
+    statusBar.setText("Status bar");
+    outputTextboxMenu.setLabel("Output to Textbox");
+    clustalColour.setLabel("Clustalx");
+
+    clustalColour.addActionListener(this);
+    zappoColour.setLabel("Zappo");
+    zappoColour.addActionListener(this);
+    taylorColour.setLabel("Taylor");
+    taylorColour.addActionListener(this);
+    hydrophobicityColour.setLabel("Hydrophobicity");
+    hydrophobicityColour.addActionListener(this);
+    helixColour.setLabel("Helix Propensity");
+    helixColour.addActionListener(this);
+    strandColour.setLabel("Strand Propensity");
+    strandColour.addActionListener(this);
+    turnColour.setLabel("Turn Propensity");
+    turnColour.addActionListener(this);
+    buriedColour.setLabel("Buried Index");
+    buriedColour.addActionListener(this);
+    userDefinedColour.setLabel("User Defined...");
+    userDefinedColour.addActionListener(this);
+    PIDColour.setLabel("Percentage Identity");
+    PIDColour.addActionListener(this);
+    BLOSUM62Colour.setLabel("BLOSUM62 Score");
+    BLOSUM62Colour.addActionListener(this);
+    avDistanceTreeBlosumMenuItem.setLabel(
+        "Average Distance Using BLOSUM62");
+    avDistanceTreeBlosumMenuItem.addActionListener(this);
+    njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
+    njTreeBlosumMenuItem.addActionListener(this);
+    annotationPanelMenuItem.setLabel("Show Annotations");
+    annotationPanelMenuItem.addItemListener(this);
+    colourTextMenuItem.setLabel("Colour Text");
+    colourTextMenuItem.addItemListener(this);
+    overviewMenuItem.setLabel("Overview Window");
+    overviewMenuItem.addActionListener(this);
+    undoMenuItem.setEnabled(false);
+    undoMenuItem.setLabel("Undo");
+    undoMenuItem.addActionListener(this);
+    redoMenuItem.setEnabled(false);
+    redoMenuItem.setLabel("Redo");
+    redoMenuItem.addActionListener(this);
+    conservationMenuItem.setLabel("by Conservation");
+    conservationMenuItem.addItemListener(this);
+    noColourmenuItem.setLabel("None");
+    noColourmenuItem.addActionListener(this);
+    wrapMenuItem.setLabel("Wrap");
+    wrapMenuItem.addItemListener(this);
+    renderGapsMenuItem.setLabel("Show Gaps");
+    renderGapsMenuItem.setState(true);
+    renderGapsMenuItem.addItemListener(this);
+    findMenuItem.setLabel("Find...");
+    findMenuItem.addActionListener(this);
     abovePIDThreshold.setLabel("Above Identity Threshold");
-        abovePIDThreshold.addItemListener(this);
-        nucleotideColour.setLabel("Nucleotide");
-        nucleotideColour.addActionListener(this);
-        deleteGroups.setLabel("Undefine Groups");
-        deleteGroups.addActionListener(this);
-        copy.setLabel("Copy");
-        copy.addActionListener(this);
-        cut.setLabel("Cut");
-        cut.addActionListener(this);
-        delete.setLabel("Delete");
-        delete.addActionListener(this);
-        pasteMenu.setLabel("Paste");
-        pasteNew.setLabel("To New Alignment");
-        pasteNew.addActionListener(this);
-        pasteThis.setLabel("Add To This Alignment");
-        pasteThis.addActionListener(this);
-        applyToAllGroups.setLabel("Apply Colour To All Groups");
-        applyToAllGroups.setState(true);
-        applyToAllGroups.addItemListener(this);
-        font.setLabel("Font...");
-        font.addActionListener(this);
-        scaleAbove.setLabel("Scale Above");
-        scaleAbove.setState(true);
-        scaleAbove.setEnabled(false);
-        scaleAbove.addItemListener(this);
-        scaleLeft.setEnabled(false);
-        scaleLeft.setState(true);
-        scaleLeft.setLabel("Scale Left");
-        scaleLeft.addItemListener(this);
-        scaleRight.setEnabled(false);
-        scaleRight.setState(true);
-        scaleRight.setLabel("Scale Right");
-        scaleRight.addItemListener(this);
-        modifyPID.setLabel("Modify Identity Threshold...");
-        modifyPID.addActionListener(this);
-        modifyConservation.setLabel("Modify Conservation Threshold...");
-        modifyConservation.addActionListener(this);
-        sortByTreeMenu.setLabel("By Tree Order");
-        sort.setLabel("Sort");
-        calculate.setLabel("Calculate Tree");
-        autoCalculate.addItemListener(this);
-        inputText.setLabel("Input from textbox");
-        inputText.addActionListener(this);
-
-        helpMenu.setLabel("Help");
-        documentation.setLabel("Documentation");
-        documentation.addActionListener(this);
-
-        about.setLabel("About...");
-        about.addActionListener(this);
-          seqLimits.setState(true);
+    abovePIDThreshold.addItemListener(this);
+    nucleotideColour.setLabel("Nucleotide");
+    nucleotideColour.addActionListener(this);
+    deleteGroups.setLabel("Undefine Groups");
+    deleteGroups.addActionListener(this);
+    copy.setLabel("Copy");
+    copy.addActionListener(this);
+    cut.setLabel("Cut");
+    cut.addActionListener(this);
+    delete.setLabel("Delete");
+    delete.addActionListener(this);
+    pasteMenu.setLabel("Paste");
+    pasteNew.setLabel("To New Alignment");
+    pasteNew.addActionListener(this);
+    pasteThis.setLabel("Add To This Alignment");
+    pasteThis.addActionListener(this);
+    applyToAllGroups.setLabel("Apply Colour To All Groups");
+    applyToAllGroups.setState(true);
+    applyToAllGroups.addItemListener(this);
+    font.setLabel("Font...");
+    font.addActionListener(this);
+    scaleAbove.setLabel("Scale Above");
+    scaleAbove.setState(true);
+    scaleAbove.setEnabled(false);
+    scaleAbove.addItemListener(this);
+    scaleLeft.setEnabled(false);
+    scaleLeft.setState(true);
+    scaleLeft.setLabel("Scale Left");
+    scaleLeft.addItemListener(this);
+    scaleRight.setEnabled(false);
+    scaleRight.setState(true);
+    scaleRight.setLabel("Scale Right");
+    scaleRight.addItemListener(this);
+    modifyPID.setLabel("Modify Identity Threshold...");
+    modifyPID.addActionListener(this);
+    modifyConservation.setLabel("Modify Conservation Threshold...");
+    modifyConservation.addActionListener(this);
+    sortByTreeMenu.setLabel("By Tree Order");
+    sort.setLabel("Sort");
+    calculate.setLabel("Calculate Tree");
+    autoCalculate.addItemListener(this);
+    inputText.setLabel("Input from textbox");
+    inputText.addActionListener(this);
+
+    helpMenu.setLabel("Help");
+    documentation.setLabel("Documentation");
+    documentation.addActionListener(this);
+
+    about.setLabel("About...");
+    about.addActionListener(this);
+    seqLimits.setState(true);
     seqLimits.setLabel("Show Sequence Limits");
     seqLimits.addItemListener(this);
     featureSettings.setLabel("Feature Settings...");
@@ -2261,41 +2483,43 @@ public void itemStateChanged(ItemEvent evt)
     newView.setLabel("New View");
     newView.addActionListener(this);
     alignFrameMenuBar.add(fileMenu);
-        alignFrameMenuBar.add(editMenu);
+    alignFrameMenuBar.add(editMenu);
     alignFrameMenuBar.add(selectMenu);
     alignFrameMenuBar.add(viewMenu);
     alignFrameMenuBar.add(formatMenu);
     alignFrameMenuBar.add(colourMenu);
-        alignFrameMenuBar.add(calculateMenu);
-        alignFrameMenuBar.add(helpMenu);
-
-        fileMenu.add(inputText);
-        fileMenu.add(loadTree);
-        fileMenu.add(loadAnnotations);
-
-        fileMenu.addSeparator();
-        fileMenu.add(outputTextboxMenu);
-        fileMenu.add(outputFeatures);
-        fileMenu.add(outputAnnotations);
-
-        if(jalviewServletURL!=null)
-          fileMenu.add(loadApplication);
-
-        fileMenu.addSeparator();
-        fileMenu.add(closeMenuItem);
-
-        editMenu.add(undoMenuItem);
-        editMenu.add(redoMenuItem);
-        editMenu.add(cut);
-        editMenu.add(copy);
-        editMenu.add(pasteMenu);
-        editMenu.add(delete);
-        editMenu.addSeparator();
-        editMenu.add(remove2LeftMenuItem);
-        editMenu.add(remove2RightMenuItem);
-        editMenu.add(removeGappedColumnMenuItem);
-        editMenu.add(removeAllGapsMenuItem);
-        editMenu.add(removeRedundancyMenuItem);
+    alignFrameMenuBar.add(calculateMenu);
+    alignFrameMenuBar.add(helpMenu);
+
+    fileMenu.add(inputText);
+    fileMenu.add(loadTree);
+    fileMenu.add(loadAnnotations);
+
+    fileMenu.addSeparator();
+    fileMenu.add(outputTextboxMenu);
+    fileMenu.add(outputFeatures);
+    fileMenu.add(outputAnnotations);
+
+    if (jalviewServletURL != null)
+    {
+      fileMenu.add(loadApplication);
+    }
+
+    fileMenu.addSeparator();
+    fileMenu.add(closeMenuItem);
+
+    editMenu.add(undoMenuItem);
+    editMenu.add(redoMenuItem);
+    editMenu.add(cut);
+    editMenu.add(copy);
+    editMenu.add(pasteMenu);
+    editMenu.add(delete);
+    editMenu.addSeparator();
+    editMenu.add(remove2LeftMenuItem);
+    editMenu.add(remove2RightMenuItem);
+    editMenu.add(removeGappedColumnMenuItem);
+    editMenu.add(removeAllGapsMenuItem);
+    editMenu.add(removeRedundancyMenuItem);
     viewMenu.add(newView);
     viewMenu.addSeparator();
     viewMenu.add(menu1);
@@ -2303,50 +2527,50 @@ public void itemStateChanged(ItemEvent evt)
     viewMenu.addSeparator();
     viewMenu.add(annotationPanelMenuItem);
     viewMenu.addSeparator();
-        viewMenu.add(sequenceFeatures);
-        viewMenu.add(featureSettings);
+    viewMenu.add(sequenceFeatures);
+    viewMenu.add(featureSettings);
     viewMenu.addSeparator();
-        viewMenu.add(overviewMenuItem);
-        colourMenu.add(applyToAllGroups);
-        colourMenu.addSeparator();
-        colourMenu.add(noColourmenuItem);
-        colourMenu.add(clustalColour);
-        colourMenu.add(BLOSUM62Colour);
-        colourMenu.add(PIDColour);
-        colourMenu.add(zappoColour);
-        colourMenu.add(taylorColour);
-        colourMenu.add(hydrophobicityColour);
-        colourMenu.add(helixColour);
-        colourMenu.add(strandColour);
-        colourMenu.add(turnColour);
-        colourMenu.add(buriedColour);
-        colourMenu.add(nucleotideColour);
-        colourMenu.add(userDefinedColour);
-        colourMenu.addSeparator();
-        colourMenu.add(conservationMenuItem);
-        colourMenu.add(modifyConservation);
-        colourMenu.add(abovePIDThreshold);
-        colourMenu.add(modifyPID);
+    viewMenu.add(overviewMenuItem);
+    colourMenu.add(applyToAllGroups);
+    colourMenu.addSeparator();
+    colourMenu.add(noColourmenuItem);
+    colourMenu.add(clustalColour);
+    colourMenu.add(BLOSUM62Colour);
+    colourMenu.add(PIDColour);
+    colourMenu.add(zappoColour);
+    colourMenu.add(taylorColour);
+    colourMenu.add(hydrophobicityColour);
+    colourMenu.add(helixColour);
+    colourMenu.add(strandColour);
+    colourMenu.add(turnColour);
+    colourMenu.add(buriedColour);
+    colourMenu.add(nucleotideColour);
+    colourMenu.add(userDefinedColour);
+    colourMenu.addSeparator();
+    colourMenu.add(conservationMenuItem);
+    colourMenu.add(modifyConservation);
+    colourMenu.add(abovePIDThreshold);
+    colourMenu.add(modifyPID);
     colourMenu.add(annotationColour);
     calculateMenu.add(sort);
-        calculateMenu.add(calculate);
-        calculateMenu.addSeparator();
-        calculateMenu.add(pairwiseAlignmentMenuItem);
-        calculateMenu.add(PCAMenuItem);
-        calculateMenu.add(autoCalculate);
-        this.add(statusBar, BorderLayout.SOUTH);
-        pasteMenu.add(pasteNew);
-        pasteMenu.add(pasteThis);
-        sort.add(sortIDMenuItem);
-        sort.add(sortByTreeMenu);
-        sort.add(sortGroupMenuItem);
-        sort.add(sortPairwiseMenuItem);
-        calculate.add(averageDistanceTreeMenuItem);
-        calculate.add(neighbourTreeMenuItem);
-        calculate.add(avDistanceTreeBlosumMenuItem);
-        calculate.add(njTreeBlosumMenuItem);
-        helpMenu.add(documentation);
-        helpMenu.add(about);
+    calculateMenu.add(calculate);
+    calculateMenu.addSeparator();
+    calculateMenu.add(pairwiseAlignmentMenuItem);
+    calculateMenu.add(PCAMenuItem);
+    calculateMenu.add(autoCalculate);
+    this.add(statusBar, BorderLayout.SOUTH);
+    pasteMenu.add(pasteNew);
+    pasteMenu.add(pasteThis);
+    sort.add(sortIDMenuItem);
+    sort.add(sortByTreeMenu);
+    sort.add(sortGroupMenuItem);
+    sort.add(sortPairwiseMenuItem);
+    calculate.add(averageDistanceTreeMenuItem);
+    calculate.add(neighbourTreeMenuItem);
+    calculate.add(avDistanceTreeBlosumMenuItem);
+    calculate.add(njTreeBlosumMenuItem);
+    helpMenu.add(documentation);
+    helpMenu.add(about);
     menu1.add(showColumns);
     menu1.add(showSeqs);
     menu2.add(hideColumns);
@@ -2420,18 +2644,17 @@ public void itemStateChanged(ItemEvent evt)
     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();
+    viewport.applet.add(alignPanel, BorderLayout.CENTER);
+    viewport.applet.validate();
 
   }
 
-
-
   PopupMenu filePopup, editPopup, searchPopup,
-      viewPopup, formatPopup, colourPopup, calculatePopup, helpPopup;
+  viewPopup, formatPopup, colourPopup, calculatePopup, helpPopup;
   MenuItem featureSettings = new MenuItem();
   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
   MenuItem annotationColour = new MenuItem();
@@ -2449,36 +2672,36 @@ public void itemStateChanged(ItemEvent evt)
   public void mousePressed(MouseEvent evt)
   {
     PopupMenu popup = null;
-    Label source = (Label)evt.getSource();
-    if(source==embeddedFile)
+    Label source = (Label) evt.getSource();
+    if (source == embeddedFile)
     {
       popup = filePopup = genPopupMenu(filePopup, fileMenu);
     }
-    else if(source==embeddedEdit)
+    else if (source == embeddedEdit)
     {
       popup = editPopup = genPopupMenu(editPopup, editMenu);
     }
-    else if(source==embeddedSelect)
+    else if (source == embeddedSelect)
     {
       popup = searchPopup = genPopupMenu(searchPopup, selectMenu);
     }
-    else if(source==embeddedView)
+    else if (source == embeddedView)
     {
       popup = viewPopup = genPopupMenu(viewPopup, viewMenu);
     }
-    else if (source ==embeddedFormat)
+    else if (source == embeddedFormat)
     {
       popup = formatPopup = genPopupMenu(formatPopup, formatMenu);
     }
-    else if(source==embeddedColour)
+    else if (source == embeddedColour)
     {
       popup = colourPopup = genPopupMenu(colourPopup, colourMenu);
     }
-    else if(source==embeddedCalculate)
+    else if (source == embeddedCalculate)
     {
       popup = calculatePopup = genPopupMenu(calculatePopup, calculateMenu);
     }
-    else if(source==embeddedHelp)
+    else if (source == embeddedHelp)
     {
       popup = helpPopup = genPopupMenu(helpPopup, helpMenu);
     }
@@ -2491,13 +2714,13 @@ public void itemStateChanged(ItemEvent evt)
 
   PopupMenu genPopupMenu(PopupMenu popup, Menu original)
   {
-    if(popup!=null)
+    if (popup != null)
     {
       return popup;
     }
     popup = new PopupMenu();
     int m, mSize = original.getItemCount();
-    for(m=0; m<mSize; m++)
+    for (m = 0; m < mSize; m++)
     {
       popup.add(original.getItem(m));
       mSize--;
@@ -2506,14 +2729,17 @@ public void itemStateChanged(ItemEvent evt)
 
     return popup;
   }
+
   public void mouseClicked(MouseEvent evt)
   {}
+
   public void mouseReleased(MouseEvent evt)
   {}
+
   public void mouseEntered(MouseEvent evt)
   {}
+
   public void mouseExited(MouseEvent evt)
   {}
 
 }
-
diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 7fc240f..4e1da95 100755
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -36,7 +36,6 @@ public class AlignViewport
   int startSeq;
   int endSeq;
 
-
   boolean cursorMode = false;
 
   boolean showJVSuffix = true;
@@ -79,15 +78,14 @@ public class AlignViewport
   boolean scaleRightWrapped = true;
 
   // The following vector holds the features which are
- // currently visible, in the correct order or rendering
+  // currently visible, in the correct order or rendering
   public Hashtable featuresDisplayed;
 
   boolean hasHiddenColumns = false;
   boolean hasHiddenRows = false;
   boolean showHiddenMarkers = true;
 
-
-  public Hashtable [] hconsensus;
+  public Hashtable[] hconsensus;
   AlignmentAnnotation consensus;
   AlignmentAnnotation conservation;
   AlignmentAnnotation quality;
@@ -96,7 +94,8 @@ public class AlignViewport
 
   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;
 
@@ -123,8 +122,10 @@ public class AlignViewport
     this.endSeq = al.getHeight() - 1;
     setFont(font);
 
-    if(System.getProperty("os.name").startsWith("Mac"))
+    if (System.getProperty("os.name").startsWith("Mac"))
+    {
       MAC = true;
+    }
 
     if (applet != null)
     {
@@ -161,8 +162,10 @@ public class AlignViewport
       param = applet.getParameter("upperCase");
       if (param != null)
       {
-        if(param.equalsIgnoreCase("bold"))
+        if (param.equalsIgnoreCase("bold"))
+        {
           upperCasebold = true;
+        }
       }
 
     }
@@ -171,14 +174,16 @@ public class AlignViewport
     {
       String colour = applet.getParameter("defaultColour");
 
-      if(colour == null)
+      if (colour == null)
       {
         colour = applet.getParameter("userDefinedColour");
-        if(colour !=null)
+        if (colour != null)
+        {
           colour = "User Defined";
+        }
       }
 
-      if(colour != null)
+      if (colour != null)
       {
         globalColourScheme = ColourSchemeProperty.getColour(alignment, colour);
         if (globalColourScheme != null)
@@ -187,27 +192,25 @@ public class AlignViewport
         }
       }
 
-      if(applet.getParameter("userDefinedColour")!=null)
+      if (applet.getParameter("userDefinedColour") != null)
       {
-        ((UserColourScheme)globalColourScheme).parseAppletParameter(
+        ( (UserColourScheme) globalColourScheme).parseAppletParameter(
             applet.getParameter("userDefinedColour"));
       }
 
-      if(hconsensus==null)
+      if (hconsensus == null)
       {
-        if(!alignment.isNucleotide())
+        if (!alignment.isNucleotide())
         {
           conservation = new AlignmentAnnotation("Conservation",
-              "Conservation of total alignment less than " +
-              ConsPercGaps + "% gaps",
-              new Annotation[1], 0f,
-              11f,
-              AlignmentAnnotation.BAR_GRAPH);
+                                                 "Conservation of total alignment less than " +
+                                                 ConsPercGaps + "% gaps",
+                                                 new Annotation[1], 0f,
+                                                 11f,
+                                                 AlignmentAnnotation.BAR_GRAPH);
           conservation.hasText = true;
           conservation.autoCalculated = true;
 
-
-
           if (showConservation)
           {
             alignment.addAnnotation(conservation);
@@ -229,15 +232,15 @@ 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;
 
-         if (showConsensus)
-         {
-           alignment.addAnnotation(consensus);
-         }
+        if (showConsensus)
+        {
+          alignment.addAnnotation(consensus);
+        }
       }
     }
   }
@@ -252,8 +255,8 @@ public class AlignViewport
     return showSequenceFeatures;
   }
 
-
-  class ConservationThread extends Thread
+  class ConservationThread
+      extends Thread
   {
     AlignmentPanel ap;
     public ConservationThread(AlignmentPanel ap)
@@ -285,24 +288,25 @@ public class AlignViewport
 
         UPDATING_CONSERVATION = true;
 
-
         int alWidth = alignment.getWidth();
-        if(alWidth<0)
+        if (alWidth < 0)
+        {
           return;
+        }
 
         Conservation cons = new jalview.analysis.Conservation("All",
             jalview.schemes.ResidueProperties.propHash, 3,
-            alignment.getSequences(), 0, alWidth -1);
+            alignment.getSequences(), 0, alWidth - 1);
 
         cons.calculate();
         cons.verdict(false, ConsPercGaps);
 
-        if (quality!=null)
+        if (quality != null)
         {
           cons.findQuality();
         }
 
-        char [] sequence = cons.getConsSequence().getSequence();
+        char[] sequence = cons.getConsSequence().getSequence();
         float minR;
         float minG;
         float minB;
@@ -325,7 +329,7 @@ public class AlignViewport
 
         conservation.annotations = new Annotation[alWidth];
 
-        if (quality!=null)
+        if (quality != null)
         {
           quality.graphMax = cons.qualityRange[1].floatValue();
           quality.annotations = new Annotation[alWidth];
@@ -340,11 +344,17 @@ public class AlignViewport
           c = sequence[i];
 
           if (Character.isDigit(c))
+          {
             value = (int) (c - '0');
+          }
           else if (c == '*')
+          {
             value = 11;
+          }
           else if (c == '+')
+          {
             value = 10;
+          }
 
           float vprop = value - min;
           vprop /= max;
@@ -356,16 +366,17 @@ public class AlignViewport
                                        minB + (maxB * vprop)));
 
           // Quality calc
-          if (quality!=null)
+          if (quality != null)
           {
             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)));
           }
         }
       }
@@ -380,7 +391,7 @@ public class AlignViewport
       UPDATING_CONSERVATION = false;
       updatingConservation = false;
 
-      if(ap!=null)
+      if (ap != null)
       {
         ap.repaint();
       }
@@ -388,7 +399,6 @@ public class AlignViewport
     }
   }
 
-
   ConservationThread conservationThread;
 
   ConsensusThread consensusThread;
@@ -408,8 +418,10 @@ public class AlignViewport
    */
   public void updateConservation(final AlignmentPanel ap)
   {
-    if (alignment.isNucleotide() || conservation==null)
+    if (alignment.isNucleotide() || conservation == null)
+    {
       return;
+    }
 
     conservationThread = new ConservationThread(ap);
     conservationThread.start();
@@ -424,14 +436,15 @@ public class AlignViewport
     consensusThread.start();
   }
 
-
-  class ConsensusThread extends Thread
+  class ConsensusThread
+      extends Thread
   {
     AlignmentPanel ap;
     public ConsensusThread(AlignmentPanel ap)
     {
       this.ap = ap;
     }
+
     public void run()
     {
       updatingConsensus = true;
@@ -452,19 +465,19 @@ public class AlignViewport
         }
       }
 
-
       UPDATING_CONSENSUS = true;
 
       try
       {
         int aWidth = alignment.getWidth();
-        if(aWidth<0)
+        if (aWidth < 0)
+        {
           return;
+        }
 
         consensus.annotations = null;
         consensus.annotations = new Annotation[aWidth];
 
-
         hconsensus = new Hashtable[aWidth];
         AAFrequency.calculate(alignment.getSequencesArray(),
                               0,
@@ -475,11 +488,15 @@ public class AlignViewport
         {
           float value = 0;
           if (ignoreGapsInConsensusCalculation)
+          {
             value = ( (Float) hconsensus[i].get(AAFrequency.PID_NOGAPS)).
                 floatValue();
+          }
           else
+          {
             value = ( (Float) hconsensus[i].get(AAFrequency.PID_GAPS)).
                 floatValue();
+          }
 
           String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE).toString();
           String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE) + " ";
@@ -491,12 +508,14 @@ public class AlignViewport
           }
 
           mouseOver += ( (int) value + "%");
-          consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);
+          consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ',
+              value);
         }
 
-
         if (globalColourScheme != null)
+        {
           globalColourScheme.setConsensus(hconsensus);
+        }
 
       }
       catch (OutOfMemoryError error)
@@ -528,21 +547,32 @@ public class AlignViewport
    */
   public SequenceI getConsensusSeq()
   {
-    if (consensus==null)
+    if (consensus == null)
+    {
       return null;
-    StringBuffer seqs=new StringBuffer();
-    for (int i=0; i<consensus.annotations.length; i++) {
-      if (consensus.annotations[i]!=null) {
+    }
+    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) == '[')
+        {
           seqs.append(consensus.annotations[i].description.charAt(1));
+        }
         else
+        {
           seqs.append(consensus.annotations[i].displayCharacter);
+        }
       }
     }
     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;
   }
+
   public SequenceGroup getSelectionGroup()
   {
     return selectionGroup;
@@ -644,7 +674,7 @@ public class AlignViewport
   public void setFont(Font f)
   {
     font = f;
-    if(nullFrame == null)
+    if (nullFrame == null)
     {
       nullFrame = new java.awt.Frame();
       nullFrame.addNotify();
@@ -654,7 +684,7 @@ public class AlignViewport
     setCharHeight(fm.getHeight());
     charWidth = fm.charWidth('M');
 
-    if(upperCasebold)
+    if (upperCasebold)
     {
       Font f2 = new Font(f.getName(), Font.BOLD, f.getSize());
       fm = nullFrame.getGraphics().getFontMetrics(f2);
@@ -783,8 +813,10 @@ public class AlignViewport
   public void setHiddenColumns(ColumnSelection colsel)
   {
     this.colSel = colsel;
-    if(colSel.getHiddenColumns()!=null)
+    if (colSel.getHiddenColumns() != null)
+    {
       hasHiddenColumns = true;
+    }
   }
 
   public ColumnSelection getColumnSelection()
@@ -871,10 +903,10 @@ public class AlignViewport
   {
     ignoreGapsInConsensusCalculation = b;
     updateConsensus(null);
-    if (globalColourScheme!=null)
+    if (globalColourScheme != null)
     {
       globalColourScheme.setThreshold(globalColourScheme.getThreshold(),
-          ignoreGapsInConsensusCalculation);
+                                      ignoreGapsInConsensusCalculation);
 
     }
   }
@@ -887,7 +919,7 @@ public class AlignViewport
   public void addPropertyChangeListener(
       java.beans.PropertyChangeListener listener)
   {
-      changeSupport.addPropertyChangeListener(listener);
+    changeSupport.addPropertyChangeListener(listener);
   }
 
   /**
@@ -898,7 +930,7 @@ public class AlignViewport
   public void removePropertyChangeListener(
       java.beans.PropertyChangeListener listener)
   {
-      changeSupport.removePropertyChangeListener(listener);
+    changeSupport.removePropertyChangeListener(listener);
   }
 
   /**
@@ -910,19 +942,20 @@ public class AlignViewport
    */
   public void firePropertyChange(String prop, Object oldvalue, Object newvalue)
   {
-      changeSupport.firePropertyChange(prop, oldvalue, newvalue);
+    changeSupport.firePropertyChange(prop, oldvalue, newvalue);
   }
 
-
-
   public boolean getIgnoreGapsConsensus()
   {
     return ignoreGapsInConsensusCalculation;
   }
+
   public void hideSelectedColumns()
   {
     if (colSel.size() < 1)
+    {
       return;
+    }
 
     colSel.hideSelectedColumns();
     setSelectionGroup(null);
@@ -935,7 +968,9 @@ public class AlignViewport
     for (int i = 0; i < alignment.getWidth(); i++)
     {
       if (colSel.contains(i))
+      {
         colSel.removeElement(i);
+      }
       else
       {
         if (!hasHiddenColumns || colSel.isVisible(i))
@@ -946,13 +981,16 @@ public class AlignViewport
     }
   }
 
-
   public void hideColumns(int start, int end)
   {
-    if(start==end)
+    if (start == end)
+    {
       colSel.hideColumns(start);
+    }
     else
+    {
       colSel.hideColumns(start, end);
+    }
 
     hasHiddenColumns = true;
   }
@@ -960,34 +998,44 @@ public class AlignViewport
   public void hideRepSequences(SequenceI repSequence, SequenceGroup sg)
   {
     int sSize = sg.getSize();
-    if(sSize < 2)
+    if (sSize < 2)
+    {
       return;
+    }
 
-    if(hiddenRepSequences==null)
+    if (hiddenRepSequences == null)
+    {
       hiddenRepSequences = new Hashtable();
+    }
 
-     hiddenRepSequences.put(repSequence, sg);
+    hiddenRepSequences.put(repSequence, sg);
 
     //Hide all sequences except the repSequence
-    SequenceI [] seqs = new SequenceI[sSize-1];
+    SequenceI[] seqs = new SequenceI[sSize - 1];
     int index = 0;
-    for(int i=0; i<sSize; i++)
-      if(sg.getSequenceAt(i)!=repSequence)
+    for (int i = 0; i < sSize; i++)
+    {
+      if (sg.getSequenceAt(i) != repSequence)
       {
-        if(index==sSize-1)
+        if (index == sSize - 1)
+        {
           return;
+        }
 
         seqs[index++] = sg.getSequenceAt(i);
       }
+    }
 
     hideSequence(seqs);
 
-    }
+  }
 
   public void hideAllSelectedSeqs()
   {
     if (selectionGroup == null)
+    {
       return;
+    }
 
     SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
 
@@ -996,12 +1044,14 @@ public class AlignViewport
     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++)
+      {
         alignment.getHiddenSequences().hideSequence(seq[i]);
+      }
 
       hasHiddenRows = true;
       firePropertyChange("alignment", null, alignment.getSequences());
@@ -1011,8 +1061,10 @@ public class AlignViewport
   public void showColumn(int col)
   {
     colSel.revealHiddenColumns(col);
-    if(colSel.getHiddenColumns()==null)
+    if (colSel.getHiddenColumns() == null)
+    {
       hasHiddenColumns = false;
+    }
   }
 
   public void showAllHiddenColumns()
@@ -1023,24 +1075,24 @@ public class AlignViewport
 
   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);
+        selectionGroup.setEndRes(alignment.getWidth() - 1);
       }
       Vector tmp = alignment.getHiddenSequences().showAll(hiddenRepSequences);
-      for(int t=0; t<tmp.size(); t++)
+      for (int t = 0; t < tmp.size(); t++)
       {
         selectionGroup.addSequence(
-            (SequenceI)tmp.elementAt(t), false
+            (SequenceI) tmp.elementAt(t), false
             );
       }
       firePropertyChange("alignment", null, alignment.getSequences());
       hasHiddenRows = false;
       hiddenRepSequences = null;
-      }
+    }
   }
 
   public int adjustForHiddenSeqs(int alignmentIndex)
@@ -1058,9 +1110,13 @@ public class AlignViewport
     SequenceI[] sequences;
 
     if (selectionGroup == null)
+    {
       sequences = alignment.getSequencesArray();
+    }
     else
+    {
       sequences = selectionGroup.getSelectionAsNewSequences(alignment);
+    }
 
     return sequences;
   }
@@ -1073,13 +1129,14 @@ public class AlignViewport
    * 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;
+    CigarArray selection = null;
+    SequenceI[] seqs = null;
     int i, iSize;
     int start = 0, end = 0;
-    if(selectedRegionOnly && selectionGroup!=null)
+    if (selectedRegionOnly && selectionGroup != null)
     {
       iSize = selectionGroup.getSize();
       seqs = selectionGroup.getSequencesInOrder(alignment);
@@ -1090,76 +1147,98 @@ public class AlignViewport
     {
       iSize = alignment.getHeight();
       seqs = alignment.getSequencesArray();
-      end = alignment.getWidth()-1;
+      end = alignment.getWidth() - 1;
     }
     SeqCigar[] selseqs = new SeqCigar[iSize];
-    for(i=0; i<iSize; i++)
+    for (i = 0; i < iSize; i++)
     {
       selseqs[i] = new SeqCigar(seqs[i], start, end);
     }
-    selection=new CigarArray(selseqs);
+    selection = new CigarArray(selseqs);
     // now construct the CigarArray operations
-    if (hasHiddenColumns) {
+    if (hasHiddenColumns)
+    {
       Vector regions = colSel.getHiddenColumns();
-      int [] region;
+      int[] region;
       int hideStart, hideEnd;
-      int last=start;
-      for (int j = 0; last<end & j < regions.size(); j++)
+      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 (hideStart < last)
+        {
           if (hideEnd > last)
           {
             hideStart = last;
-          } else
+          }
+          else
+          {
             continue;
+          }
         }
 
-        if (hideStart>end)
+        if (hideStart > end)
+        {
           break;
+        }
 
-        if (hideEnd>end)
-          hideEnd=end;
+        if (hideEnd > end)
+        {
+          hideEnd = end;
+        }
 
-        if (hideStart>hideEnd)
+        if (hideStart > hideEnd)
+        {
           break;
+        }
         /**
          * form operations...
          */
-        if (last<hideStart)
-          selection.addOperation(CigarArray.M, hideStart-last);
-        selection.addOperation(CigarArray.D, 1+hideEnd-hideStart);
-        last = hideEnd+1;
+        if (last < hideStart)
+        {
+          selection.addOperation(CigarArray.M, hideStart - last);
+        }
+        selection.addOperation(CigarArray.D, 1 + hideEnd - hideStart);
+        last = hideEnd + 1;
       }
       // Final match if necessary.
-      if (last<end)
-        selection.addOperation(CigarArray.M, end-last+1);
-    } else {
-      selection.addOperation(CigarArray.M, end-start+1);
+      if (last < end)
+      {
+        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
    */
-  jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly) {
+  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);
-    if (aligview!=null) {
+    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
@@ -1168,18 +1247,18 @@ public class AlignViewport
    * which contain hidden columns.
    * @return String[]
    */
-  public String [] getViewAsString(boolean selectedRegionOnly)
+  public String[] getViewAsString(boolean selectedRegionOnly)
   {
-    String [] selection = null;
-    SequenceI [] seqs= null;
+    String[] selection = null;
+    SequenceI[] seqs = null;
     int i, iSize;
     int start = 0, end = 0;
-    if(selectedRegionOnly && selectionGroup!=null)
+    if (selectedRegionOnly && selectionGroup != null)
     {
       iSize = selectionGroup.getSize();
       seqs = selectionGroup.getSequencesInOrder(alignment);
       start = selectionGroup.getStartRes();
-      end = selectionGroup.getEndRes()+1;
+      end = selectionGroup.getEndRes() + 1;
     }
     else
     {
@@ -1190,48 +1269,48 @@ public class AlignViewport
 
     selection = new String[iSize];
 
-
-    for(i=0; i<iSize; i++)
+    for (i = 0; i < iSize; i++)
     {
       if (hasHiddenColumns)
       {
-           StringBuffer visibleSeq = new StringBuffer();
-           Vector regions = colSel.getHiddenColumns();
-
-           int blockStart = start, blockEnd=end;
-           int [] region;
-           int hideStart, hideEnd;
+        StringBuffer visibleSeq = new StringBuffer();
+        Vector regions = colSel.getHiddenColumns();
 
-           for (int j = 0; j < regions.size(); j++)
-           {
-             region = (int[]) regions.elementAt(j);
-             hideStart = region[0];
-             hideEnd = region[1];
+        int blockStart = start, blockEnd = end;
+        int[] region;
+        int hideStart, hideEnd;
 
-             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);
 
+          if (blockStart > blockEnd)
+          {
+            break;
+          }
 
-             visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));
+          visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));
 
-             blockStart = hideEnd+1;
-             blockEnd = end;
-           }
+          blockStart = hideEnd + 1;
+          blockEnd = end;
+        }
 
-           if(end>blockStart)
-             visibleSeq.append(seqs[i].getSequence(blockStart, end));
+        if (end > blockStart)
+        {
+          visibleSeq.append(seqs[i].getSequence(blockStart, end));
+        }
 
-           selection[i] = visibleSeq.toString();
+        selection[i] = visibleSeq.toString();
       }
       else
       {
@@ -1255,26 +1334,38 @@ public class AlignViewport
   public Color getSequenceColour(SequenceI seq)
   {
     if (sequenceColours == null || !sequenceColours.containsKey(seq))
+    {
       return Color.white;
+    }
     else
+    {
       return (Color) sequenceColours.get(seq);
+    }
   }
 
   public void setSequenceColour(SequenceI seq, Color col)
   {
     if (sequenceColours == null)
+    {
       sequenceColours = new Hashtable();
+    }
 
     if (col == null)
+    {
       sequenceColours.remove(seq);
+    }
     else
+    {
       sequenceColours.put(seq, col);
+    }
   }
 
   public String getSequenceSetId()
   {
     if (sequenceSetID == null)
+    {
       sequenceSetID = alignment.hashCode() + "";
+    }
 
     return sequenceSetID;
   }
@@ -1292,28 +1383,32 @@ public class AlignViewport
     //Reset endRes of groups if beyond alignment width
     int alWidth = alignment.getWidth();
     Vector groups = alignment.getGroups();
-    if(groups!=null)
+    if (groups != null)
     {
-      for(int i=0; i<groups.size(); i++)
+      for (int i = 0; i < groups.size(); i++)
       {
-        SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
-        if(sg.getEndRes()>alWidth)
-          sg.setEndRes(alWidth-1);
+        SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
+        if (sg.getEndRes() > alWidth)
+        {
+          sg.setEndRes(alWidth - 1);
+        }
       }
     }
 
-    if(selectionGroup!=null && selectionGroup.getEndRes()>alWidth)
-      selectionGroup.setEndRes(alWidth-1);
+    if (selectionGroup != null && selectionGroup.getEndRes() > alWidth)
+    {
+      selectionGroup.setEndRes(alWidth - 1);
+    }
 
     resetAllColourSchemes();
 
-  //AW  alignment.adjustSequenceAnnotations();
+    //AW  alignment.adjustSequenceAnnotations();
   }
 
   void resetAllColourSchemes()
   {
     ColourSchemeI cs = globalColourScheme;
-    if(cs!=null)
+    if (cs != null)
     {
       if (cs instanceof ClustalxColourScheme)
       {
@@ -1338,17 +1433,16 @@ public class AlignViewport
     }
 
     int s, sSize = alignment.getGroups().size();
-    for(s=0; s<sSize; s++)
+    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(
+        ( (ClustalxColourScheme) sg.cs).resetClustalX(
             sg.getSequences(hiddenRepSequences), sg.getWidth());
       }
       sg.recalcConservation();
     }
   }
 
-
 }
diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index 39e9d03..db3cb8c 100755
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -24,7 +24,8 @@ import java.awt.event.*;
 
 import jalview.datamodel.*;
 
-public class AlignmentPanel extends Panel implements AdjustmentListener
+public class AlignmentPanel
+    extends Panel implements AdjustmentListener
 {
 
   AlignViewport av;
@@ -40,8 +41,6 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
   // this value is set false when selection area being dragged
   boolean fastPaint = true;
 
-
-
   public AlignmentPanel(AlignFrame af, final AlignViewport av)
   {
     try
@@ -53,7 +52,6 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
       e.printStackTrace();
     }
 
-
     alignFrame = af;
     this.av = av;
     seqPanel = new SeqPanel(av, this);
@@ -117,13 +115,14 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
 
   }
 
-
   public void alignmentChanged()
   {
     av.alignmentChanged(this);
 
     if (overviewPanel != null)
+    {
       overviewPanel.updateOverviewImage();
+    }
 
     alignFrame.updateEditMenuBar();
 
@@ -145,15 +144,17 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
     annotationPanel.repaint();
     Dimension d = calculateIdWidth();
     d.setSize(d.width + 4, seqPanel.seqCanvas.getSize().height);
-    alabels.setSize(d.width+4, ap );
+    alabels.setSize(d.width + 4, ap);
     idPanel.idCanvas.setSize(d);
     hscrollFillerPanel.setSize(d);
 
     validate();
     repaint();
 
-    if(overviewPanel!=null)
-          overviewPanel.updateOverviewImage();
+    if (overviewPanel != null)
+    {
+      overviewPanel.updateOverviewImage();
+    }
   }
 
   public void setIdWidth(int w, int h)
@@ -215,7 +216,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
   {
     seqPanel.seqCanvas.highlightSearchResults(results);
 
-   // do we need to scroll the panel?
+    // do we need to scroll the panel?
     if (results != null)
     {
       SequenceI seq = results.getResultSequence(0);
@@ -223,30 +224,34 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
       int start = seq.findIndex(results.getResultStart(0)) - 1;
       int end = seq.findIndex(results.getResultEnd(0)) - 1;
 
-        if(!av.wrapAlignment)
+      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)
           {
-            if (start > av.alignment.getWidth() - hextent)
+            start = av.alignment.getWidth() - hextent;
+            if (start < 0)
             {
-              start = av.alignment.getWidth() - hextent;
-              if (start < 0)
-                start = 0;
+              start = 0;
             }
-            if (seqIndex > av.alignment.getHeight() - vextent)
+          }
+          if (seqIndex > av.alignment.getHeight() - vextent)
+          {
+            seqIndex = av.alignment.getHeight() - vextent;
+            if (seqIndex < 0)
             {
-              seqIndex = av.alignment.getHeight() - vextent;
-              if (seqIndex < 0)
-                seqIndex = 0;
+              seqIndex = 0;
             }
-            setScrollValues(start, seqIndex);
           }
+          setScrollValues(start, seqIndex);
         }
-        else
-        {
-          scrollToWrappedVisible(start);
-        }
+      }
+      else
+      {
+        scrollToWrappedVisible(start);
+      }
     }
 
     repaint();
@@ -254,7 +259,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
 
   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);
@@ -262,7 +268,6 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
     }
   }
 
-
   public OverviewPanel getOverviewPanel()
   {
     return overviewPanel;
@@ -290,7 +295,6 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
     av.startRes = 0;
     scalePanelHolder.setVisible(!wrap);
 
-
     hscroll.setVisible(!wrap);
     idwidthAdjuster.setVisible(!wrap);
 
@@ -305,17 +309,15 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
       annotationSpaceFillerHolder.setVisible(true);
     }
 
-
     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();
 
   }
 
-
   int hextent = 0;
   int vextent = 0;
 
@@ -328,7 +330,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
       {
         return false;
       }
-      setScrollValues(hscroll.getValue(), vscroll.getValue()-1);
+      setScrollValues(hscroll.getValue(), vscroll.getValue() - 1);
     }
     else
     {
@@ -336,7 +338,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
       {
         return false;
       }
-      setScrollValues(hscroll.getValue(), vscroll.getValue()+1);
+      setScrollValues(hscroll.getValue(), vscroll.getValue() + 1);
     }
 
     repaint();
@@ -351,7 +353,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
       {
         return false;
       }
-      setScrollValues(hscroll.getValue()-1, vscroll.getValue());
+      setScrollValues(hscroll.getValue() - 1, vscroll.getValue());
     }
     else
     {
@@ -359,7 +361,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
       {
         return false;
       }
-      setScrollValues(hscroll.getValue()+1, vscroll.getValue());
+      setScrollValues(hscroll.getValue() + 1, vscroll.getValue());
     }
 
     repaint();
@@ -371,11 +373,13 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
     int width = av.alignment.getWidth();
     int height = av.alignment.getHeight();
 
-    if(av.hasHiddenColumns)
-     width = av.getColumnSelection().findColumnPosition(width);
+    if (av.hasHiddenColumns)
+    {
+      width = av.getColumnSelection().findColumnPosition(width);
+    }
 
     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;
@@ -422,8 +426,10 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
     hscroll.setValues(x, hextent, 0, width);
     vscroll.setValues(y, vextent, 0, height);
 
-    if(overviewPanel!=null)
-          overviewPanel.setBoxPosition();
+    if (overviewPanel != null)
+    {
+      overviewPanel.setBoxPosition();
+    }
 
   }
 
@@ -432,8 +438,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
     int oldX = av.getStartRes();
     int oldY = av.getStartSeq();
 
-
-    if (evt==null || evt.getSource() == hscroll)
+    if (evt == null || evt.getSource() == hscroll)
     {
       int x = hscroll.getValue();
       av.setStartRes(x);
@@ -441,8 +446,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
                    1);
     }
 
-
-    if (evt==null || evt.getSource() == vscroll)
+    if (evt == null || evt.getSource() == vscroll)
     {
       int offy = vscroll.getValue();
       if (av.getWrapAlignment())
@@ -476,12 +480,14 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
     {
       // Make sure we're not trying to draw a panel
       // larger than the visible window
-      if(scrollX>av.endRes-av.startRes)
+      if (scrollX > av.endRes - av.startRes)
       {
         scrollX = av.endRes - av.startRes;
       }
-      else if(scrollX<av.startRes-av.endRes)
+      else if (scrollX < av.startRes - av.endRes)
+      {
         scrollX = av.startRes - av.endRes;
+      }
 
       idPanel.idCanvas.fastPaint(scrollY);
       seqPanel.seqCanvas.fastPaint(scrollX,
@@ -516,12 +522,14 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
       int maxwidth = av.alignment.getWidth();
 
       if (av.hasHiddenColumns)
+      {
         maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+      }
 
       int canvasWidth = seqPanel.seqCanvas.getWrappedCanvasWidth
           (seqPanel.seqCanvas.getSize().width);
 
-      if(canvasWidth>0)
+      if (canvasWidth > 0)
       {
         int max = maxwidth / canvasWidth;
         vscroll.setMaximum(max);
@@ -544,7 +552,9 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
     if (getBounds() == g.getClipBounds())
     {
       if (overviewPanel != null)
+      {
         overviewPanel.updateOverviewImage();
+      }
     }
 
   }
@@ -569,49 +579,51 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
   BorderLayout borderLayout4 = new BorderLayout();
   BorderLayout borderLayout2 = new BorderLayout();
 
-  private void jbInit() throws Exception {
-      //  idPanelHolder.setPreferredSize(new Dimension(70, 10));
-      this.setLayout(borderLayout7);
-
-      //   sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));
-      sequenceHolderPanel.setLayout(borderLayout3);
-      seqPanelHolder.setLayout(borderLayout1);
-      scalePanelHolder.setBackground(Color.white);
-
-      // 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(Scrollbar.HORIZONTAL);
-      hscrollHolder.setLayout(borderLayout10);
-      hscrollFillerPanel.setBackground(Color.white);
-
-      //  hscrollFillerPanel.setPreferredSize(new Dimension(70, 10));
-      hscrollHolder.setBackground(Color.white);
-
-      //    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);
-      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);
+  private void jbInit()
+      throws Exception
+  {
+    //  idPanelHolder.setPreferredSize(new Dimension(70, 10));
+    this.setLayout(borderLayout7);
+
+    //   sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));
+    sequenceHolderPanel.setLayout(borderLayout3);
+    seqPanelHolder.setLayout(borderLayout1);
+    scalePanelHolder.setBackground(Color.white);
+
+    // 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(Scrollbar.HORIZONTAL);
+    hscrollHolder.setLayout(borderLayout10);
+    hscrollFillerPanel.setBackground(Color.white);
+
+    //  hscrollFillerPanel.setPreferredSize(new Dimension(70, 10));
+    hscrollHolder.setBackground(Color.white);
+
+    //    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);
+    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/appletgui/AnnotationColourChooser.java b/src/jalview/appletgui/AnnotationColourChooser.java
index ab3b379..80d39e8 100755
--- a/src/jalview/appletgui/AnnotationColourChooser.java
+++ b/src/jalview/appletgui/AnnotationColourChooser.java
@@ -1,31 +1,33 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 jalview.appletgui;
 
-import java.awt.event.*;
+import java.util.*;
+
 import java.awt.*;
+import java.awt.event.*;
 
+import jalview.datamodel.*;
 import jalview.schemes.*;
-import java.util.*;
-import jalview.datamodel.SequenceGroup;
 
-public class AnnotationColourChooser extends Panel implements ActionListener,
+public class AnnotationColourChooser
+    extends Panel implements ActionListener,
     AdjustmentListener, ItemListener
 {
   Frame frame;
@@ -63,7 +65,9 @@ public class AnnotationColourChooser extends Panel implements ActionListener,
     slider.addAdjustmentListener(this);
 
     if (av.alignment.getAlignmentAnnotation() == null)
+    {
       return;
+    }
 
     if (oldcs instanceof AnnotationColourGradient)
     {
@@ -81,7 +85,9 @@ public class AnnotationColourChooser extends Panel implements ActionListener,
     for (int i = 0; i < av.alignment.getAlignmentAnnotation().length; i++)
     {
       if (av.alignment.getAlignmentAnnotation()[i].graph > 0)
+      {
         annotations.addItem(av.alignment.getAlignmentAnnotation()[i].label);
+      }
     }
 
     threshold.addItem("No Threshold");
@@ -178,10 +184,9 @@ public class AnnotationColourChooser extends Panel implements ActionListener,
   Checkbox currentColours = new Checkbox();
   BorderLayout borderLayout1 = new BorderLayout();
 
-
   public void actionPerformed(ActionEvent evt)
   {
-    if(evt.getSource() == thresholdValue)
+    if (evt.getSource() == thresholdValue)
     {
       try
       {
@@ -193,9 +198,13 @@ public class AnnotationColourChooser extends Panel implements ActionListener,
       {}
     }
     else if (evt.getSource() == minColour)
+    {
       minColour_actionPerformed(null);
+    }
     else if (evt.getSource() == maxColour)
+    {
       maxColour_actionPerformed(null);
+    }
 
     else if (evt.getSource() == ok)
     {
@@ -210,10 +219,11 @@ public class AnnotationColourChooser extends Panel implements ActionListener,
     }
 
     else
+    {
       changeColour();
+    }
   }
 
-
   public void itemStateChanged(ItemEvent evt)
   {
     if (evt.getSource() == currentColours)
@@ -256,8 +266,10 @@ public class AnnotationColourChooser extends Panel implements ActionListener,
       changeColour();
     }
     else
+    {
       new UserDefinedColours(this, "Min Colour",
-                              minColour.getBackground());
+                             minColour.getBackground());
+    }
 
   }
 
@@ -270,16 +282,19 @@ public class AnnotationColourChooser extends Panel implements ActionListener,
       changeColour();
     }
     else
+    {
       new UserDefinedColours(this, "Max Colour",
-                              maxColour.getBackground());
+                             maxColour.getBackground());
+    }
   }
 
-
   void changeColour()
   {
     // Check if combobox is still adjusting
     if (adjusting)
+    {
       return;
+    }
 
     // We removed the non-graph annotations when filling the combobox
     // so allow for them again here
@@ -287,21 +302,31 @@ public class AnnotationColourChooser extends Panel implements ActionListener,
     for (int i = 0; i < av.alignment.getAlignmentAnnotation().length; i++)
     {
       if (av.alignment.getAlignmentAnnotation()[i].graph == 0)
+      {
         nograph++;
+      }
       else
+      {
         graph++;
+      }
 
       if (graph == annotations.getSelectedIndex())
+      {
         break;
+      }
     }
 
     currentAnnotation = av.alignment.getAlignmentAnnotation()[graph + nograph];
 
     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);
@@ -322,7 +347,7 @@ public class AnnotationColourChooser extends Panel implements ActionListener,
                                       Color.black));
     }
 
-    if(aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
+    if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
     {
       adjusting = true;
 
@@ -337,16 +362,20 @@ public class AnnotationColourChooser extends Panel implements ActionListener,
 
     AnnotationColourGradient acg = null;
     if (currentColours.getState())
+    {
       acg = new AnnotationColourGradient(
           currentAnnotation,
           av.getGlobalColourScheme(), aboveThreshold);
+    }
     else
+    {
       acg =
           new AnnotationColourGradient(
               currentAnnotation,
               minColour.getBackground(),
               maxColour.getBackground(),
               aboveThreshold);
+    }
 
     av.setGlobalColourScheme(acg);
 
@@ -364,15 +393,19 @@ public class AnnotationColourChooser extends Panel implements ActionListener,
         }
 
         if (currentColours.getState())
+        {
           sg.cs = new AnnotationColourGradient(
               currentAnnotation,
               sg.cs, aboveThreshold);
+        }
         else
+        {
           sg.cs = new AnnotationColourGradient(
               currentAnnotation,
               minColour.getBackground(),
               maxColour.getBackground(),
               aboveThreshold);
+        }
 
       }
     }
@@ -380,7 +413,6 @@ public class AnnotationColourChooser extends Panel implements ActionListener,
     ap.repaint();
   }
 
-
   void reset()
   {
     av.setGlobalColourScheme(oldcs);
@@ -391,13 +423,11 @@ public class AnnotationColourChooser extends Panel implements ActionListener,
       for (int g = 0; g < allGroups.size(); g++)
       {
         sg = (SequenceGroup) allGroups.elementAt(g);
-        sg.cs = (ColourSchemeI)oldgroupColours.get(sg);
+        sg.cs = (ColourSchemeI) oldgroupColours.get(sg);
       }
     }
     ap.repaint();
 
   }
 
-
-
 }
diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java
index 7bf438f..bf6d38d 100755
--- a/src/jalview/appletgui/AnnotationLabels.java
+++ b/src/jalview/appletgui/AnnotationLabels.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -19,9 +19,10 @@
 
 package jalview.appletgui;
 
+import java.util.*;
+
 import java.awt.*;
 import java.awt.event.*;
-import java.util.Vector;
 
 import jalview.datamodel.*;
 
@@ -56,10 +57,9 @@ public class AnnotationLabels
   }
 
   public AnnotationLabels(AlignViewport av)
-{
-  this.av = av;
-}
-
+  {
+    this.av = av;
+  }
 
   public void setScrollOffset(int y)
   {
@@ -72,8 +72,10 @@ public class AnnotationLabels
     selectedRow = -1;
     AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
 
-    if(aa==null)
+    if (aa == null)
+    {
       return;
+    }
 
     int height = 0;
     for (int i = 0; i < aa.length; i++)
@@ -96,7 +98,7 @@ public class AnnotationLabels
   {
     AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
 
-    if(evt.getActionCommand().equals(EDITNAME))
+    if (evt.getActionCommand().equals(EDITNAME))
     {
       EditNameDialog dialog = new EditNameDialog(
           aa[selectedRow].label,
@@ -136,9 +138,11 @@ public class AnnotationLabels
     }
     else if (evt.getActionCommand().equals(COPYCONS_SEQ))
     {
-      SequenceI cons=av.getConsensusSeq();
-      if (cons!=null)
+      SequenceI cons = av.getConsensusSeq();
+      if (cons != null)
+      {
         copy_annotseqtoclipboard(cons);
+      }
 
     }
     ap.annotationPanel.adjustPanelHeight();
@@ -154,13 +158,17 @@ public class AnnotationLabels
     if (selectedRow > -1)
     {
       if (tooltip == null)
+      {
         tooltip = new Tooltip(ap.av.alignment.
-                                          getAlignmentAnnotation()[selectedRow].
-                                          description,
-                                          this);
+                              getAlignmentAnnotation()[selectedRow].
+                              description,
+                              this);
+      }
       else
+      {
         tooltip.setTip(ap.av.alignment.
-                     getAlignmentAnnotation()[selectedRow].description);
+                       getAlignmentAnnotation()[selectedRow].description);
+      }
     }
     else if (tooltip != null)
     {
@@ -171,14 +179,19 @@ 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)
   {
     AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
@@ -199,7 +212,7 @@ public class AnnotationLabels
     item.addActionListener(this);
     pop.add(item);
 
-    if (aa[selectedRow]==ap.av.consensus)
+    if (aa[selectedRow] == ap.av.consensus)
     {
       pop.addSeparator();
       final CheckboxMenuItem cbmi = new CheckboxMenuItem(
@@ -215,46 +228,50 @@ public class AnnotationLabels
         }
       });
       pop.add(cbmi);
-      final MenuItem cpcons=new MenuItem(COPYCONS_SEQ);
+      final MenuItem cpcons = new MenuItem(COPYCONS_SEQ);
       cpcons.addActionListener(this);
       pop.add(cpcons);
     }
 
-     pop.show(this, evt.getX(), evt.getY());
+    pop.show(this, evt.getX(), evt.getY());
 
   }
-/**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void copy_annotseqtoclipboard(SequenceI sq)
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void copy_annotseqtoclipboard(SequenceI sq)
+  {
+    if (sq == null || sq.getLength() < 1)
+    {
+      return;
+    }
+    jalview.appletgui.AlignFrame.copiedSequences = new StringBuffer();
+    jalview.appletgui.AlignFrame.copiedSequences.append(sq.getName() + "\t" +
+        sq.getStart() + "\t" +
+        sq.getEnd() + "\t" +
+        sq.getSequenceAsString() + "\n");
+    if (av.hasHiddenColumns)
     {
-      if (sq==null || sq.getLength()<1)
-        return;
-      jalview.appletgui.AlignFrame.copiedSequences = new StringBuffer();
-      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++)
       {
-        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]});
       }
     }
+  }
 
-    public void update(Graphics g)
-    {
-      paint(g);
-    }
+  public void update(Graphics g)
+  {
+    paint(g);
+  }
 
   public void paint(Graphics g)
   {
@@ -265,7 +282,7 @@ public class AnnotationLabels
     }
 
     drawComponent(image.getGraphics(), w);
-    g.drawImage(image,0,0,this);
+    g.drawImage(image, 0, 0, this);
   }
 
   public void drawComponent(Graphics g, int width)
@@ -293,14 +310,14 @@ public class AnnotationLabels
 
         x = width - fm.stringWidth(aa[i].label) - 3;
 
-        if (aa[i].graph>0)
+        if (aa[i].graph > 0)
         {
           y += (aa[i].height / 3);
         }
 
         g.drawString(aa[i].label, x, y);
 
-        if (aa[i].graph>0)
+        if (aa[i].graph > 0)
         {
           y += (2 * aa[i].height / 3);
         }
diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java
index 17c0c8a..9c45d5e 100755
--- a/src/jalview/appletgui/AnnotationPanel.java
+++ b/src/jalview/appletgui/AnnotationPanel.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -56,7 +56,9 @@ public class AnnotationPanel
   public AnnotationPanel(AlignmentPanel ap)
   {
     if (System.getProperty("os.name").startsWith("Mac"))
+    {
       MAC = true;
+    }
 
     this.ap = ap;
     av = ap.av;
@@ -74,13 +76,11 @@ public class AnnotationPanel
     // ap.annotationScroller.getVAdjustable().addAdjustmentListener( this );
   }
 
-
   public AnnotationPanel(AlignViewport av)
   {
     this.av = av;
   }
 
-
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
     ap.alabels.setScrollOffset( -evt.getValue());
@@ -91,7 +91,6 @@ public class AnnotationPanel
     // setHeight of panels
     AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
 
-
     int height = 0;
     if (aa != null)
     {
@@ -113,7 +112,7 @@ public class AnnotationPanel
           aa[i].height += 16;
         }
 
-        if (aa[i].graph>0)
+        if (aa[i].graph > 0)
         {
           aa[i].height += GRAPH_HEIGHT;
         }
@@ -143,8 +142,10 @@ public class AnnotationPanel
     if (activeRow == -1)
     {
       AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
-      if(aa ==null)
+      if (aa == null)
+      {
         return;
+      }
 
       for (int j = 0; j < aa.length; j++)
       {
@@ -193,16 +194,20 @@ public class AnnotationPanel
 
     int res = evt.getX() / av.getCharWidth() + av.getStartRes();
 
-    if(av.hasHiddenColumns)
-          res = av.getColumnSelection().adjustForHiddenColumns(res);
+    if (av.hasHiddenColumns)
+    {
+      res = av.getColumnSelection().adjustForHiddenColumns(res);
+    }
 
-        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)
-            text.append("  " + aa[row].annotations[res].description);
-          ap.alignFrame.statusBar.setText(text.toString());
-        }
+    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)
+      {
+        text.append("  " + aa[row].annotations[res].description);
+      }
+      ap.alignFrame.statusBar.setText(text.toString());
+    }
   }
 
   public void update(Graphics g)
@@ -214,7 +219,7 @@ 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))
     {
@@ -225,7 +230,6 @@ public class AnnotationPanel
       fastPaint = false;
     }
 
-
     if (fastPaint)
     {
       g.drawImage(image, 0, 0, this);
@@ -237,7 +241,6 @@ public class AnnotationPanel
     gg.fillRect(0, 0, getSize().width, getSize().height);
     drawComponent(gg, av.startRes, av.endRes + 1);
 
-
     g.drawImage(image, 0, 0, this);
   }
 
@@ -286,218 +289,137 @@ public class AnnotationPanel
   {
     g.setFont(av.getFont());
 
-
     g.setColor(Color.white);
     g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getSize().height);
 
-
     if (fm == null)
+    {
       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);
+      g.setColor(Color.black);
+      if (av.validCharWidth)
       {
-          g.setColor(Color.white);
-          g.fillRect(0, 0, getSize().width, getSize().height);
-          g.setColor(Color.black);
-          if(av.validCharWidth)
-            g.drawString("Alignment has no annotations", 20, 15);
-
-          return;
+        g.drawString("Alignment has no annotations", 20, 15);
       }
 
-      AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+      return;
+    }
 
-      int x = 0;
-      int y = 0;
-      int column=0;
-      char lastSS;
-      int lastSSX;
-      int iconOffset = av.charHeight / 2;
-      boolean validRes = false;
+    AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
 
-      boolean [] graphGroupDrawn = new boolean[aa.length];
+    int x = 0;
+    int y = 0;
+    int column = 0;
+    char lastSS;
+    int lastSSX;
+    int iconOffset = av.charHeight / 2;
+    boolean validRes = false;
 
+    boolean[] graphGroupDrawn = new boolean[aa.length];
 
-      //\u03B2 \u03B1
-      for (int i = 0; i < aa.length; i++)
+    //\u03B2 \u03B1
+    for (int i = 0; i < aa.length; i++)
+    {
+      AlignmentAnnotation row = aa[i];
+
+      if (!row.visible)
       {
-          AlignmentAnnotation row = aa[i];
+        continue;
+      }
 
-          if (!row.visible)
-          {
-              continue;
-          }
+      lastSS = ' ';
+      lastSSX = 0;
 
-          lastSS = ' ';
-          lastSSX = 0;
+      if (row.graph > 0)
+      {
+        if (row.graphGroup > -1 && graphGroupDrawn[row.graphGroup])
+        {
+          continue;
+        }
 
-          if (row.graph>0)
-          {
-              if(row.graphGroup>-1 && graphGroupDrawn[ row.graphGroup ] )
-                continue;
+        // this is so that we draw the characters below the graph
+        y += row.height;
 
-              // this is so that we draw the characters below the graph
-              y += row.height;
+        if (row.hasText)
+        {
+          y -= av.charHeight;
+        }
+      }
 
-              if (row.hasText)
-              {
-                  y -= av.charHeight;
-              }
-          }
+      if (row.hasText)
+      {
+        iconOffset = av.charHeight / 2;
+      }
+      else
+      {
+        iconOffset = 0;
+      }
 
-          if (row.hasText)
-          {
-              iconOffset = av.charHeight / 2;
-          }
-          else
+      x = 0;
+      while (x < endRes - startRes)
+      {
+        if (av.hasHiddenColumns)
+        {
+          column = av.getColumnSelection().adjustForHiddenColumns(startRes + x);
+          if (column > row.annotations.length - 1)
           {
-              iconOffset = 0;
+            break;
           }
+        }
+        else
+        {
+          column = startRes + x;
+        }
 
-           x = 0;
-          while(x < endRes-startRes)
-          {
-            if (av.hasHiddenColumns)
-            {
-              column = av.getColumnSelection().adjustForHiddenColumns(startRes+x);
-              if (column > row.annotations.length-1)
-              {
-                break;
-              }
-            }
-            else
-                column = startRes+x;
-
-              if ( (row.annotations.length <= column) ||
-                  (row.annotations[column] == null))
-              {
-                validRes = false;
-              }
-              else
-              {
-                validRes = true;
-              }
-
-
-              if (av.validCharWidth && validRes &&
-                        (row.annotations[column].displayCharacter.length() > 0))
-              {
-                int charOffset = (av.charWidth -
-                    fm.charWidth(row.annotations[column].displayCharacter.charAt(
-                            0))) / 2;
-                g.setColor(row.annotations[column].colour);
-
-                if (column == 0 || row.graph>0)
-                {
-                    g.drawString(row.annotations[column].displayCharacter,
-                                (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==' ')))
-                {
-                    g.drawString(row.annotations[column].displayCharacter,
-                       (x*av.charWidth)+charOffset,
-                        y + iconOffset + 3);
-                    }
-              }
-
-              if (row.hasIcons)
-              {
-                  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);
-                            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)
-                      {
-                          lastSS = row.annotations[column].secondaryStructure;
-                      }
-                      else
-                      {
-                          lastSS = ' ';
-                      }
-
-                      lastSSX = (x*av.charWidth);
-                  }
-              }
+        if ( (row.annotations.length <= column) ||
+            (row.annotations[column] == null))
+        {
+          validRes = false;
+        }
+        else
+        {
+          validRes = true;
+        }
 
+        if (av.validCharWidth && validRes &&
+            (row.annotations[column].displayCharacter.length() > 0))
+        {
+          int charOffset = (av.charWidth -
+                            fm.charWidth(row.annotations[column].
+                                         displayCharacter.charAt(
+                                             0))) / 2;
+          g.setColor(row.annotations[column].colour);
 
-          column++;
-          x++;
+          if (column == 0 || row.graph > 0)
+          {
+            g.drawString(row.annotations[column].displayCharacter,
+                         (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 == ' ')))
+          {
+            g.drawString(row.annotations[column].displayCharacter,
+                         (x * av.charWidth) + charOffset,
+                         y + iconOffset + 3);
+          }
+        }
 
-          if(column>=row.annotations.length)
-              column = row.annotations.length-1;
-
-        //  x ++;
-
-          if (row.hasIcons)
+        if (row.hasIcons)
+        {
+          if (!validRes ||
+              (row.annotations[column].secondaryStructure != lastSS))
           {
             switch (lastSS)
             {
@@ -508,122 +430,223 @@ public class AnnotationPanel
                   //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);
+                                  (x * av.charWidth) - lastSSX, 7, 8, 8);
                   break;
                 }
 
                 int sCol = (lastSSX / av.charWidth) + startRes;
                 int x1 = lastSSX;
-                int x2 = (x*av.charWidth);
+                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);
+                  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);
+                  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);
-
                 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);
 
-                if (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);
+                           (x * av.charWidth) - lastSSX, 2);
 
                 break;
             }
+
+            if (validRes)
+            {
+              lastSS = row.annotations[column].secondaryStructure;
+            }
+            else
+            {
+              lastSS = ' ';
+            }
+
+            lastSSX = (x * av.charWidth);
           }
+        }
+
+        column++;
+        x++;
+      }
+
+      if (column >= row.annotations.length)
+      {
+        column = row.annotations.length - 1;
+      }
+
+      //  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;
+            }
+
+            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.graph>0)
+            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);
+
+            break;
+
+          case 'E':
+            g.setColor(SHEET_COLOUR);
+
+            if (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);
+            }
+
+            break;
+        }
+      }
+
+      if (row.graph > 0)
+      {
+        if (row.graph == AlignmentAnnotation.LINE_GRAPH)
+        {
+          if (row.graphGroup > -1 && !graphGroupDrawn[row.graphGroup])
           {
-              if(row.graph == AlignmentAnnotation.LINE_GRAPH )
+            float groupmax = -999999, groupmin = 9999999;
+            for (int gg = 0; gg < aa.length; gg++)
+            {
+              if (aa[gg].graphGroup != row.graphGroup)
               {
-                if(row.graphGroup>-1 && !graphGroupDrawn[row.graphGroup])
-                 {
-                   float groupmax=-999999, groupmin=9999999;
-                   for(int gg=0; gg<aa.length; gg++)
-                   {
-                     if(aa[gg].graphGroup!=row.graphGroup)
-                       continue;
-
-                     if(aa[gg]!=row)
-                       aa[gg].visible = false;
-
-                     if(aa[gg].graphMax>groupmax)
-                       groupmax = aa[gg].graphMax;
-                     if(aa[gg].graphMin<groupmin)
-                       groupmin = aa[gg].graphMin;
-                   }
-
-                   for (int gg = 0; gg < aa.length; gg++)
-                   {
-                     if (aa[gg].graphGroup == row.graphGroup)
-                     {
-                       drawLineGraph(g, aa[gg], startRes, endRes, y,
-                                     groupmin, groupmax,
-                                     row.graphHeight);
-                     }
-                   }
-
-                   graphGroupDrawn[ row.graphGroup ] = true;
-                 }
-                 else
-                   drawLineGraph(g, row, startRes, endRes,
-                                 y, row.graphMin, row.graphMax, row.graphHeight  );
+                continue;
               }
-              else if(row.graph == AlignmentAnnotation.BAR_GRAPH )
-                 drawBarGraph(g, row, startRes, endRes,
-                              row.graphMin, row.graphMax, y);
-          }
 
-          if (row.graph>0 && row.hasText)
-          {
-              y += av.charHeight;
-          }
+              if (aa[gg] != row)
+              {
+                aa[gg].visible = false;
+              }
 
-          if (row.graph==0)
+              if (aa[gg].graphMax > groupmax)
+              {
+                groupmax = aa[gg].graphMax;
+              }
+              if (aa[gg].graphMin < groupmin)
+              {
+                groupmin = aa[gg].graphMin;
+              }
+            }
+
+            for (int gg = 0; gg < aa.length; gg++)
+            {
+              if (aa[gg].graphGroup == row.graphGroup)
+              {
+                drawLineGraph(g, aa[gg], startRes, endRes, y,
+                              groupmin, groupmax,
+                              row.graphHeight);
+              }
+            }
+
+            graphGroupDrawn[row.graphGroup] = true;
+          }
+          else
           {
-              y += aa[i].height;
+            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);
+        }
+      }
+
+      if (row.graph > 0 && row.hasText)
+      {
+        y += av.charHeight;
+      }
+
+      if (row.graph == 0)
+      {
+        y += aa[i].height;
       }
+    }
   }
 
   public void drawLineGraph(Graphics g, AlignmentAnnotation aa,
@@ -632,45 +655,48 @@ public class AnnotationPanel
                             float min, float max,
                             int graphHeight)
   {
-    if(sRes>aa.annotations.length)
+    if (sRes > aa.annotations.length)
+    {
       return;
-
-
+    }
 
     int x = 0;
 
     //Adjustment for fastpaint to left
-    if(eRes<av.endRes)
+    if (eRes < av.endRes)
+    {
       eRes++;
+    }
 
     eRes = Math.min(eRes, aa.annotations.length);
 
-
-    if(sRes==0)
+    if (sRes == 0)
     {
       sRes++;
-      x+=av.charWidth;
+      x += av.charWidth;
     }
 
-    int y1=y, y2=y;
+    int y1 = y, y2 = y;
     float range = max - min;
 
     ////Draw origin
-    if(min<0)
-      y2 = y - (int)((0-min / range)*graphHeight);
+    if (min < 0)
+    {
+      y2 = y - (int) ( (0 - min / range) * graphHeight);
+    }
 
     g.setColor(Color.gray);
-    g.drawLine(x-av.charWidth,y2,(eRes-sRes)*av.charWidth,y2);
+    g.drawLine(x - av.charWidth, y2, (eRes - sRes) * av.charWidth, y2);
 
     eRes = Math.min(eRes, aa.annotations.length);
 
     int column;
-    int aaMax = aa.annotations.length-1;
+    int aaMax = aa.annotations.length - 1;
 
-    while( x < eRes - sRes )
+    while (x < eRes - sRes)
     {
       column = sRes + x;
-      if(av.hasHiddenColumns)
+      if (av.hasHiddenColumns)
       {
         column = av.getColumnSelection().adjustForHiddenColumns(column);
       }
@@ -680,26 +706,29 @@ 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;
       }
 
-        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);
+      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);
 
-        g.drawLine(x*av.charWidth-av.charWidth/2, y1, x*av.charWidth+av.charWidth/2, y2);
-        x ++;
-     }
+      g.drawLine(x * av.charWidth - av.charWidth / 2, y1,
+                 x * av.charWidth + av.charWidth / 2, y2);
+      x++;
+    }
 
-     if(aa.threshold!=null)
-     {
-         g.setColor(aa.threshold.colour);
+    if (aa.threshold != null)
+    {
+      g.setColor(aa.threshold.colour);
 
-         y2 = (int)(y - ((aa.threshold.value-min) / range)*graphHeight);
-         g.drawLine(0,y2,(eRes-sRes)*av.charWidth,y2);
+      y2 = (int) (y - ( (aa.threshold.value - min) / range) * graphHeight);
+      g.drawLine(0, y2, (eRes - sRes) * av.charWidth, y2);
     }
   }
 
@@ -708,81 +737,93 @@ public class AnnotationPanel
                            float min, float max,
                            int y)
   {
-    if(sRes>aa.annotations.length)
+    if (sRes > aa.annotations.length)
+    {
       return;
+    }
 
     eRes = Math.min(eRes, aa.annotations.length);
 
-    int x=0, y1=y, y2=y;
+    int x = 0, y1 = y, y2 = y;
 
     float range = max - min;
 
-    if(min<0)
-      y2 = y - (int)((0-min / (range))*aa.graphHeight);
+    if (min < 0)
+    {
+      y2 = y - (int) ( (0 - min / (range)) * aa.graphHeight);
+    }
 
     g.setColor(Color.gray);
 
-    g.drawLine(x,y2,(eRes-sRes)*av.charWidth,y2);
+    g.drawLine(x, y2, (eRes - sRes) * av.charWidth, y2);
 
     int column;
-    int aaMax = aa.annotations.length-1;
+    int aaMax = aa.annotations.length - 1;
 
-    while( x < eRes-sRes )
+    while (x < eRes - sRes)
     {
       column = sRes + x;
-      if(av.hasHiddenColumns)
+      if (av.hasHiddenColumns)
       {
         column = av.getColumnSelection().adjustForHiddenColumns(column);
       }
 
-      if(column > aaMax)
+      if (column > aaMax)
       {
-          break;
+        break;
       }
 
       if (aa.annotations[column] == null)
       {
-        x ++;
+        x++;
         continue;
       }
 
-        g.setColor(aa.annotations[column].colour);
-        y1 = y - (int) (((aa.annotations[column].value-min) / (range)) * aa.graphHeight);
+      g.setColor(aa.annotations[column].colour);
+      y1 = y -
+          (int) ( ( (aa.annotations[column].value - min) / (range)) * aa.graphHeight);
 
-        if(y1-y2>0)
-          g.fillRect(x*av.charWidth, y2, av.charWidth, y1-y2 );
-        else
-          g.fillRect(x*av.charWidth, y1, av.charWidth, y2-y1 );
+      if (y1 - y2 > 0)
+      {
+        g.fillRect(x * av.charWidth, y2, av.charWidth, y1 - y2);
+      }
+      else
+      {
+        g.fillRect(x * av.charWidth, y1, av.charWidth, y2 - y1);
+      }
 
-        x ++ ;
+      x++;
 
     }
-    if(aa.threshold!=null)
+    if (aa.threshold != null)
     {
-        g.setColor(aa.threshold.colour);
-        y2 = (int)(y - ((aa.threshold.value-min) / range)*aa.graphHeight);
-        g.drawLine(0,y2,(eRes-sRes)*av.charWidth,y2);
-      }
+      g.setColor(aa.threshold.colour);
+      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)
   {
-      g.setColor(Color.white);
-      g.fillRect(0, 0, width, y);
-      g.setColor(new Color(0, 0, 180));
+    g.setColor(Color.white);
+    g.fillRect(0, 0, width, y);
+    g.setColor(new Color(0, 0, 180));
 
-      int x = 0, height;
+    int x = 0, height;
 
-      for (int j = sRes; j < eRes; j++)
-      {
-          g.setColor(aa.annotations[j].colour);
+    for (int j = sRes; j < eRes; j++)
+    {
+      g.setColor(aa.annotations[j].colour);
 
-          height = (int) ((aa.annotations[j].value / aa.graphMax) * GRAPH_HEIGHT);
-          if(height>y)
-              height = y;
-          g.fillRect(x, y - height, av.charWidth, height);
-          x += av.charWidth;
+      height = (int) ( (aa.annotations[j].value / aa.graphMax) * GRAPH_HEIGHT);
+      if (height > y)
+      {
+        height = y;
       }
+      g.fillRect(x, y - height, av.charWidth, height);
+      x += av.charWidth;
     }
+  }
 }
diff --git a/src/jalview/appletgui/CutAndPasteTransfer.java b/src/jalview/appletgui/CutAndPasteTransfer.java
index 9f12b87..b6e7460 100755
--- a/src/jalview/appletgui/CutAndPasteTransfer.java
+++ b/src/jalview/appletgui/CutAndPasteTransfer.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -25,7 +25,8 @@ import java.awt.event.*;
 import jalview.datamodel.*;
 import jalview.io.*;
 
-public class CutAndPasteTransfer extends Panel implements ActionListener, MouseListener
+public class CutAndPasteTransfer
+    extends Panel implements ActionListener, MouseListener
 {
   boolean pdbImport = false;
   boolean treeImport = false;
@@ -35,10 +36,13 @@ public class CutAndPasteTransfer extends Panel implements ActionListener, MouseL
 
   public CutAndPasteTransfer(boolean forImport, AlignFrame alignFrame)
   {
-    try {
-        jbInit();
-    } catch (Exception e) {
-        e.printStackTrace();
+    try
+    {
+      jbInit();
+    }
+    catch (Exception e)
+    {
+      e.printStackTrace();
     }
 
     this.alignFrame = alignFrame;
@@ -81,15 +85,20 @@ public class CutAndPasteTransfer extends Panel implements ActionListener, MouseL
     addSequences.setVisible(false);
   }
 
-
   public void actionPerformed(ActionEvent evt)
   {
-    if(evt.getSource()==accept)
+    if (evt.getSource() == accept)
+    {
       ok(true);
-    else if(evt.getSource() == addSequences)
+    }
+    else if (evt.getSource() == addSequences)
+    {
       ok(false);
-    else if(evt.getSource() == cancel)
+    }
+    else if (evt.getSource() == cancel)
+    {
       cancel();
+    }
   }
 
   protected void ok(boolean newWindow)
@@ -97,35 +106,39 @@ public class CutAndPasteTransfer extends Panel implements ActionListener, MouseL
     String text = getText();
     int length = text.length();
     textarea.append("\n");
-    if(textarea.getText().length()==length)
+    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);
+      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)
+    if (pdbImport)
     {
       new MCview.AppletPDBViewer(text, AppletFormatAdapter.PASTE,
                                  seq,
                                  alignFrame.getSeqcanvas());
     }
-    else if(treeImport)
+    else if (treeImport)
     {
-      try{
+      try
+      {
         jalview.io.NewickFile fin = new jalview.io.NewickFile(textarea.getText(),
             "Paste");
 
         fin.parse();
-        if(fin.getTree()!=null)
+        if (fin.getTree() != null)
+        {
           alignFrame.loadTree(fin, "Pasted tree file");
+        }
 
       }
       catch (Exception ex)
@@ -134,7 +147,7 @@ public class CutAndPasteTransfer extends Panel implements ActionListener, MouseL
         return;
       }
     }
-    else if(annotationImport)
+    else if (annotationImport)
     {
       if (new AnnotationFile().readAnnotationFile(
           alignFrame.viewport.alignment, textarea.getText(),
@@ -150,23 +163,25 @@ public class CutAndPasteTransfer extends Panel implements ActionListener, MouseL
                                      jalview.io.AppletFormatAdapter.PASTE);
       }
     }
-    else if(alignFrame!=null)
+    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)
+      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)
+        if (newWindow)
         {
           AlignFrame af = new AlignFrame(al, alignFrame.viewport.applet,
                                          "Cut & Paste input - " + format,
@@ -174,23 +189,33 @@ public class CutAndPasteTransfer extends Panel implements ActionListener, MouseL
           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);
+    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);
+    if (this.getParent() instanceof Frame)
+    {
+      ( (Frame)this.getParent()).setVisible(false);
+    }
     else
-     ((Dialog)this.getParent()).setVisible(false);
+    {
+      ( (Dialog)this.getParent()).setVisible(false);
+    }
   }
 
   protected TextArea textarea = new TextArea();
@@ -201,29 +226,40 @@ public class CutAndPasteTransfer extends Panel implements ActionListener, MouseL
   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);
+  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 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){}
+
+  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 56dcbc3..3e197f0 100644
--- a/src/jalview/appletgui/EditNameDialog.java
+++ b/src/jalview/appletgui/EditNameDialog.java
@@ -22,7 +22,8 @@ package jalview.appletgui;
 import java.awt.*;
 import java.awt.event.*;
 
-public class EditNameDialog extends Dialog implements ActionListener
+public class EditNameDialog
+    extends Dialog implements ActionListener
 {
   TextField id, description;
   Button ok = new Button("Accept");
@@ -37,9 +38,13 @@ public class EditNameDialog extends Dialog implements ActionListener
   public String getDescription()
   {
     if (description.getText().length() < 1)
+    {
       return null;
+    }
     else
+    {
       return description.getText();
+    }
   }
 
   public EditNameDialog(String name,
@@ -56,13 +61,13 @@ public class EditNameDialog extends Dialog implements ActionListener
     Panel panel = new Panel(new BorderLayout());
     Panel panel2 = new Panel(new BorderLayout());
     Label label = new Label(label1);
-    label.setFont(new Font("Monospaced",Font.PLAIN, 12));
+    label.setFont(new Font("Monospaced", Font.PLAIN, 12));
     panel2.add(label, BorderLayout.WEST);
     panel2.add(id, BorderLayout.CENTER);
     panel.add(panel2, BorderLayout.NORTH);
     panel2 = new Panel(new BorderLayout());
     label = new Label(label2);
-    label.setFont(new Font("Monospaced",Font.PLAIN, 12));
+    label.setFont(new Font("Monospaced", Font.PLAIN, 12));
     panel2.add(label, BorderLayout.WEST);
     panel2.add(description, BorderLayout.CENTER);
     panel.add(panel2, BorderLayout.CENTER);
@@ -78,12 +83,11 @@ public class EditNameDialog extends Dialog implements ActionListener
 
     add(panel, BorderLayout.NORTH);
 
-
-    int width = 500, height=100;
+    int width = 500, height = 100;
 
     pack();
 
-    height+=getInsets().top+getInsets().bottom;
+    height += getInsets().top + getInsets().bottom;
 
     setBounds(ap.alignFrame.getBounds().x
               + (ap.alignFrame.getSize().width - width) / 2,
@@ -93,13 +97,14 @@ public class EditNameDialog extends Dialog implements ActionListener
 
     show();
 
-
   }
 
   public void actionPerformed(ActionEvent evt)
   {
-    if(evt.getSource()==ok)
+    if (evt.getSource() == ok)
+    {
       accept = true;
+    }
 
     setVisible(false);
   }
diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java
index 47fbb0d..7ad5f4d 100755
--- a/src/jalview/appletgui/FeatureRenderer.java
+++ b/src/jalview/appletgui/FeatureRenderer.java
@@ -1,7 +1,6 @@
-
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -19,11 +18,11 @@
  */
 package jalview.appletgui;
 
-import jalview.datamodel.*;
+import java.util.*;
 
 import java.awt.*;
 
-import java.util.*;
+import jalview.datamodel.*;
 
 /**
  * DOCUMENT ME!
@@ -33,392 +32,426 @@ import java.util.*;
  */
 public class FeatureRenderer
 {
-    AlignViewport av;
+  AlignViewport av;
 
-    Hashtable featureColours = new Hashtable();
+  Hashtable featureColours = new Hashtable();
 
-    // A higher level for grouping features of a
-    // particular type
-    Hashtable featureGroups = null;
+  // A higher level for grouping features of a
+  // particular type
+  Hashtable featureGroups = null;
 
-    // Holds web links for feature groups and feature types
-    // in the form label|link
-    Hashtable featureLinks = null;
+  // Holds web links for feature groups and feature types
+  // in the form label|link
+  Hashtable featureLinks = null;
 
+  // This is actually an Integer held in the hashtable,
+  // Retrieved using the key feature type
+  Object currentColour;
 
-    // This is actually an Integer held in the hashtable,
-    // Retrieved using the key feature type
-    Object currentColour;
+  String[] renderOrder;
 
-    String [] renderOrder;
+  FontMetrics fm;
+  int charOffset;
 
-    FontMetrics fm;
-    int charOffset;
+  float transparency = 1f;
 
-    float transparency = 1f;
+  TransparencySetter transparencySetter = null;
 
-    TransparencySetter transparencySetter = null;
+  /**
+   * Creates a new FeatureRenderer object.
+   *
+   * @param av DOCUMENT ME!
+   */
+  public FeatureRenderer(AlignViewport av)
+  {
+    this.av = av;
 
-    /**
-     * Creates a new FeatureRenderer object.
-     *
-     * @param av DOCUMENT ME!
-     */
-    public FeatureRenderer(AlignViewport av)
+    if (!System.getProperty("java.version").startsWith("1.1"))
     {
-        this.av = av;
-
-        if(!System.getProperty("java.version").startsWith("1.1"))
-             transparencySetter = new TransparencySetter();
+      transparencySetter = new TransparencySetter();
     }
+  }
 
+  public void transferSettings(FeatureRenderer fr)
+  {
+    renderOrder = fr.renderOrder;
+    featureGroups = fr.featureGroups;
+    featureColours = fr.featureColours;
+    transparency = fr.transparency;
+  }
 
-    public void transferSettings(FeatureRenderer fr)
+  public Color findFeatureColour(Color initialCol, SequenceI seq, int i)
+  {
+    overview = true;
+    if (!av.showSequenceFeatures)
     {
-      renderOrder = fr.renderOrder;
-      featureGroups = fr.featureGroups;
-      featureColours = fr.featureColours;
-      transparency =  fr.transparency;
+      return initialCol;
     }
 
-
-    public Color findFeatureColour(Color initialCol, SequenceI seq, int i)
+    lastSequence = seq;
+    sequenceFeatures = lastSequence.getSequenceFeatures();
+    if (sequenceFeatures == null)
     {
-      overview = true;
-      if(!av.showSequenceFeatures)
-        return initialCol;
-
-        lastSequence = seq;
-        sequenceFeatures = lastSequence.getSequenceFeatures();
-        if(sequenceFeatures==null)
-          return initialCol;
-
-        sfSize = sequenceFeatures.length;
+      return initialCol;
+    }
 
-      if(jalview.util.Comparison.isGap(lastSequence.getCharAt(i)))
-        return Color.white;
+    sfSize = sequenceFeatures.length;
 
-      currentColour = null;
+    if (jalview.util.Comparison.isGap(lastSequence.getCharAt(i)))
+    {
+      return Color.white;
+    }
 
-      drawSequence(null, lastSequence, lastSequence.findPosition(i), -1,-1);
+    currentColour = null;
 
-      if(currentColour==null)
-        return initialCol;
+    drawSequence(null, lastSequence, lastSequence.findPosition(i), -1, -1);
 
-      return new Color( ((Integer)currentColour).intValue() );
+    if (currentColour == null)
+    {
+      return initialCol;
     }
 
-    /**
-     * This is used by the Molecule Viewer to get the accurate colour
-     * of the rendered sequence
-     */
-    boolean overview = false;
+    return new Color( ( (Integer) currentColour).intValue());
+  }
+
+  /**
+   * This is used by the Molecule Viewer to get the accurate colour
+   * of the rendered sequence
+   */
+  boolean overview = false;
 
-    int white = Color.white.getRGB();
-    public int findFeatureColour(int initialCol, int seqIndex, int column)
+  int white = Color.white.getRGB();
+  public int findFeatureColour(int initialCol, int seqIndex, int column)
+  {
+    if (!av.showSequenceFeatures)
     {
-      if(!av.showSequenceFeatures)
-        return initialCol;
+      return initialCol;
+    }
 
-      if(seqIndex!=lastSequenceIndex)
+    if (seqIndex != lastSequenceIndex)
+    {
+      lastSequence = av.alignment.getSequenceAt(seqIndex);
+      lastSequenceIndex = seqIndex;
+      sequenceFeatures = lastSequence.getSequenceFeatures();
+      if (sequenceFeatures == null)
       {
-        lastSequence = av.alignment.getSequenceAt(seqIndex);
-        lastSequenceIndex = seqIndex;
-        sequenceFeatures = lastSequence.getSequenceFeatures();
-        if(sequenceFeatures==null)
-          return initialCol;
-
-        sfSize = sequenceFeatures.length;
+        return initialCol;
       }
 
+      sfSize = sequenceFeatures.length;
+    }
 
-      if(jalview.util.Comparison.isGap(lastSequence.getCharAt(column)))
-        return Color.white.getRGB();
-
-      currentColour = null;
+    if (jalview.util.Comparison.isGap(lastSequence.getCharAt(column)))
+    {
+      return Color.white.getRGB();
+    }
 
-      drawSequence(null, lastSequence, lastSequence.findPosition(column), -1,-1);
+    currentColour = null;
 
-      if(currentColour==null)
-        return initialCol;
+    drawSequence(null, lastSequence, lastSequence.findPosition(column), -1, -1);
 
-      return  ((Integer)currentColour).intValue();
+    if (currentColour == null)
+    {
+      return initialCol;
     }
 
+    return ( (Integer) currentColour).intValue();
+  }
 
-    /**
-     * 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;
-    int lastSequenceIndex=-1;
-    SequenceI lastSequence;
-    SequenceFeature [] sequenceFeatures;
-    int sfSize, sfindex, spos, epos;
-
-    public void drawSequence(Graphics g, SequenceI seq,
-                             int start, int end, int y1)
+  /**
+   * 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;
+  int lastSequenceIndex = -1;
+  SequenceI lastSequence;
+  SequenceFeature[] sequenceFeatures;
+  int sfSize, sfindex, spos, epos;
+
+  public void drawSequence(Graphics g, SequenceI seq,
+                           int start, int end, int y1)
+  {
+    if (seq.getSequenceFeatures() == null
+        || seq.getSequenceFeatures().length == 0)
     {
-      if (   seq.getSequenceFeatures() == null
-          || seq.getSequenceFeatures().length==0)
-        return;
+      return;
+    }
 
-      if(transparencySetter!=null && g!=null)
+    if (transparencySetter != null && g != null)
+    {
+      transparencySetter.setTransparency(g, transparency);
+    }
+
+    if (av.featuresDisplayed == null || renderOrder == null)
+    {
+      findAllFeatures();
+      if (av.featuresDisplayed.size() < 1)
       {
-        transparencySetter.setTransparency(g, transparency);
+        return;
       }
 
-      if (av.featuresDisplayed == null || renderOrder==null)
-       {
-         findAllFeatures();
-         if(av.featuresDisplayed.size()<1)
-           return;
-
-         sequenceFeatures = seq.getSequenceFeatures();
-         sfSize = sequenceFeatures.length;
-       }
-       if(lastSequence==null || seq!=lastSequence)
+      sequenceFeatures = seq.getSequenceFeatures();
+      sfSize = sequenceFeatures.length;
+    }
+    if (lastSequence == null || seq != lastSequence)
+    {
+      lastSequence = seq;
+      sequenceFeatures = seq.getSequenceFeatures();
+      sfSize = sequenceFeatures.length;
+    }
+    if (!overview)
+    {
+      spos = lastSequence.findPosition(start);
+      epos = lastSequence.findPosition(end);
+      if (g != null)
       {
-        lastSequence = seq;
-        sequenceFeatures = seq.getSequenceFeatures();
-        sfSize = sequenceFeatures.length;
+        fm = g.getFontMetrics();
       }
-      if(!overview)
+    }
+    String type;
+    for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++)
+    {
+      type = renderOrder[renderIndex];
+      if (!av.featuresDisplayed.containsKey(type))
       {
-        spos = lastSequence.findPosition(start);
-        epos = lastSequence.findPosition(end);
-        if(g!=null)
-          fm = g.getFontMetrics();
+        continue;
       }
-      String type;
-      for(int renderIndex=0; renderIndex<renderOrder.length; renderIndex++)
-       {
-        type =  renderOrder[renderIndex];
-        if(!av.featuresDisplayed.containsKey(type))
+
+      // loop through all features in sequence to find
+      // current feature to render
+      for (sfindex = 0; sfindex < sfSize; sfindex++)
+      {
+        if (!sequenceFeatures[sfindex].type.equals(type))
+        {
           continue;
+        }
 
-        // loop through all features in sequence to find
-        // current feature to render
-        for (sfindex = 0; sfindex < sfSize; sfindex++)
+        if (featureGroups != null
+            && sequenceFeatures[sfindex].featureGroup != null
+            &&
+            featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)
+            &&
+            ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].
+                                            featureGroup)).
+            booleanValue())
         {
-          if (!sequenceFeatures[sfindex].type.equals(type))
-            continue;
-
-          if (featureGroups != null
-              && sequenceFeatures[sfindex].featureGroup != null
-              &&
-              featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)
-              &&
-              ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].featureGroup)).
-              booleanValue())
-          {
-            continue;
-          }
+          continue;
+        }
 
-          if (!overview && (sequenceFeatures[sfindex].getBegin() > epos
-                            || sequenceFeatures[sfindex].getEnd() < spos))
-            continue;
+        if (!overview && (sequenceFeatures[sfindex].getBegin() > epos
+                          || sequenceFeatures[sfindex].getEnd() < spos))
+        {
+          continue;
+        }
 
-          if (overview)
+        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);
+        }
+        else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))
+        {
 
-          }
-          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].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);
+        }
 
-      if(transparencySetter!=null && g!=null)
-      {
-        transparencySetter.setTransparency(g, 1.0f);
       }
     }
 
+    if (transparencySetter != null && g != null)
+    {
+      transparencySetter.setTransparency(g, 1.0f);
+    }
+  }
+
+  char s;
+  int i;
+  void renderFeature(Graphics g, SequenceI seq,
+                     int fstart, int fend, Color featureColour, int start,
+                     int end, int y1)
+  {
 
-    char s;
-    int i;
-    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 < start)
+      { // fix for if the feature we have starts before the sequence start,
+        fstart = start; // but the feature end is still valid!!
+      }
 
-      if (((fstart <= end) && (fend >= start)))
+      if (fend >= end)
       {
-        if (fstart < start)
-        { // fix for if the feature we have starts before the sequence start,
-          fstart = start; // but the feature end is still valid!!
-        }
+        fend = end;
+      }
+
+      for (i = fstart; i <= fend; i++)
+      {
+        s = seq.getCharAt(i);
 
-        if (fend >= end)
+        if (jalview.util.Comparison.isGap(s))
         {
-          fend = end;
+          continue;
         }
 
-          for (i = fstart; i <= fend; i++)
-          {
-            s = seq.getCharAt(i);
-
-            if (jalview.util.Comparison.isGap(s))
-            {
-              continue;
-            }
+        g.setColor(featureColour);
 
-            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)
-              continue;
+        if (!av.validCharWidth)
+        {
+          continue;
+        }
 
-            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.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;
 
-          }
       }
     }
+  }
+
+  void findAllFeatures()
+  {
+    jalview.schemes.UserColourScheme ucs = new
+        jalview.schemes.UserColourScheme();
 
-    void findAllFeatures()
+    av.featuresDisplayed = new Hashtable();
+    Vector allfeatures = new Vector();
+    for (int i = 0; i < av.alignment.getHeight(); i++)
     {
-      jalview.schemes.UserColourScheme ucs = new
-          jalview.schemes.UserColourScheme();
+      SequenceFeature[] features = av.alignment.getSequenceAt(i).
+          getSequenceFeatures();
 
-      av.featuresDisplayed = new Hashtable();
-      Vector allfeatures = new Vector();
-      for (int i = 0; i < av.alignment.getHeight(); i++)
+      if (features == null)
       {
-        SequenceFeature [] features = av.alignment.getSequenceAt(i).getSequenceFeatures();
-
-        if (features == null)
-          continue;
+        continue;
+      }
 
-        int index = 0;
-        while (index < features.length)
+      int index = 0;
+      while (index < features.length)
+      {
+        if (!av.featuresDisplayed.containsKey(features[index].getType()))
         {
-          if (!av.featuresDisplayed.containsKey(features[index].getType()))
+          if (getColour(features[index].getType()) == null)
           {
-            if (getColour(features[index].getType()) == null)
-            {
-              featureColours.put(features[index].getType(),
-                                 ucs.createColourFromName(features[index].
-                  getType()));
-            }
-
-
-            av.featuresDisplayed.put(features[index].getType(),
-                                  new Integer( getColour(features[index].getType()).getRGB()) );
-            allfeatures.addElement(features[index].getType());
+            featureColours.put(features[index].getType(),
+                               ucs.createColourFromName(features[index].
+                getType()));
           }
-          index++;
-        }
-      }
 
-      renderOrder = new String[allfeatures.size()];
-      Enumeration en = allfeatures.elements();
-      int i = allfeatures.size()-1;
-      while(en.hasMoreElements())
-      {
-        renderOrder[i] = en.nextElement().toString();
-        i--;
+          av.featuresDisplayed.put(features[index].getType(),
+                                   new Integer(getColour(features[index].
+              getType()).getRGB()));
+          allfeatures.addElement(features[index].getType());
+        }
+        index++;
       }
     }
 
-    public Color getColour(String featureType)
+    renderOrder = new String[allfeatures.size()];
+    Enumeration en = allfeatures.elements();
+    int i = allfeatures.size() - 1;
+    while (en.hasMoreElements())
     {
-      return (Color)featureColours.get(featureType);
+      renderOrder[i] = en.nextElement().toString();
+      i--;
     }
+  }
 
-    public void addNewFeature(String name, Color col)
-    {
-
-      setColour(name, col);
-      if(av.featuresDisplayed==null)
-        av.featuresDisplayed = new Hashtable();
+  public Color getColour(String featureType)
+  {
+    return (Color) featureColours.get(featureType);
+  }
 
+  public void addNewFeature(String name, Color col)
+  {
 
-      av.featuresDisplayed.put(name, "NOGROUP");
+    setColour(name, col);
+    if (av.featuresDisplayed == null)
+    {
+      av.featuresDisplayed = new Hashtable();
     }
 
-    public void setColour(String featureType, Color col)
+    av.featuresDisplayed.put(name, "NOGROUP");
+  }
+
+  public void setColour(String featureType, Color col)
+  {
+    featureColours.put(featureType, col);
+  }
+
+  public void setFeaturePriority(Object[][] data)
+  {
+    // The feature table will display high priority
+    // features at the top, but theses are the ones
+    // we need to render last, so invert the data
+    if (av.featuresDisplayed != null)
     {
-      featureColours.put(featureType, col);
+      av.featuresDisplayed.clear();
     }
 
-    public void setFeaturePriority(Object [][] data)
-    {
-        // The feature table will display high priority
-        // features at the top, but theses are the ones
-        // we need to render last, so invert the data
-        if(av.featuresDisplayed!=null)
-          av.featuresDisplayed.clear();
+    renderOrder = new String[data.length];
 
-        renderOrder = new String[data.length];
+    if (data.length > 0)
+    {
+      for (int i = 0; i < data.length; i++)
+      {
+        String type = data[i][0].toString();
+        setColour(type, (Color) data[i][1]);
+        if ( ( (Boolean) data[i][2]).booleanValue())
+        {
+          av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB()));
+        }
 
-        if (data.length > 0)
-          for (int i = 0; i < data.length; i++)
-          {
-            String type = data[i][0].toString();
-            setColour(type, (Color) data[i][1]);
-            if ( ( (Boolean) data[i][2]).booleanValue())
-            {
-              av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB()));
-            }
-
-            renderOrder[data.length - i - 1] = type;
-          }
+        renderOrder[data.length - i - 1] = type;
+      }
     }
+  }
 }
 
-  class TransparencySetter
+class TransparencySetter
+{
+  void setTransparency(Graphics g, float value)
   {
-    void setTransparency(Graphics g, float 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 c855672..9e40b1a 100755
--- a/src/jalview/appletgui/FeatureSettings.java
+++ b/src/jalview/appletgui/FeatureSettings.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,13 +18,15 @@
  */
 package jalview.appletgui;
 
-import jalview.datamodel.*;
-import java.awt.*;
 import java.util.*;
+
+import java.awt.*;
 import java.awt.event.*;
 
+import jalview.datamodel.*;
 
-public class FeatureSettings extends Panel implements ItemListener,
+public class FeatureSettings
+    extends Panel implements ItemListener,
     MouseListener, MouseMotionListener, ActionListener, AdjustmentListener
 {
   FeatureRenderer fr;
@@ -36,7 +38,7 @@ public class FeatureSettings extends Panel implements ItemListener,
   ScrollPane scrollPane;
   boolean alignmentHasFeatures = false;
   Image linkImage;
-  Scrollbar transparency ;
+  Scrollbar transparency;
 
   public FeatureSettings(final AlignmentPanel ap)
   {
@@ -45,14 +47,16 @@ public class FeatureSettings extends Panel implements ItemListener,
     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)
+    if (fr.transparencySetter != null)
     {
       transparency.addAdjustmentListener(this);
     }
     else
+    {
       transparency.setEnabled(false);
+    }
 
     java.net.URL url = getClass().getResource("/images/link.gif");
     if (url != null)
@@ -60,9 +64,10 @@ public class FeatureSettings extends Panel implements ItemListener,
       linkImage = java.awt.Toolkit.getDefaultToolkit().getImage(url);
     }
 
-
-    if(av.featuresDisplayed==null)
+    if (av.featuresDisplayed == null)
+    {
       fr.findAllFeatures();
+    }
 
     setTableData();
 
@@ -70,42 +75,44 @@ public class FeatureSettings extends Panel implements ItemListener,
     scrollPane = new ScrollPane();
     scrollPane.add(featurePanel);
     if (alignmentHasFeatures)
+    {
       add(scrollPane, BorderLayout.CENTER);
+    }
 
     Button invert = new Button("Invert Selection");
     invert.addActionListener(this);
 
-    Panel lowerPanel = new Panel(new GridLayout(2,1,5,10));
+    Panel lowerPanel = new Panel(new GridLayout(2, 1, 5, 10));
     lowerPanel.add(invert);
 
     Panel tPanel = new Panel(new BorderLayout());
 
-    if(fr.transparencySetter!=null)
+    if (fr.transparencySetter != null)
     {
       tPanel.add(transparency, BorderLayout.CENTER);
       tPanel.add(new Label("Transparency"), BorderLayout.EAST);
     }
     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);
 
     add(lowerPanel, BorderLayout.SOUTH);
 
-
-
-    if(groupPanel!=null)
+    if (groupPanel != null)
     {
       groupPanel.setLayout(
-          new GridLayout( fr.featureGroups.size() / 4 + 1, 4));
+          new GridLayout(fr.featureGroups.size() / 4 + 1, 4));
       groupPanel.validate();
 
       add(groupPanel, BorderLayout.NORTH);
     }
     frame = new Frame();
     frame.add(this);
-    int height = featurePanel.getComponentCount()*50 +60;
-
+    int height = featurePanel.getComponentCount() * 50 + 60;
 
     height = Math.max(200, height);
     height = Math.min(400, height);
@@ -126,19 +133,22 @@ public class FeatureSettings extends Panel implements ItemListener,
   {
     alignmentHasFeatures = false;
 
-    if(fr.featureGroups==null)
+    if (fr.featureGroups == null)
+    {
       fr.featureGroups = new Hashtable();
+    }
 
     Vector allFeatures = new Vector();
     Vector allGroups = new Vector();
     SequenceFeature[] tmpfeatures;
     String group;
 
-
     for (int i = 0; i < av.alignment.getHeight(); i++)
     {
       if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null)
+      {
         continue;
+      }
 
       alignmentHasFeatures = true;
 
@@ -146,141 +156,145 @@ public class FeatureSettings extends Panel implements ItemListener,
       int index = 0;
       while (index < tmpfeatures.length)
       {
-        if(tmpfeatures[index].getFeatureGroup()!=null)
+        if (tmpfeatures[index].getFeatureGroup() != null)
         {
           group = tmpfeatures[index].featureGroup;
-          if(!allGroups.contains(group))
-           {
-             allGroups.addElement(group);
+          if (!allGroups.contains(group))
+          {
+            allGroups.addElement(group);
 
-             boolean visible = true;
-             if (fr.featureGroups.containsKey(group))
-             {
-               visible = ( (Boolean) fr.featureGroups.get(group)).booleanValue();
-             }
+            boolean visible = true;
+            if (fr.featureGroups.containsKey(group))
+            {
+              visible = ( (Boolean) fr.featureGroups.get(group)).booleanValue();
+            }
 
-             fr.featureGroups.put(group, new Boolean(visible));
+            fr.featureGroups.put(group, new Boolean(visible));
 
-             if (groupPanel == null)
-             {
-               groupPanel = new Panel();
-             }
+            if (groupPanel == null)
+            {
+              groupPanel = new Panel();
+            }
 
-             Checkbox check =  new MyCheckbox(
+            Checkbox check = new MyCheckbox(
                 group,
                 visible,
-                (fr.featureLinks!=null && fr.featureLinks.containsKey(group))
-                 );
-
-
-             check.addMouseListener(this);
-             check.setFont(new Font("Serif", Font.BOLD, 12));
-             check.addItemListener(this);
-             groupPanel.add(check);
-           }
+                (fr.featureLinks != null && fr.featureLinks.containsKey(group))
+                );
+
+            check.addMouseListener(this);
+            check.setFont(new Font("Serif", Font.BOLD, 12));
+            check.addItemListener(this);
+            groupPanel.add(check);
+          }
         }
 
         if (!allFeatures.contains(tmpfeatures[index].getType()))
         {
-            allFeatures.addElement(tmpfeatures[index].getType());
+          allFeatures.addElement(tmpfeatures[index].getType());
         }
-         index ++;
+        index++;
       }
     }
 
     resetTable(false);
   }
 
- //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;
-    String group=null, type;
+    SequenceFeature[] tmpfeatures;
+    String group = null, type;
     Vector visibleChecks = new Vector();
 
-     for (int i = 0; i < av.alignment.getHeight(); i++)
-     {
-         if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null)
-           continue;
-
-         tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures();
-         int index = 0;
-         while (index < tmpfeatures.length)
-         {
-           group = tmpfeatures[index].featureGroup;
-
-           if (group==null || fr.featureGroups.get(group)==null ||
-               ((Boolean) fr.featureGroups.get(group)).booleanValue())
-           {
-             type = tmpfeatures[index].getType();
-             if(!visibleChecks.contains(type) )
-             {
-               visibleChecks.addElement(type);
-             }
-           }
-           index++;
-         }
-     }
-
-       Component[] comps;
-       int cSize = featurePanel.getComponentCount();
-       Checkbox check;
-       //This will remove any checkboxes which shouldn't be
-       //visible
-       for (int i = 0; i < cSize; i++)
-       {
-         comps = featurePanel.getComponents();
-         check = (Checkbox) comps[i];
-         if (!visibleChecks.contains(check.getLabel()))
-         {
-           featurePanel.remove(i);
-           cSize --;
-           i--;
-         }
-       }
-
-       if(fr.renderOrder!=null)
-       {
-         //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];
-
-              if(!visibleChecks.contains(item))
-                continue;
-
-              visibleChecks.removeElement(item);
-
-              addCheck(false, item);
-         }
-       }
-
-       // now add checkboxes which should be visible,
-       // if they have not already been added
-       Enumeration en = visibleChecks.elements();
-
-       while(en.hasMoreElements())
-       {
-         addCheck(groupsChanged, en.nextElement().toString());
-       }
-
-
-   featurePanel.setLayout(new GridLayout(featurePanel.getComponentCount(), 1, 10,5));
-   featurePanel.validate();
-
-
-   if(scrollPane!=null)
-     scrollPane.validate();
-
-   itemStateChanged(null);
+    for (int i = 0; i < av.alignment.getHeight(); i++)
+    {
+      if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null)
+      {
+        continue;
+      }
+
+      tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures();
+      int index = 0;
+      while (index < tmpfeatures.length)
+      {
+        group = tmpfeatures[index].featureGroup;
+
+        if (group == null || fr.featureGroups.get(group) == null ||
+            ( (Boolean) fr.featureGroups.get(group)).booleanValue())
+        {
+          type = tmpfeatures[index].getType();
+          if (!visibleChecks.contains(type))
+          {
+            visibleChecks.addElement(type);
+          }
+        }
+        index++;
+      }
+    }
+
+    Component[] comps;
+    int cSize = featurePanel.getComponentCount();
+    Checkbox check;
+    //This will remove any checkboxes which shouldn't be
+    //visible
+    for (int i = 0; i < cSize; i++)
+    {
+      comps = featurePanel.getComponents();
+      check = (Checkbox) comps[i];
+      if (!visibleChecks.contains(check.getLabel()))
+      {
+        featurePanel.remove(i);
+        cSize--;
+        i--;
+      }
+    }
+
+    if (fr.renderOrder != null)
+    {
+      //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];
+
+        if (!visibleChecks.contains(item))
+        {
+          continue;
+        }
+
+        visibleChecks.removeElement(item);
+
+        addCheck(false, item);
+      }
+    }
+
+    // now add checkboxes which should be visible,
+    // if they have not already been added
+    Enumeration en = visibleChecks.elements();
+
+    while (en.hasMoreElements())
+    {
+      addCheck(groupsChanged, en.nextElement().toString());
+    }
+
+    featurePanel.setLayout(new GridLayout(featurePanel.getComponentCount(), 1,
+                                          10, 5));
+    featurePanel.validate();
+
+    if (scrollPane != null)
+    {
+      scrollPane.validate();
+    }
+
+    itemStateChanged(null);
   }
 
   void addCheck(boolean groupsChanged, String type)
   {
     boolean addCheck;
-    Component [] comps = featurePanel.getComponents();
+    Component[] comps = featurePanel.getComponents();
     Checkbox check;
     addCheck = true;
     for (int i = 0; i < featurePanel.getComponentCount(); i++)
@@ -303,8 +317,9 @@ public class FeatureSettings extends Panel implements ItemListener,
 
       check = new MyCheckbox(type,
                              selected,
-          (fr.featureLinks!=null && fr.featureLinks.containsKey(type))
-           );
+                             (fr.featureLinks != null &&
+                              fr.featureLinks.containsKey(type))
+          );
 
       check.addMouseListener(this);
       check.addMouseMotionListener(this);
@@ -316,9 +331,9 @@ public class FeatureSettings extends Panel implements ItemListener,
 
   public void actionPerformed(ActionEvent evt)
   {
-    for(int i=0; i<featurePanel.getComponentCount(); i++)
+    for (int i = 0; i < featurePanel.getComponentCount(); i++)
     {
-      Checkbox check = (Checkbox)featurePanel.getComponent(i);
+      Checkbox check = (Checkbox) featurePanel.getComponent(i);
       check.setState(!check.getState());
     }
     selectionChanged();
@@ -335,7 +350,9 @@ public class FeatureSettings extends Panel implements ItemListener,
         fr.featureGroups.put(source.getLabel(), new Boolean(source.getState()));
         ap.seqPanel.seqCanvas.repaint();
         if (ap.overviewPanel != null)
+        {
           ap.overviewPanel.updateOverviewImage();
+        }
 
         resetTable(true);
         return;
@@ -346,27 +363,29 @@ public class FeatureSettings extends Panel implements ItemListener,
 
   void selectionChanged()
   {
-      Component[] comps = featurePanel.getComponents();
-      int cSize = comps.length;
+    Component[] comps = featurePanel.getComponents();
+    int cSize = comps.length;
 
-      Object[][] tmp = new Object[cSize][3];
-      int tmpSize = 0;
-      for (int i = 0; i < cSize; i++)
-      {
-        Checkbox check = (Checkbox) comps[i];
-        tmp[tmpSize][0] = check.getLabel();
-        tmp[tmpSize][1] = fr.getColour(check.getLabel());
-        tmp[tmpSize][2] = new Boolean(check.getState());
-        tmpSize++;
-      }
+    Object[][] tmp = new Object[cSize][3];
+    int tmpSize = 0;
+    for (int i = 0; i < cSize; i++)
+    {
+      Checkbox check = (Checkbox) comps[i];
+      tmp[tmpSize][0] = check.getLabel();
+      tmp[tmpSize][1] = fr.getColour(check.getLabel());
+      tmp[tmpSize][2] = new Boolean(check.getState());
+      tmpSize++;
+    }
 
-      Object[][]data = new Object[tmpSize][3];
-      System.arraycopy(tmp, 0, data,0, tmpSize);
+    Object[][] data = new Object[tmpSize][3];
+    System.arraycopy(tmp, 0, data, 0, tmpSize);
 
-      fr.setFeaturePriority(data);
-      ap.seqPanel.seqCanvas.repaint();
-      if (ap.overviewPanel != null)
-        ap.overviewPanel.updateOverviewImage();
+    fr.setFeaturePriority(data);
+    ap.seqPanel.seqCanvas.repaint();
+    if (ap.overviewPanel != null)
+    {
+      ap.overviewPanel.updateOverviewImage();
+    }
   }
 
   MyCheckbox selectedCheck;
@@ -375,65 +394,74 @@ public class FeatureSettings extends Panel implements ItemListener,
   public void mousePressed(MouseEvent evt)
   {
 
-    selectedCheck = (MyCheckbox)evt.getSource();
+    selectedCheck = (MyCheckbox) evt.getSource();
 
-    if(fr.featureLinks!=null
-       && fr.featureLinks.containsKey(selectedCheck.getLabel() )
+    if (fr.featureLinks != null
+        && fr.featureLinks.containsKey(selectedCheck.getLabel())
         )
+    {
+      if (evt.getX() > selectedCheck.stringWidth + 20)
       {
-        if(evt.getX()>selectedCheck.stringWidth+20)
-        {
-          evt.consume();
-        }
+        evt.consume();
       }
+    }
 
   }
 
   public void mouseDragged(MouseEvent evt)
   {
-    if(((Component)evt.getSource()).getParent()!=featurePanel)
+    if ( ( (Component) evt.getSource()).getParent() != featurePanel)
+    {
       return;
-      dragging = true;
+    }
+    dragging = true;
   }
 
   public void mouseReleased(MouseEvent evt)
   {
-    if(((Component)evt.getSource()).getParent()!=featurePanel)
+    if ( ( (Component) evt.getSource()).getParent() != featurePanel)
+    {
       return;
+    }
 
     Component comp = null;
-    Checkbox  target = null;
-
-    int height = evt.getY()+evt.getComponent().getLocation().y;
-
-    if(height > featurePanel.getSize().height)
-     {
-
-       comp = featurePanel.getComponent(featurePanel.getComponentCount()-1);
-     }
-     else if(height < 0)
-     {
-       comp = featurePanel.getComponent(0);
-     }
-     else
-     {
-       comp = featurePanel.getComponentAt(evt.getX(),
-                                  evt.getY() +
-                                  evt.getComponent().getLocation().y);
-     }
-
-    if(comp!=null && comp instanceof Checkbox)
-      target = (Checkbox)comp;
-
-    if (   selectedCheck != null
+    Checkbox target = null;
+
+    int height = evt.getY() + evt.getComponent().getLocation().y;
+
+    if (height > featurePanel.getSize().height)
+    {
+
+      comp = featurePanel.getComponent(featurePanel.getComponentCount() - 1);
+    }
+    else if (height < 0)
+    {
+      comp = featurePanel.getComponent(0);
+    }
+    else
+    {
+      comp = featurePanel.getComponentAt(evt.getX(),
+                                         evt.getY() +
+                                         evt.getComponent().getLocation().y);
+    }
+
+    if (comp != null && comp instanceof Checkbox)
+    {
+      target = (Checkbox) comp;
+    }
+
+    if (selectedCheck != null
         && target != null
         && selectedCheck != target)
     {
       int targetIndex = -1;
-      for(int i=0; i<featurePanel.getComponentCount(); i++)
+      for (int i = 0; i < featurePanel.getComponentCount(); i++)
       {
-          if(target==featurePanel.getComponent(i))
-          { targetIndex = i; break; }
+        if (target == featurePanel.getComponent(i))
+        {
+          targetIndex = i;
+          break;
+        }
       }
 
       featurePanel.remove(selectedCheck);
@@ -451,13 +479,17 @@ public class FeatureSettings extends Panel implements ItemListener,
     ap.repaint();
   }
 
-  public void mouseEntered(MouseEvent evt){}
-  public void mouseExited(MouseEvent evt){}
+  public void mouseEntered(MouseEvent evt)
+  {}
+
+  public void mouseExited(MouseEvent evt)
+  {}
+
   public void mouseClicked(MouseEvent evt)
   {
     MyCheckbox check = (MyCheckbox) evt.getSource();
 
-    if (fr.featureLinks!=null
+    if (fr.featureLinks != null
         && fr.featureLinks.containsKey(check.getLabel()))
     {
       if (evt.getX() > check.stringWidth + 20)
@@ -469,16 +501,20 @@ public class FeatureSettings extends Panel implements ItemListener,
       }
     }
 
-    if(check.getParent()!=featurePanel)
+    if (check.getParent() != featurePanel)
+    {
       return;
+    }
 
-    if(evt.getClickCount()>1)
+    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 mouseMoved(MouseEvent evt)
+  {}
 
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
@@ -487,7 +523,8 @@ public class FeatureSettings extends Panel implements ItemListener,
 
   }
 
-  class MyCheckbox extends Checkbox
+  class MyCheckbox
+      extends Checkbox
   {
     public int stringWidth;
     boolean hasLink;
@@ -503,11 +540,11 @@ public class FeatureSettings extends Panel implements ItemListener,
     public void paint(Graphics g)
     {
       if (hasLink)
-        g.drawImage(linkImage, stringWidth + 25,(
-        getSize().height-linkImage.getHeight(this))/2,
+      {
+        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 25b924a..e1236c9 100755
--- a/src/jalview/appletgui/Finder.java
+++ b/src/jalview/appletgui/Finder.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -25,9 +25,9 @@ import java.awt.*;
 import java.awt.event.*;
 
 import jalview.datamodel.*;
-import java.awt.Rectangle;
 
-public class Finder extends Panel implements ActionListener
+public class Finder
+    extends Panel implements ActionListener
 {
   AlignViewport av;
   AlignmentPanel ap;
@@ -66,10 +66,14 @@ public class Finder extends Panel implements ActionListener
   public void actionPerformed(ActionEvent evt)
   {
     if (evt.getSource() == textfield)
+    {
       doSearch(false);
+    }
 
     else if (evt.getSource() == findNext)
+    {
       doSearch(false);
+    }
 
     else if (evt.getSource() == findAll)
     {
@@ -77,11 +81,12 @@ public class Finder extends Panel implements ActionListener
       seqIndex = 0;
       doSearch(true);
     }
-    else if(evt.getSource() == createNewGroup)
+    else if (evt.getSource() == createNewGroup)
+    {
       createNewGroup_actionPerformed();
+    }
   }
 
-
   public void createNewGroup_actionPerformed()
   {
 
@@ -92,28 +97,29 @@ public class Finder extends Panel implements ActionListener
 
     cap.setText(textfield.getText());
 
-    dialog.setBounds( frame.getLocation().x+frame.getSize().width+5,
-                      frame.getLocation().y+20,300,100);
+    dialog.setBounds(frame.getLocation().x + frame.getSize().width + 5,
+                     frame.getLocation().y + 20, 300, 100);
     dialog.show();
 
-
     String featureName = cap.getText().trim();
-    if(featureName.length()<1)
+    if (featureName.length() < 1)
+    {
       return;
+    }
 
-
-    for (int i = 0; i < searchResults.getSize(); i ++ )
+    for (int i = 0; i < searchResults.getSize(); i++)
     {
-        SequenceI seq = searchResults.getResultSequence(i);
+      SequenceI seq = searchResults.getResultSequence(i);
 
-        SequenceFeature sf = new SequenceFeature(featureName,
-            null, null,
-            searchResults.getResultStart(i),
-           searchResults.getResultEnd(i), "Search Results");
+      SequenceFeature sf = new SequenceFeature(featureName,
+                                               null, null,
+                                               searchResults.getResultStart(i),
+                                               searchResults.getResultEnd(i),
+                                               "Search Results");
 
-        ap.seqPanel.seqCanvas.getFeatureRenderer().addNewFeature(
-            featureName, new Color(60,160,115));
-        seq.addSequenceFeature(sf);
+      ap.seqPanel.seqCanvas.getFeatureRenderer().addNewFeature(
+          featureName, new Color(60, 160, 115));
+      seq.addSequenceFeature(sf);
     }
 
     ap.seqPanel.seqCanvas.getFeatureRenderer().findAllFeatures();
@@ -124,24 +130,25 @@ public class Finder extends Panel implements ActionListener
 
   void doSearch(boolean findAll)
   {
-    if(jalview.bin.JalviewLite.currentAlignFrame!=null)
+    if (jalview.bin.JalviewLite.currentAlignFrame != null)
     {
       ap = jalview.bin.JalviewLite.currentAlignFrame.alignPanel;
       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);
-    
+
     String searchString = textfield.getText();
-    
+
     finder.find(searchString);
-    seqIndex=finder.getSeqIndex();
-    resIndex=finder.getResIndex();
+    seqIndex = finder.getSeqIndex();
+    resIndex = finder.getResIndex();
     searchResults = finder.getSearchResults();
     Vector idMatch = finder.getIdMatch();
-    
+
     if (searchResults.getSize() == 0 && idMatch.size() > 0)
     {
       ap.idPanel.highlightSearchResults(idMatch);
@@ -150,7 +157,7 @@ public class Finder extends Panel implements ActionListener
     if (searchResults.getSize() > 0)
     {
       createNewGroup.setEnabled(true);
-      
+
     }
     else
     {
@@ -164,8 +171,10 @@ public class Finder extends Panel implements ActionListener
 
     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);
     }
 
   }
@@ -179,49 +188,54 @@ public class Finder extends Panel implements ActionListener
   protected Button createNewGroup = new Button();
   Checkbox caseSensitive = new Checkbox();
 
-  private void jbInit() throws Exception {
-      jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
-      jLabel1.setText("Find");
-      jLabel1.setBounds(new Rectangle(3, 30, 34, 15));
-      this.setLayout(null);
-      textfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
-      textfield.setText("");
-      textfield.setBounds(new Rectangle(40, 27, 133, 21));
-      textfield.addKeyListener(new java.awt.event.KeyAdapter() {
-              public void keyTyped(KeyEvent e) {
-                  textfield_keyTyped(e);
-              }
-          });
-      textfield.addActionListener(this);
-      findAll.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
-      findAll.setLabel("Find all");
-      findAll.addActionListener(this);
-      findNext.setEnabled(false);
-      findNext.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
-      findNext.setLabel("Find Next");
-      findNext.addActionListener(this);
-      jPanel1.setBounds(new Rectangle(180, 5, 141, 64));
-      jPanel1.setLayout(gridLayout1);
-      gridLayout1.setHgap(0);
-      gridLayout1.setRows(3);
-      gridLayout1.setVgap(2);
-      createNewGroup.setEnabled(false);
-      createNewGroup.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
-      createNewGroup.setLabel("New Feature");
-      createNewGroup.addActionListener(this);
+  private void jbInit()
+      throws Exception
+  {
+    jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
+    jLabel1.setText("Find");
+    jLabel1.setBounds(new Rectangle(3, 30, 34, 15));
+    this.setLayout(null);
+    textfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
+    textfield.setText("");
+    textfield.setBounds(new Rectangle(40, 27, 133, 21));
+    textfield.addKeyListener(new java.awt.event.KeyAdapter()
+    {
+      public void keyTyped(KeyEvent e)
+      {
+        textfield_keyTyped(e);
+      }
+    });
+    textfield.addActionListener(this);
+    findAll.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
+    findAll.setLabel("Find all");
+    findAll.addActionListener(this);
+    findNext.setEnabled(false);
+    findNext.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
+    findNext.setLabel("Find Next");
+    findNext.addActionListener(this);
+    jPanel1.setBounds(new Rectangle(180, 5, 141, 64));
+    jPanel1.setLayout(gridLayout1);
+    gridLayout1.setHgap(0);
+    gridLayout1.setRows(3);
+    gridLayout1.setVgap(2);
+    createNewGroup.setEnabled(false);
+    createNewGroup.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
+    createNewGroup.setLabel("New Feature");
+    createNewGroup.addActionListener(this);
     caseSensitive.setLabel("Match Case");
     caseSensitive.setBounds(new Rectangle(40, 49, 126, 23));
     jPanel1.add(findNext, null);
-      jPanel1.add(findAll, null);
-      jPanel1.add(createNewGroup, null);
+    jPanel1.add(findAll, null);
+    jPanel1.add(createNewGroup, null);
     this.add(caseSensitive);
     this.add(textfield, null);
-      this.add(jLabel1, null);
-      this.add(jPanel1, null);
+    this.add(jLabel1, null);
+    this.add(jPanel1, null);
   }
 
-  void textfield_keyTyped(KeyEvent e) {
-      findNext.setEnabled(true);
+  void textfield_keyTyped(KeyEvent e)
+  {
+    findNext.setEnabled(true);
   }
 
 }
diff --git a/src/jalview/appletgui/FontChooser.java b/src/jalview/appletgui/FontChooser.java
index 5fb6fb6..112e1d4 100755
--- a/src/jalview/appletgui/FontChooser.java
+++ b/src/jalview/appletgui/FontChooser.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -20,7 +20,6 @@
 package jalview.appletgui;
 
 import java.awt.*;
-
 import java.awt.event.*;
 
 public class FontChooser
@@ -95,23 +94,32 @@ public class FontChooser
 
   public void actionPerformed(ActionEvent evt)
   {
-    if(evt.getSource()==ok)
+    if (evt.getSource() == ok)
+    {
       ok_actionPerformed();
-    else if(evt.getSource()==cancel)
+    }
+    else if (evt.getSource() == cancel)
+    {
       cancel_actionPerformed();
+    }
   }
 
   public void itemStateChanged(ItemEvent evt)
   {
-    if(evt.getSource()==fontName)
+    if (evt.getSource() == fontName)
+    {
       fontName_actionPerformed();
-    else if(evt.getSource()==fontSize)
+    }
+    else if (evt.getSource() == fontSize)
+    {
       fontSize_actionPerformed();
-    else if(evt.getSource()==fontStyle)
+    }
+    else if (evt.getSource() == fontStyle)
+    {
       fontStyle_actionPerformed();
+    }
   }
 
-
   protected void ok_actionPerformed()
   {
     frame.setVisible(false);
@@ -127,12 +135,12 @@ public class FontChooser
 
   protected void cancel_actionPerformed()
   {
-    if(ap!=null)
+    if (ap != null)
     {
       ap.av.setFont(oldFont);
       ap.repaint();
     }
-    else if(tp!=null)
+    else if (tp != null)
     {
       tp.setTreeFont(oldFont);
       tp.treeCanvas.repaint();
@@ -157,10 +165,10 @@ public class FontChooser
       ap.av.setFont(newFont);
       ap.fontChanged();
     }
-    else if(tp != null)
+    else if (tp != null)
     {
       tp.setTreeFont(newFont);
-      }
+    }
   }
 
   protected void fontName_actionPerformed()
@@ -189,6 +197,7 @@ public class FontChooser
     }
     changeFont();
   }
+
   Label label1 = new Label();
   protected Choice fontSize = new Choice();
   protected Choice fontStyle = new Choice();
@@ -207,52 +216,53 @@ public class FontChooser
   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);
+  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 a1bc873..ac82e12 100755
--- a/src/jalview/appletgui/IdCanvas.java
+++ b/src/jalview/appletgui/IdCanvas.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -54,7 +54,7 @@ public class IdCanvas
     if (searchResults != null && searchResults.contains(s))
     {
       gg.setColor(Color.black);
-      gg.fillRect(0, ((i - starty) * charHeight) + ypos,
+      gg.fillRect(0, ( (i - starty) * charHeight) + ypos,
                   getSize().width, charHeight);
       gg.setColor(Color.white);
     }
@@ -62,25 +62,26 @@ public class IdCanvas
              av.getSelectionGroup().getSequences(null).contains(s))
     {
       gg.setColor(Color.lightGray);
-      gg.fillRect(0, ((i - starty) * charHeight) + ypos,
+      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,
+      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 +
+    gg.drawString(s.getDisplayId(av.getShowJVSuffix()), 0,
+                  ( (i - starty) * charHeight) + ypos +
                   charHeight - (charHeight / 5));
 
     if (av.hasHiddenRows && av.showHiddenMarkers)
-          drawMarker(i, starty, ypos);
+    {
+      drawMarker(i, starty, ypos);
+    }
 
   }
 
@@ -186,7 +187,9 @@ public class IdCanvas
       int alheight = av.alignment.getHeight();
 
       if (av.hasHiddenColumns)
+      {
         maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+      }
 
       int annotationHeight = 0;
       AnnotationLabels labels = null;
@@ -200,7 +203,9 @@ public class IdCanvas
 
       int hgap = av.charHeight;
       if (av.scaleAboveWrapped)
+      {
         hgap += av.charHeight;
+      }
 
       int cHeight = alheight * av.charHeight
           + hgap
@@ -220,7 +225,9 @@ public class IdCanvas
             setHiddenFont(i);
           }
           else
+          {
             gg.setFont(italic);
+          }
 
           SequenceI s = av.alignment.getSequenceAt(i);
           drawIdString(gg, s, i, 0, ypos);
@@ -249,8 +256,10 @@ public class IdCanvas
         }
 
         seq = av.alignment.getSequenceAt(i);
-        if(seq==null)
+        if (seq == null)
+        {
           continue;
+        }
 
         // Selected sequence colours
         if ( (searchResults != null) &&
@@ -267,7 +276,7 @@ public class IdCanvas
         }
         else
         {
-          currentColor =  av.getSequenceColour(seq);
+          currentColor = av.getSequenceColour(seq);
           currentTextColor = Color.black;
         }
 
@@ -278,14 +287,15 @@ public class IdCanvas
 
         gg.setColor(currentTextColor);
 
-
         gg.drawString(seq.getDisplayId(av.getShowJVSuffix()),
                       0,
                       ( ( (i - starty) * av.charHeight) + av.charHeight) -
                       (av.charHeight / 5));
 
         if (av.hasHiddenRows && av.showHiddenMarkers)
+        {
           drawMarker(i, starty, 0);
+        }
       }
     }
   }
@@ -298,7 +308,7 @@ public class IdCanvas
 
   void drawMarker(int i, int starty, int yoffset)
   {
-    SequenceI [] hseqs = av.alignment.getHiddenSequences().hiddenSequences;
+    SequenceI[] hseqs = av.alignment.getHiddenSequences().hiddenSequences;
     //Use this method here instead of calling hiddenSeq adjust
     //3 times.
     int hSize = hseqs.length;
@@ -310,59 +320,64 @@ public class IdCanvas
     boolean below = (hiddenIndex > lastIndex + 1);
     boolean above = (nextIndex > hiddenIndex + 1);
 
-
-
-    for(int j=0; j<hSize; j++)
+    for (int j = 0; j < hSize; j++)
     {
       if (hseqs[j] != null)
       {
-        if(j-1<hiddenIndex)
+        if (j - 1 < hiddenIndex)
+        {
           hiddenIndex++;
-        if(j-1<lastIndex)
+        }
+        if (j - 1 < lastIndex)
+        {
           lastIndex++;
-        if(j-1<nextIndex)
+        }
+        if (j - 1 < nextIndex)
+        {
           nextIndex++;
+        }
       }
-      }
+    }
 
-      gg.setColor(Color.blue);
-      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);
-      }
-      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);
+    gg.setColor(Color.blue);
+    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);
+    }
+    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);
 
-      }
+    }
   }
 
   void setHiddenFont(int i)
   {
-  /*  System.out.println(i+" "+av.alignment.getHeight());
-    if (av.alignment.getSequenceAt(i).getHiddenSequences() != null)
-      gg.setFont(new Font(av.getFont().getName(), Font.BOLD,
-                          av.getFont().getSize()));
-    else
-      gg.setFont(new Font(av.getFont().getName(), Font.ITALIC,
-                          av.getFont().getSize()));*/
+    /*  System.out.println(i+" "+av.alignment.getHeight());
+      if (av.alignment.getSequenceAt(i).getHiddenSequences() != null)
+        gg.setFont(new Font(av.getFont().getName(), Font.BOLD,
+                            av.getFont().getSize()));
+      else
+        gg.setFont(new Font(av.getFont().getName(), Font.ITALIC,
+                            av.getFont().getSize()));*/
   }
 }
diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java
index 26daf21..2acfa39 100755
--- a/src/jalview/appletgui/IdPanel.java
+++ b/src/jalview/appletgui/IdPanel.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -50,7 +50,7 @@ public class IdPanel
     idCanvas.addMouseMotionListener(this);
 
     String label, url;
-    if(av.applet!=null)
+    if (av.applet != null)
     {
       for (int i = 1; i < 10; i++)
       {
@@ -58,7 +58,9 @@ public class IdPanel
         url = av.applet.getParameter("linkURL_" + i);
 
         if (label != null && url != null)
+        {
           links.addElement(label + "|" + url);
+        }
 
       }
     }
@@ -76,21 +78,27 @@ public class IdPanel
 
     SequenceI sequence = av.getAlignment().getSequenceAt(seq);
 
-    if(sequence.getDescription()==null)
+    if (sequence.getDescription() == null)
     {
-      if(tooltip!=null)
+      if (tooltip != null)
+      {
         tooltip.setVisible(false);
+      }
       tooltip = null;
       return;
     }
 
     if (tooltip == null)
+    {
       tooltip = new Tooltip(
           sequence.getDisplayId(true)
           + "\n" + sequence.getDescription(), idCanvas);
+    }
     else
+    {
       tooltip.setTip(sequence.getDisplayId(true)
                      + "\n" + sequence.getDescription());
+    }
   }
 
   public void mouseDragged(MouseEvent e)
@@ -115,22 +123,25 @@ public class IdPanel
   public void mouseClicked(MouseEvent e)
   {
     if (e.getClickCount() < 2)
-        return;
-
+    {
+      return;
+    }
 
     //DEFAULT LINK IS FIRST IN THE LINK LIST
     int seq = alignPanel.seqPanel.findSeq(e);
     String id = av.getAlignment().getSequenceAt(seq).getName();
     if (id.indexOf("|") > -1)
-        id = id.substring(id.lastIndexOf("|") + 1);
+    {
+      id = id.substring(id.lastIndexOf("|") + 1);
+    }
 
     String target = links.elementAt(0).toString();
     target = target.substring(0, target.indexOf("|"));
     String url = links.elementAt(0).toString();
-    url = url.substring(url.indexOf("|")+1);
+    url = url.substring(url.indexOf("|") + 1);
 
     int index = url.indexOf("$SEQUENCE_ID$");
-    url = url.substring(0, index)+ id + url.substring(index+13);
+    url = url.substring(0, index) + id + url.substring(index + 13);
 
     try
     {
@@ -172,7 +183,7 @@ public class IdPanel
 
   public void mousePressed(MouseEvent e)
   {
-    if (e.getClickCount() >1 )
+    if (e.getClickCount() > 1)
     {
       return;
     }
@@ -188,22 +199,22 @@ public class IdPanel
     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);
       av.getSelectionGroup().setEndRes(av.alignment.getWidth() - 1);
     }
 
-
     if (e.isShiftDown() && lastid != -1)
     {
       selectSeqs(lastid, seq);
@@ -255,8 +266,10 @@ public class IdPanel
       scrollThread.running = false;
     }
 
-    if(av.getSelectionGroup()!=null)
+    if (av.getSelectionGroup() != null)
+    {
       av.getSelectionGroup().recalcConservation();
+    }
 
     mouseDragging = false;
     PaintRefresher.Refresh(this, av.getSequenceSetId());
@@ -315,12 +328,11 @@ public class IdPanel
           {
             selectSeqs(lastid - 1, seq);
           }
-          else if (seq > lastid && seq<av.alignment.getHeight())
+          else if (seq > lastid && seq < av.alignment.getHeight())
           {
             selectSeqs(lastid + 1, seq);
           }
 
-
           lastid = seq;
         }
         else
diff --git a/src/jalview/appletgui/IdwidthAdjuster.java b/src/jalview/appletgui/IdwidthAdjuster.java
index 844a9cb..052a95e 100755
--- a/src/jalview/appletgui/IdwidthAdjuster.java
+++ b/src/jalview/appletgui/IdwidthAdjuster.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index 867ce56..0f70a51 100755
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -43,7 +43,6 @@ public class OverviewPanel
   SequenceRenderer sr;
   FeatureRenderer fr;
 
-
   Frame nullFrame;
 
   public OverviewPanel(AlignmentPanel ap)
@@ -54,7 +53,6 @@ public class OverviewPanel
     nullFrame = new Frame();
     nullFrame.addNotify();
 
-
     sr = new SequenceRenderer(av);
     sr.graphics = nullFrame.getGraphics();
     sr.renderGaps = false;
@@ -62,22 +60,24 @@ public class OverviewPanel
     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.hconsensus == null)
+    {
+      graphHeight = 0;
+    }
 
     if (av.alignment.getWidth() > av.alignment.getHeight())
     {
       // wider
       width = 400;
       sequencesHeight = (int) (400f / initialScale);
-      if(sequencesHeight<40)
-              sequencesHeight = 40;
+      if (sequencesHeight < 40)
+      {
+        sequencesHeight = 40;
+      }
     }
     else
     {
@@ -112,15 +112,18 @@ public class OverviewPanel
 
   }
 
-
   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();
@@ -146,26 +149,26 @@ public class OverviewPanel
   {
     if (boxY < 0)
     {
-        boxY = 0;
+      boxY = 0;
     }
 
     if (boxY > (sequencesHeight - boxHeight))
     {
-        boxY = sequencesHeight - boxHeight + 1;
+      boxY = sequencesHeight - boxHeight + 1;
     }
 
     if (boxX < 0)
     {
-        boxX = 0;
+      boxX = 0;
     }
 
     if (boxX > (width - boxWidth))
     {
-      if(av.hasHiddenColumns)
+      if (av.hasHiddenColumns)
       {
         //Try smallest possible box
         boxWidth = (int) ( (av.endRes - av.startRes + 1) *
-                               av.getCharWidth() * scalew);
+                          av.getCharWidth() * scalew);
       }
       boxX = width - boxWidth;
     }
@@ -183,12 +186,12 @@ public class OverviewPanel
       col = av.getColumnSelection().findColumnPosition(col);
     }
 
-    if( av.hasHiddenRows )
+    if (av.hasHiddenRows)
     {
       row = av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(row);
     }
 
-    ap.setScrollValues( col, row );
+    ap.setScrollValues(col, row);
     ap.repaint();
   }
 
@@ -199,15 +202,17 @@ public class OverviewPanel
   {
     if (resizing)
     {
-        resizeAgain = true;
-        return;
+      resizeAgain = true;
+      return;
     }
 
     if (av.showSequenceFeatures)
-   {
-     fr.featureGroups = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups;
-     fr.featureColours = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours;
-   }
+    {
+      fr.featureGroups = ap.seqPanel.seqCanvas.getFeatureRenderer().
+          featureGroups;
+      fr.featureColours = ap.seqPanel.seqCanvas.getFeatureRenderer().
+          featureColours;
+    }
 
     resizing = true;
 
@@ -225,7 +230,7 @@ public class OverviewPanel
 
   // This is set true if the user resizes whilst
   // the overview is being calculated
-    boolean resizeAgain = false;
+  boolean resizeAgain = false;
 
   public void run()
   {
@@ -235,7 +240,7 @@ public class OverviewPanel
 
     if (av.showSequenceFeatures)
     {
-      fr.transferSettings( ap.seqPanel.seqCanvas.getFeatureRenderer() );
+      fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
     }
 
     if (getSize().width > 0 && getSize().height > 0)
@@ -259,17 +264,17 @@ public class OverviewPanel
     float sampleCol = (float) alwidth / (float) width;
     float sampleRow = (float) alheight / (float) sequencesHeight;
 
-    int lastcol=0, lastrow=0;
-    int xstart=0, ystart=0;
+    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)
+      if ( (int) (row * sampleRow) == lastrow)
       {
-        sameRow ++;
+        sameRow++;
         continue;
       }
 
@@ -280,9 +285,10 @@ public class OverviewPanel
         if (seq == null)
         {
           int index =
-             av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(lastrow);
+              av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(
+              lastrow);
 
-         seq = av.alignment.getSequenceAt(index);
+          seq = av.alignment.getSequenceAt(index);
         }
         else
         {
@@ -290,47 +296,56 @@ public class OverviewPanel
         }
       }
       else
+      {
         seq = av.alignment.getSequenceAt(lastrow);
+      }
 
-        for (col = 0; col < width; col++)
+      for (col = 0; col < width; col++)
+      {
+        if ( (int) (col * sampleCol) == lastcol &&
+            (int) (row * sampleRow) == lastrow)
         {
-          if ( (int) (col * sampleCol) == lastcol && (int) (row * sampleRow) == lastrow)
-          {
-            sameCol ++;
-            continue;
-          }
+          sameCol++;
+          continue;
+        }
 
-          lastcol = (int) (col * sampleCol);
+        lastcol = (int) (col * sampleCol);
 
-          if (seq.getLength() > lastcol)
-          {
-            color = sr.getResidueBoxColour(
-                seq, lastcol);
+        if (seq.getLength() > lastcol)
+        {
+          color = sr.getResidueBoxColour(
+              seq, lastcol);
 
-            if (av.showSequenceFeatures)
-              color = fr.findFeatureColour(color, seq, lastcol);
-          }
-          else
+          if (av.showSequenceFeatures)
           {
-            color = Color.white; //White
+            color = fr.findFeatureColour(color, seq, lastcol);
           }
+        }
+        else
+        {
+          color = Color.white; //White
+        }
 
-          if (hiddenRow ||
-              (av.hasHiddenColumns && !av.getColumnSelection().isVisible(lastcol)))
-          {
-            color = color.darker().darker();
-          }
+        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);
+        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;
+        xstart = col;
+        sameCol = 1;
       }
-      lastrow = (int)(row*sampleRow);
+      lastrow = (int) (row * sampleRow);
       ystart = row;
       sameRow = 1;
     }
@@ -357,12 +372,12 @@ public class OverviewPanel
 
     setBoxPosition();
 
-    if(resizeAgain)
+    if (resizeAgain)
     {
       resizeAgain = false;
       updateOverviewImage();
     }
-}
+  }
 
   public void setBoxPosition()
   {
@@ -400,9 +415,13 @@ public class OverviewPanel
     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);
 
@@ -423,7 +442,7 @@ public class OverviewPanel
       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);
+      g.drawImage(offscreen, 0, 0, this);
     }
     else
     {
diff --git a/src/jalview/appletgui/PCAPanel.java b/src/jalview/appletgui/PCAPanel.java
index 845e880..b121828 100755
--- a/src/jalview/appletgui/PCAPanel.java
+++ b/src/jalview/appletgui/PCAPanel.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -27,7 +27,6 @@ import java.awt.event.*;
 import jalview.analysis.*;
 import jalview.datamodel.*;
 
-
 public class PCAPanel
     extends Frame implements Runnable, ActionListener, ItemListener
 {
@@ -35,10 +34,9 @@ public class PCAPanel
   int top;
   RotatableCanvas rc;
   AlignViewport av;
-  SequenceI [] seqs;
+  SequenceI[] seqs;
   AlignmentView seqstrings;
 
-
   public PCAPanel(AlignViewport av)
   {
     try
@@ -58,8 +56,8 @@ public class PCAPanel
     }
 
     this.av = av;
-    seqstrings = av.getAlignmentView(av.getSelectionGroup()!=null);
-    if(av.getSelectionGroup()==null)
+    seqstrings = av.getAlignmentView(av.getSelectionGroup() != null);
+    if (av.getSelectionGroup() == null)
     {
       seqs = av.alignment.getSequencesArray();
     }
@@ -67,7 +65,7 @@ public class PCAPanel
     {
       seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
     }
-    SeqCigar sq[]=seqstrings.getSequences();
+    SeqCigar sq[] = seqstrings.getSequences();
     int length = sq[0].getWidth();
 
     for (int i = 0; i < seqs.length; i++)
@@ -79,13 +77,11 @@ public class PCAPanel
       }
     }
 
-
     rc = new RotatableCanvas(av);
     add(rc, BorderLayout.CENTER);
 
     jalview.bin.JalviewLite.addFrame(this, "Principal component analysis",
-                                       400, 400);
-
+                                     400, 400);
 
     Thread worker = new Thread(this);
     worker.start();
@@ -96,47 +92,47 @@ public class PCAPanel
    */
   public void run()
   {
-              pca = new PCA(seqstrings.getSequenceStrings(' '));
-              pca.run();
-
-              // Now find the component coordinates
-              int ii = 0;
-
-              while ((ii < seqs.length) && (seqs[ii] != null))
-              {
-                  ii++;
-              }
-
-              double[][] comps = new double[ii][ii];
-
-              for (int i = 0; i < ii; i++)
-              {
-                  if (pca.getEigenvalue(i) > 1e-4)
-                  {
-                      comps[i] = pca.component(i);
-                  }
-              }
-
-              //////////////////
-              xCombobox.select(0);
-              yCombobox.select(1);
-              zCombobox.select(2);
-
-              top = pca.getM().rows - 1;
-
-              Vector points = new Vector();
-              float[][] scores = pca.getComponents(top - 1, top - 2, top - 3, 100);
-
-              for (int i = 0; i < pca.getM().rows; i++)
-              {
-                  SequencePoint sp = new SequencePoint(seqs[i], scores[i]);
-                  points.addElement(sp);
-              }
-
-              rc.setPoints(points, pca.getM().rows);
-              rc.repaint();
-              seqs = null;
-              this.repaint();
+    pca = new PCA(seqstrings.getSequenceStrings(' '));
+    pca.run();
+
+    // Now find the component coordinates
+    int ii = 0;
+
+    while ( (ii < seqs.length) && (seqs[ii] != null))
+    {
+      ii++;
+    }
+
+    double[][] comps = new double[ii][ii];
+
+    for (int i = 0; i < ii; i++)
+    {
+      if (pca.getEigenvalue(i) > 1e-4)
+      {
+        comps[i] = pca.component(i);
+      }
+    }
+
+    //////////////////
+    xCombobox.select(0);
+    yCombobox.select(1);
+    zCombobox.select(2);
+
+    top = pca.getM().rows - 1;
+
+    Vector points = new Vector();
+    float[][] scores = pca.getComponents(top - 1, top - 2, top - 3, 100);
+
+    for (int i = 0; i < pca.getM().rows; i++)
+    {
+      SequencePoint sp = new SequencePoint(seqs[i], scores[i]);
+      points.addElement(sp);
+    }
+
+    rc.setPoints(points, pca.getM().rows);
+    rc.repaint();
+    seqs = null;
+    this.repaint();
   }
 
   void doDimensionChange()
@@ -164,23 +160,32 @@ public class PCAPanel
 
   public void actionPerformed(ActionEvent evt)
   {
-    if(evt.getSource()==inputData)
+    if (evt.getSource() == inputData)
+    {
       showOriginalData();
+    }
     else
+    {
       values_actionPerformed();
+    }
   }
 
   public void itemStateChanged(ItemEvent evt)
   {
-    if(evt.getSource()==xCombobox)
+    if (evt.getSource() == xCombobox)
+    {
       xCombobox_actionPerformed();
-    else if(evt.getSource()==yCombobox)
+    }
+    else if (evt.getSource() == yCombobox)
+    {
       yCombobox_actionPerformed();
-    else if(evt.getSource()==zCombobox)
+    }
+    else if (evt.getSource() == zCombobox)
+    {
       zCombobox_actionPerformed();
+    }
   }
 
-
   protected void xCombobox_actionPerformed()
   {
     doDimensionChange();
@@ -204,7 +209,7 @@ public class PCAPanel
     frame.add(cap);
     jalview.bin.JalviewLite.addFrame(frame, "PCA details", 500, 500);
 
-      cap.setText(pca.getDetails());
+    cap.setText(pca.getDetails());
   }
 
   void showOriginalData()
@@ -216,23 +221,23 @@ public class PCAPanel
     Object[] alAndColsel = seqstrings.getAlignmentAndColumnSelection(av.
         getGapCharacter());
 
+    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);
 
-    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);
-
-      af.viewport.setHiddenColumns( (ColumnSelection) alAndColsel[1] );
-     }
+      af.viewport.setHiddenColumns( (ColumnSelection) alAndColsel[1]);
+    }
   }
 
   public void labels_itemStateChanged(ItemEvent itemEvent)
   {
-    rc.showLabels( labels.getState() );
+    rc.showLabels(labels.getState());
   }
+
   Panel jPanel2 = new Panel();
   Label jLabel1 = new Label();
   Label jLabel2 = new Label();
diff --git a/src/jalview/appletgui/PaintRefresher.java b/src/jalview/appletgui/PaintRefresher.java
index 1195210..f7bec98 100755
--- a/src/jalview/appletgui/PaintRefresher.java
+++ b/src/jalview/appletgui/PaintRefresher.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,12 +18,11 @@
  */
 package jalview.appletgui;
 
-import jalview.datamodel.*;
+import java.util.*;
 
 import java.awt.*;
 
-import java.util.*;
-
+import jalview.datamodel.*;
 
 /**
  * DOCUMENT ME!
@@ -33,171 +32,197 @@ import java.util.*;
  */
 public class PaintRefresher
 {
-    static Hashtable components;
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param comp DOCUMENT ME!
-     * @param al DOCUMENT ME!
-     */
-    public static void Register(Component comp, String seqSetId)
+  static Hashtable components;
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param comp DOCUMENT ME!
+   * @param al DOCUMENT ME!
+   */
+  public static void Register(Component comp, String seqSetId)
+  {
+    if (components == null)
     {
-      if (components == null)
-        components = new Hashtable();
+      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);
-        }
+    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)
+  public static void RemoveComponent(Component comp)
+  {
+    if (components == null)
     {
-      if (components == null)
-        return;
+      return;
+    }
 
-      Enumeration en = components.keys();
-      while(en.hasMoreElements())
+    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)
       {
-        String id = en.nextElement().toString();
-        Vector comps = (Vector) components.get(id);
-        comps.removeElement(comp);
-        if(comps.size()==0)
-        {
-          components.remove(id);
-        }
+        components.remove(id);
       }
     }
-
-    public static void Refresh(Component source, String 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)
     {
-      Refresh( source, id, false, false);
+      return;
     }
 
-    public static void Refresh(Component source,
-                               String id,
-                               boolean alignmentChanged,
-                               boolean validateSequences)
+    Component comp;
+    Vector comps = (Vector) components.get(id);
+
+    if (comps == null)
     {
-      if (components == null)
-        return;
+      return;
+    }
 
-      Component comp;
-      Vector comps = (Vector) components.get(id);
+    Enumeration e = comps.elements();
+    while (e.hasMoreElements())
+    {
+      comp = (Component) e.nextElement();
 
-      if(comps==null)
+      if (comp == source)
       {
-        return;
+        continue;
       }
 
-      Enumeration e = comps.elements();
-      while (e.hasMoreElements())
+      if (!comp.isValid())
       {
-        comp = (Component) e.nextElement();
-
-        if(comp==source)
-        {
-          continue;
-        }
+        comps.removeElement(comp);
+      }
+      else if (validateSequences
+               && comp instanceof AlignmentPanel
+               && source instanceof AlignmentPanel)
+      {
+        validateSequences( ( (AlignmentPanel) source).av.alignment,
+                          ( (AlignmentPanel) comp).av.alignment);
+      }
 
-        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();
+      }
 
-        if(comp instanceof AlignmentPanel && alignmentChanged)
-        {
-          ((AlignmentPanel)comp).alignmentChanged();
-        }
+      comp.repaint();
+    }
+  }
 
-        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();
     }
 
-    static void validateSequences(AlignmentI source, AlignmentI comp)
+    SequenceI[] a2;
+    if (comp.getHiddenSequences().getSize() > 0)
     {
-      SequenceI[] a1;
-      if(source.getHiddenSequences().getSize()>0)
-        a1 = source.getHiddenSequences().getFullAlignment().getSequencesArray();
-      else
-        a1 = source.getSequencesArray();
+      a2 = comp.getHiddenSequences().getFullAlignment().getSequencesArray();
+    }
+    else
+    {
+      a2 = comp.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;
 
-      int i, iSize=a1.length, j, jSize=a2.length;
+    if (iSize == jSize)
+    {
+      return;
+    }
 
-      if(iSize == jSize)
-        return;
+    boolean exists = false;
+    for (i = 0; i < iSize; i++)
+    {
+      exists = false;
 
-      boolean exists = false;
-      for(i=0; i<iSize; i++)
+      for (j = 0; j < jSize; j++)
       {
-        exists = false;
-
-        for(j=0; j<jSize; j++)
-          if (a2[j]==a1[i] )
-          {
-            exists = true;
-            break;
-          }
+        if (a2[j] == a1[i])
+        {
+          exists = true;
+          break;
+        }
+      }
 
-        if(!exists)
+      if (!exists)
+      {
+        if (i < jSize)
         {
-          if (i < jSize)
-            comp.getSequences().insertElementAt(a1[i], i);
-          else
-            comp.addSequence(a1[i]);
+          comp.getSequences().insertElementAt(a1[i], i);
+        }
+        else
+        {
+          comp.addSequence(a1[i]);
+        }
 
-          jSize++;
+        jSize++;
 
-          if (comp.getHiddenSequences().getSize() > 0)
-            a2 = comp.getHiddenSequences().getFullAlignment().getSequencesArray();
-          else
-            a2 = comp.getSequencesArray();
+        if (comp.getHiddenSequences().getSize() > 0)
+        {
+          a2 = comp.getHiddenSequences().getFullAlignment().getSequencesArray();
+        }
+        else
+        {
+          a2 = comp.getSequencesArray();
         }
       }
+    }
 
-      iSize=a1.length;
-      jSize=a2.length;
+    iSize = a1.length;
+    jSize = a2.length;
 
-      for(j=0; j<jSize; j++)
+    for (j = 0; j < jSize; j++)
+    {
+      exists = false;
+      for (i = 0; i < iSize; i++)
       {
-        exists = false;
-        for(i=0; i<iSize; i++)
+        if (a2[j] == a1[i])
         {
-          if (a2[j]==a1[i])
-          {
-            exists = true;
-            break;
-          }
+          exists = true;
+          break;
         }
+      }
 
-        if(!exists)
-        {
-          comp.deleteSequence(a2[j]);
-        }
+      if (!exists)
+      {
+        comp.deleteSequence(a2[j]);
       }
     }
+  }
 }
diff --git a/src/jalview/appletgui/PairwiseAlignPanel.java b/src/jalview/appletgui/PairwiseAlignPanel.java
index 480f719..05372a4 100755
--- a/src/jalview/appletgui/PairwiseAlignPanel.java
+++ b/src/jalview/appletgui/PairwiseAlignPanel.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -21,11 +21,11 @@ package jalview.appletgui;
 
 import java.util.*;
 
+import java.awt.*;
 import java.awt.event.*;
 
 import jalview.analysis.*;
 import jalview.datamodel.*;
-import java.awt.*;
 
 public class PairwiseAlignPanel
     extends Panel implements ActionListener
@@ -61,7 +61,8 @@ 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++)
@@ -126,10 +127,13 @@ public class PairwiseAlignPanel
       System.out.println("\n");
     }
   }
+
   public void actionPerformed(ActionEvent evt)
   {
-    if(evt.getSource()==viewInEditorButton)
+    if (evt.getSource() == viewInEditorButton)
+    {
       viewInEditorButton_actionPerformed();
+    }
   }
 
   protected void viewInEditorButton_actionPerformed()
@@ -143,28 +147,31 @@ public class PairwiseAlignPanel
     }
 
     new AlignFrame(new Alignment(seq),
-                                   ap.av.applet,
-                                   "Pairwise Aligned Sequences",
-                                   false);
+                   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 {
-      this.setLayout(borderLayout1);
-      textarea.setFont(new java.awt.Font("Monospaced", 0, 12));
-      textarea.setText("");
-      viewInEditorButton.setFont(new java.awt.Font("Verdana", 0, 12));
-      viewInEditorButton.setLabel("View in alignment editor");
-      viewInEditorButton.addActionListener(this);
-      this.add(scrollPane, BorderLayout.CENTER);
-      scrollPane.add(textarea);
-      this.add(jPanel1, BorderLayout.SOUTH);
-      jPanel1.add(viewInEditorButton, null);
+  private void jbInit()
+      throws Exception
+  {
+    this.setLayout(borderLayout1);
+    textarea.setFont(new java.awt.Font("Monospaced", 0, 12));
+    textarea.setText("");
+    viewInEditorButton.setFont(new java.awt.Font("Verdana", 0, 12));
+    viewInEditorButton.setLabel("View in alignment editor");
+    viewInEditorButton.addActionListener(this);
+    this.add(scrollPane, BorderLayout.CENTER);
+    scrollPane.add(textarea);
+    this.add(jPanel1, BorderLayout.SOUTH);
+    jPanel1.add(viewInEditorButton, null);
   }
 
 }
diff --git a/src/jalview/appletgui/RedundancyPanel.java b/src/jalview/appletgui/RedundancyPanel.java
index 2e8811a..d2d4384 100755
--- a/src/jalview/appletgui/RedundancyPanel.java
+++ b/src/jalview/appletgui/RedundancyPanel.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -21,21 +21,20 @@ package jalview.appletgui;
 
 import java.util.*;
 
-import java.awt.event.*;
-
 import java.awt.*;
+import java.awt.event.*;
 
-import jalview.datamodel.*;
-import jalview.appletgui.PaintRefresher;
 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;
+  float[] redundancy;
+  SequenceI[] originalSequences;
   Frame frame;
   Vector redundantSeqs;
 
@@ -54,7 +53,7 @@ public class RedundancyPanel extends SliderPanel implements Runnable, WindowList
 
     slider.setVisibleAmount(1);
     slider.setMinimum(0);
-    slider.setMaximum(100+slider.getVisibleAmount());
+    slider.setMaximum(100 + slider.getVisibleAmount());
     slider.setValue(100);
 
     slider.addAdjustmentListener(new AdjustmentListener()
@@ -76,6 +75,7 @@ public class RedundancyPanel extends SliderPanel implements Runnable, WindowList
     Thread worker = new Thread(this);
     worker.start();
   }
+
   /**
    * This is a copy of remove redundancy in jalivew.datamodel.Alignment
    * except we dont want to remove redundancy, just calculate once
@@ -88,103 +88,113 @@ public class RedundancyPanel extends SliderPanel implements Runnable, WindowList
    */
   public void run()
   {
-      label.setText("Calculating....");
+    label.setText("Calculating....");
 
-      slider.setVisible(false);
-      applyButton.setEnabled(false);
-      valueField.setVisible(false);
+    slider.setVisible(false);
+    applyButton.setEnabled(false);
+    valueField.setVisible(false);
 
-      validate();
+    validate();
 
-      String[] omitHidden = null;
+    String[] omitHidden = null;
 
-      SequenceGroup sg = ap.av.getSelectionGroup();
-      int height;
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    int height;
 
-      int start, end;
+    int start, end;
 
-      if ( (sg != null) && (sg.getSize() >= 1))
-      {
-         originalSequences = sg.getSequencesInOrder(ap.av.alignment);
-         start = sg.getStartRes();
-         end = sg.getEndRes();
-      }
-      else
-      {
-        originalSequences = ap.av.alignment.getSequencesArray();
-        start = 0;
-        end = ap.av.alignment.getWidth();
-      }
+    if ( (sg != null) && (sg.getSize() >= 1))
+    {
+      originalSequences = sg.getSequencesInOrder(ap.av.alignment);
+      start = sg.getStartRes();
+      end = sg.getEndRes();
+    }
+    else
+    {
+      originalSequences = ap.av.alignment.getSequencesArray();
+      start = 0;
+      end = ap.av.alignment.getWidth();
+    }
 
-      height = originalSequences.length;
+    height = originalSequences.length;
 
-      redundancy = new float[height];
-      for (int i = 0; i < height; i++)
-      {
-        redundancy[i] = 0f;
-      }
+    redundancy = new float[height];
+    for (int i = 0; i < height; i++)
+    {
+      redundancy[i] = 0f;
+    }
 
     //  if (ap.av.hasHiddenColumns)
+    {
+      //   omitHidden = ap.av.getSelectionAsString();
+    }
+
+    // long start = System.currentTimeMillis();
+
+    float pid;
+    String seqi, seqj;
+    for (int i = 0; i < height; i++)
+    {
+      for (int j = 0; j < i; j++)
       {
-     //   omitHidden = ap.av.getSelectionAsString();
-      }
+        if (i == j)
+        {
+          continue;
+        }
 
+        if (omitHidden == null)
+        {
+          seqi = originalSequences[i].getSequenceAsString(start, end);
+          seqj = originalSequences[j].getSequenceAsString(start, end);
+        }
+        else
+        {
+          seqi = omitHidden[i];
+          seqj = omitHidden[j];
+        }
 
-     // long start = System.currentTimeMillis();
+        pid = jalview.util.Comparison.PID(seqi, seqj);
 
-      float pid;
-      String seqi, seqj;
-      for (int i = 0; i < height; i++)
-      {
-          for (int j = 0; j < i; j++)
-          {
-            if(i==j)
-              continue;
-
-            if(omitHidden==null)
-            {
-              seqi = originalSequences[i].getSequenceAsString(start, end);
-              seqj = originalSequences[j].getSequenceAsString(start, end);
-            }
-            else
-            {
-              seqi = omitHidden[i];
-              seqj = omitHidden[j];
-            }
-
-            pid = jalview.util.Comparison.PID( seqi,  seqj );
-
-            if(seqj.length() < seqi.length())
-              redundancy[j] = Math.max(pid, redundancy[j]);
-            else
-              redundancy[i] = Math.max(pid, redundancy[i]);
-
-          }
-      }
+        if (seqj.length() < seqi.length())
+        {
+          redundancy[j] = Math.max(pid, redundancy[j]);
+        }
+        else
+        {
+          redundancy[i] = Math.max(pid, redundancy[i]);
+        }
 
+      }
+    }
 
-      label.setText("Enter the redundancy threshold");
-      slider.setVisible(true);
-      applyButton.setEnabled(true);
-      valueField.setVisible(true);
+    label.setText("Enter the redundancy threshold");
+    slider.setVisible(true);
+    applyButton.setEnabled(true);
+    valueField.setVisible(true);
 
-      validate();
-     // System.out.println("blob done "+ (System.currentTimeMillis()-start));
+    validate();
+    // System.out.println("blob done "+ (System.currentTimeMillis()-start));
   }
 
   void sliderValueChanged()
   {
-    if(redundancy==null)
+    if (redundancy == null)
+    {
       return;
+    }
 
     float value = slider.getValue();
 
-    for(int i=0; i<redundancy.length; i++)
+    for (int i = 0; i < redundancy.length; i++)
     {
       if (value > redundancy[i])
-         redundantSeqs.removeElement(originalSequences[i]);
-      else if(!redundantSeqs.contains(originalSequences[i]))
-         redundantSeqs.addElement(originalSequences[i]);
+      {
+        redundantSeqs.removeElement(originalSequences[i]);
+      }
+      else if (!redundantSeqs.contains(originalSequences[i]))
+      {
+        redundantSeqs.addElement(originalSequences[i]);
+      }
     }
 
     ap.idPanel.idCanvas.setHighlighted(redundantSeqs);
@@ -193,59 +203,65 @@ public class RedundancyPanel extends SliderPanel implements Runnable, WindowList
                            true,
                            true);
 
-    }
+  }
+
   public void applyButton_actionPerformed()
-  {        Vector del = new Vector();
+  {
+    Vector del = new Vector();
+
+    undoButton.setEnabled(true);
 
-        undoButton.setEnabled(true);
+    float value = slider.getValue();
+    SequenceGroup sg = ap.av.getSelectionGroup();
+
+    for (int i = 0; i < redundancy.length; i++)
+    {
+      if (value <= redundancy[i])
+      {
+        del.addElement(originalSequences[i]);
+      }
+    }
 
-        float value = slider.getValue();
-        SequenceGroup sg = ap.av.getSelectionGroup();
+    // This has to be done before the restoreHistoryItem method of alignFrame will
+    // actually restore these sequences.
+    if (del.size() > 0)
+    {
+      SequenceI[] deleted = new SequenceI[del.size()];
 
-        for (int i = 0; i < redundancy.length; i++)
+      int width = 0;
+      for (int i = 0; i < del.size(); i++)
+      {
+        deleted[i] = (SequenceI) del.elementAt(i);
+        if (deleted[i].getLength() > width)
         {
-          if (value <= redundancy[i])
-          {
-            del.addElement(originalSequences[i]);
-          }
+          width = deleted[i].getLength();
         }
+      }
 
-        // This has to be done before the restoreHistoryItem method of alignFrame will
-        // actually restore these sequences.
-        if (del.size() > 0)
+      EditCommand cut = new EditCommand("Remove Redundancy",
+                                        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);
+        if (sg != null)
         {
-          SequenceI [] deleted = new SequenceI[del.size()];
-
-          int width = 0;
-          for (int i = 0; i < del.size(); i++)
-          {
-            deleted[i] = (SequenceI)del.elementAt(i);
-            if(deleted[i].getLength()>width)
-              width = deleted[i].getLength();
-          }
-
-          EditCommand cut = new EditCommand("Remove Redundancy",
-              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);
-            if (sg != null)
-            {
-              sg.deleteSequence(deleted[i], false);
-            }
-          }
-
-          historyList.push(cut);
-
-          ap.alignFrame.addHistoryItem(cut);
-
-          ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences());
+          sg.deleteSequence(deleted[i], false);
         }
+      }
+
+      historyList.push(cut);
+
+      ap.alignFrame.addHistoryItem(cut);
+
+      ap.av.firePropertyChange("alignment", null,
+                               ap.av.getAlignment().getSequences());
+    }
 
   }
 
@@ -265,7 +281,7 @@ public class RedundancyPanel extends SliderPanel implements Runnable, WindowList
     if (historyList.size() == 0)
     {
       undoButton.setEnabled(false);
-      }
+    }
   }
 
   public void valueField_actionPerformed(ActionEvent e)
@@ -281,7 +297,6 @@ public class RedundancyPanel extends SliderPanel implements Runnable, WindowList
     }
   }
 
-
   public void windowOpened(WindowEvent evt)
   {}
 
@@ -295,10 +310,13 @@ public class RedundancyPanel extends SliderPanel implements Runnable, WindowList
 
   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 36e0859..a2463e8 100755
--- a/src/jalview/appletgui/RotatableCanvas.java
+++ b/src/jalview/appletgui/RotatableCanvas.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -297,6 +297,7 @@ public class RotatableCanvas
   {
     paint(g);
   }
+
   public void paint(Graphics g)
   {
     if (points == null)
@@ -329,7 +330,7 @@ public class RotatableCanvas
         drawAxes(ig);
       }
 
-      if(tooltip!=null)
+      if (tooltip != null)
       {
         ig.setColor(Color.red);
         ig.drawString(tooltip, toolx, tooly);
@@ -382,7 +383,8 @@ public class RotatableCanvas
 
       if (av.getSelectionGroup() != null)
       {
-        if (av.getSelectionGroup().getSequences(null).contains( ( (SequencePoint) points.
+        if (av.getSelectionGroup().getSequences(null).contains( ( (
+            SequencePoint) points.
             elementAt(i)).sequence))
         {
           g.setColor(Color.gray);
@@ -497,33 +499,34 @@ public class RotatableCanvas
       if (av.getSelectionGroup() != null)
       {
         av.getSelectionGroup().addOrRemove(found, true);
-        av.getSelectionGroup().setEndRes(av.alignment.getWidth()-1);
+        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);
+        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();
+    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)
@@ -531,35 +534,35 @@ public class RotatableCanvas
     mx = evt.getX();
     my = evt.getY();
 
-      rotmat.setIdentity();
+    rotmat.setIdentity();
 
-      rotmat.rotate( (float) (my - omy), 'x');
-      rotmat.rotate( (float) (mx - omx), 'y');
+    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 < npoint; i++)
+    {
+      SequencePoint sp = (SequencePoint) points.elementAt(i);
+      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;
+      //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());
+    paint(this.getGraphics());
   }
 
   public void rectSelect(int x1, int y1, int x2, int y2)
diff --git a/src/jalview/appletgui/ScalePanel.java b/src/jalview/appletgui/ScalePanel.java
index 9cde175..07e83e7 100755
--- a/src/jalview/appletgui/ScalePanel.java
+++ b/src/jalview/appletgui/ScalePanel.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -38,7 +38,7 @@ public class ScalePanel
   int min; //used by mouseDragged to see if user
   int max; //used by mouseDragged to see if user
   boolean mouseDragging = false;
-  int [] reveal;
+  int[] reveal;
 
   public ScalePanel(AlignViewport av, AlignmentPanel ap)
   {
@@ -57,13 +57,17 @@ public class ScalePanel
     final int res;
 
     if (av.hasHiddenColumns)
+    {
       res = av.getColumnSelection().adjustForHiddenColumns(x);
+    }
     else
+    {
       res = x;
+    }
 
     min = res;
     max = res;
-    if ((evt.getModifiers() & InputEvent.BUTTON3_MASK)
+    if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK)
         == InputEvent.BUTTON3_MASK)
     {
       PopupMenu pop = new PopupMenu();
@@ -78,7 +82,9 @@ public class ScalePanel
             reveal = null;
             ap.repaint();
             if (ap.overviewPanel != null)
+            {
               ap.overviewPanel.updateOverviewImage();
+            }
           }
         });
         pop.add(item);
@@ -94,7 +100,9 @@ public class ScalePanel
               reveal = null;
               ap.repaint();
               if (ap.overviewPanel != null)
+              {
                 ap.overviewPanel.updateOverviewImage();
+              }
             }
           });
           pop.add(item);
@@ -113,11 +121,15 @@ public class ScalePanel
             if (av.getSelectionGroup() != null
                 &&
                 av.getSelectionGroup().getSize() == av.alignment.getHeight())
+            {
               av.setSelectionGroup(null);
+            }
 
             ap.repaint();
             if (ap.overviewPanel != null)
+            {
               ap.overviewPanel.updateOverviewImage();
+            }
           }
         });
         pop.add(item);
@@ -143,13 +155,13 @@ public class ScalePanel
       sg.setEndRes(res);
       av.setSelectionGroup(sg);
 
-      if(evt.isShiftDown())
+      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++)
+        for (int i = min; i < max; i++)
         {
-            av.getColumnSelection().addElement(i);
+          av.getColumnSelection().addElement(i);
         }
         sg.setStartRes(min);
         sg.setEndRes(max);
@@ -165,30 +177,32 @@ public class ScalePanel
 
     int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
 
-    if(res> av.alignment.getWidth())
+    if (res > av.alignment.getWidth())
     {
-      res = av.alignment.getWidth()-1;
+      res = av.alignment.getWidth() - 1;
     }
 
-    if(av.hasHiddenColumns)
+    if (av.hasHiddenColumns)
+    {
       res = av.getColumnSelection().adjustForHiddenColumns(res);
+    }
 
     if (!stretchingGroup)
     {
-        ap.repaint();
+      ap.repaint();
 
-        return;
+      return;
     }
 
     SequenceGroup sg = av.getSelectionGroup();
 
     if (res > sg.getStartRes())
     {
-        sg.setEndRes(res);
+      sg.setEndRes(res);
     }
     else if (res < sg.getStartRes())
     {
-        sg.setStartRes(res);
+      sg.setStartRes(res);
     }
 
     stretchingGroup = false;
@@ -201,10 +215,14 @@ public class ScalePanel
 
     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())
     {
@@ -257,17 +275,20 @@ public class ScalePanel
     }
   }
 
-
   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)
@@ -278,7 +299,9 @@ public class ScalePanel
   public void mouseMoved(MouseEvent evt)
   {
     if (!av.hasHiddenColumns)
+    {
       return;
+    }
 
     int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
 
@@ -316,7 +339,6 @@ public class ScalePanel
   {
     gg.setFont(av.getFont());
 
-
     //Fill in the background
     gg.setColor(Color.white);
     gg.fillRect(0, 0, width, height);
@@ -328,16 +350,17 @@ public class ScalePanel
 
     for (int i = 0; i < cs.size(); i++)
     {
-        int sel = cs.columnAt(i);
-        if(av.hasHiddenColumns)
-          sel = av.getColumnSelection().findColumnPosition(sel);
-
+      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);
-        }
+      if ( (sel >= startx) && (sel <= endx))
+      {
+        gg.fillRect( (sel - startx) * av.charWidth, 0, av.charWidth,
+                    getSize().height);
+      }
     }
 
     // Draw the scale numbers
@@ -348,47 +371,48 @@ 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;
+      scalestartx += 5;
     }
 
     String string;
-    int maxX=0;
+    int maxX = 0;
 
     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);
-              maxX = (i - startx + 1) * av.charWidth + fm.stringWidth(string);
-            }
+          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));
-        }
+      }
+      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())
+      if (av.getShowHiddenMarkers())
       {
         for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size();
              i++)
@@ -397,8 +421,10 @@ public class ScalePanel
           res = av.getColumnSelection().findHiddenRegionPosition(i) -
               startx;
 
-          if(res < 0 || res > endx-scalestartx)
+          if (res < 0 || res > endx - scalestartx)
+          {
             continue;
+          }
 
           gg.fillPolygon(new int[]
                          {res * av.charWidth - av.charHeight / 4,
diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index f36cc6a..b9d3dfe 100755
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -39,11 +39,9 @@ public class SeqCanvas
 
   boolean fastPaint = false;
 
-
   int cursorX = 0;
   int cursorY = 0;
 
-
   public SeqCanvas(AlignViewport av)
   {
     this.av = av;
@@ -73,7 +71,6 @@ public class SeqCanvas
     pdbCanvas = pc;
   }
 
-
   void drawNorthScale(Graphics g, int startx, int endx, int ypos)
   {
     int scalestartx = startx - startx % 10 + 10;
@@ -84,16 +81,18 @@ public class SeqCanvas
     for (int i = scalestartx; i < endx; i += 10)
     {
       int value = i;
-      if(av.hasHiddenColumns)
-          value = av.getColumnSelection().adjustForHiddenColumns(value);
+      if (av.hasHiddenColumns)
+      {
+        value = av.getColumnSelection().adjustForHiddenColumns(value);
+      }
 
-      g.drawString( String.valueOf(value), (i - startx - 1) * av.charWidth,
-          ypos - (av.charHeight / 2));
+      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);
+      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);
     }
   }
 
@@ -109,88 +108,92 @@ public class SeqCanvas
 
     int maxwidth = av.alignment.getWidth();
     if (av.hasHiddenColumns)
-        maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+    {
+      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;
+    // 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)
+      while (index < endx)
+      {
+        if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
         {
-          if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
-          {
-            index++;
+          index++;
 
-            continue;
-          }
+          continue;
+        }
 
-          value = av.alignment.getSequenceAt(i).findPosition(index);
+        value = av.alignment.getSequenceAt(i).findPosition(index);
 
-          break;
-        }
+        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));
-        }
+      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;
+    ypos += av.charHeight;
+
+    if (av.hasHiddenColumns)
+    {
+      endx = av.getColumnSelection().adjustForHiddenColumns(endx);
+    }
 
-        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;
 
-        SequenceI seq;
-        // EAST SCALE
-        for (int i = 0; i < av.alignment.getHeight(); i++)
+      while (index > startx)
+      {
+        if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
         {
-            seq = av.alignment.getSequenceAt(i);
-            int index = endx;
-            int value = -1;
+          index--;
 
-            while (index > startx)
-            {
-                if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
-                {
-                    index--;
-
-                    continue;
-                }
+          continue;
+        }
 
-                value = seq.findPosition(index);
+        value = seq.findPosition(index);
 
-                break;
-            }
+        break;
+      }
 
-            if (value != -1)
-            {
-                g.drawString(String.valueOf(value), 0,
-                    (ypos + (i * av.charHeight)) - (av.charHeight / 5));
-            }
-        }
+      if (value != -1)
+      {
+        g.drawString(String.valueOf(value), 0,
+                     (ypos + (i * av.charHeight)) - (av.charHeight / 5));
+      }
     }
+  }
 
-  int lastsr=0;
+  int lastsr = 0;
   void fastPaint(int horizontal, int vertical)
   {
-    if ( fastPaint || gg == null)
+    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)
+    if (lastsr + horizontal != av.startRes)
     {
       horizontal = av.startRes - lastsr;
     }
@@ -205,8 +208,6 @@ public class SeqCanvas
                 -horizontal * av.charWidth,
                 -vertical * av.charHeight);
 
-
-
     int sr = av.startRes, er = av.endRes, ss = av.startSeq, es = av.endSeq,
         transX = 0, transY = 0;
 
@@ -307,7 +308,6 @@ public class SeqCanvas
     gg.setColor(Color.white);
     gg.fillRect(0, 0, imgWidth, imgHeight);
 
-
     if (av.getWrapAlignment())
     {
       drawWrappedPanel(gg, imgWidth, imgHeight, av.startRes);
@@ -328,27 +328,26 @@ public class SeqCanvas
   int LABEL_WEST, LABEL_EAST;
   public int getWrappedCanvasWidth(int cwidth)
   {
-      cwidth -= cwidth % av.charWidth;
+    cwidth -= cwidth % av.charWidth;
 
-      FontMetrics fm = getFontMetrics(av.getFont());
+    FontMetrics fm = getFontMetrics(av.getFont());
 
-      LABEL_EAST = 0;
-      LABEL_WEST = 0;
+    LABEL_EAST = 0;
+    LABEL_WEST = 0;
 
-      if (av.scaleRightWrapped)
-      {
-          LABEL_EAST = fm.stringWidth(getMask());
-      }
+    if (av.scaleRightWrapped)
+    {
+      LABEL_EAST = fm.stringWidth(getMask());
+    }
 
-      if (av.scaleLeftWrapped)
-      {
-          LABEL_WEST = fm.stringWidth(getMask());
-      }
+    if (av.scaleLeftWrapped)
+    {
+      LABEL_WEST = fm.stringWidth(getMask());
+    }
 
-      return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
+    return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
   }
 
-
   /**
    * Generates a string of zeroes.
    * @return String
@@ -362,7 +361,9 @@ public class SeqCanvas
     {
       tmp = av.alignment.getSequenceAt(i).getEnd();
       if (tmp > maxWidth)
+      {
         maxWidth = tmp;
+      }
     }
 
     for (int i = maxWidth; i > 0; i /= 10)
@@ -379,20 +380,21 @@ public class SeqCanvas
 
     FontMetrics fm = getFontMetrics(av.getFont());
 
-
     if (av.scaleRightWrapped)
     {
-        LABEL_EAST = fm.stringWidth(getMask());
+      LABEL_EAST = fm.stringWidth(getMask());
     }
 
     if (av.scaleLeftWrapped)
     {
-        LABEL_WEST = fm.stringWidth(getMask());
+      LABEL_WEST = fm.stringWidth(getMask());
     }
 
     int hgap = av.charHeight;
-    if(av.scaleAboveWrapped)
+    if (av.scaleAboveWrapped)
+    {
       hgap += av.charHeight;
+    }
 
     int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
     int cHeight = av.getAlignment().getHeight() * av.charHeight;
@@ -401,396 +403,427 @@ public class SeqCanvas
 
     av.endRes = av.startRes + cWidth;
 
-
     int endx;
     int ypos = hgap;
 
-    int maxwidth = av.alignment.getWidth()-1;
+    int maxwidth = av.alignment.getWidth() - 1;
 
-    if(av.hasHiddenColumns)
-          maxwidth = av.getColumnSelection().findColumnPosition(maxwidth)-1;
+    if (av.hasHiddenColumns)
+    {
+      maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+    }
 
-    while ((ypos <= canvasHeight) && (startRes < maxwidth))
+    while ( (ypos <= canvasHeight) && (startRes < maxwidth))
     {
-      endx = startRes + cWidth -1;
+      endx = startRes + cWidth - 1;
 
       if (endx > maxwidth)
       {
         endx = maxwidth;
       }
 
-        g.setColor(Color.black);
+      g.setColor(Color.black);
 
-        if (av.scaleLeftWrapped)
-        {
-            drawWestScale(g, startRes, endx, ypos);
-        }
+      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);
-        }
+      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);
+      g.translate(LABEL_WEST, 0);
 
-        if (av.scaleAboveWrapped)
-        {
-          drawNorthScale(g, startRes, endx, ypos);
-        }
-        if (av.hasHiddenColumns && av.showHiddenMarkers)
+      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++)
         {
-          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);
+          res = av.getColumnSelection().findHiddenRegionPosition(i) -
+              startRes;
 
+          if (res < 0 || res > endx - startRes)
+          {
+            continue;
           }
-        }
 
-        if(g.getClip()==null)
-          g.setClip(0, 0, cWidth * av.charWidth, canvasHeight);
+          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);
 
-        drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);
-         g.setClip(null);
+        }
+      }
 
+      if (g.getClip() == null)
+      {
+        g.setClip(0, 0, cWidth * av.charWidth, canvasHeight);
+      }
 
-        if(av.showAnnotation)
-        {
-          g.translate(0, cHeight + ypos+4);
-          if(annotations==null)
-            annotations = new AnnotationPanel(av);
+      drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);
+      g.setClip(null);
 
-          annotations.drawComponent( g, startRes, endx+1 );
-          g.translate(0, -cHeight - ypos-4);
+      if (av.showAnnotation)
+      {
+        g.translate(0, cHeight + ypos + 4);
+        if (annotations == null)
+        {
+          annotations = new AnnotationPanel(av);
         }
-        g.translate(-LABEL_WEST, 0);
 
-        ypos += cHeight+getAnnotationHeight()+hgap;
+        annotations.drawComponent(g, startRes, endx + 1);
+        g.translate(0, -cHeight - ypos - 4);
+      }
+      g.translate( -LABEL_WEST, 0);
 
+      ypos += cHeight + getAnnotationHeight() + hgap;
 
-        startRes += cWidth;
-        }
+      startRes += cWidth;
+    }
 
   }
 
   AnnotationPanel annotations;
   int getAnnotationHeight()
   {
-    if(!av.showAnnotation)
+    if (!av.showAnnotation)
+    {
       return 0;
+    }
 
-    if(annotations==null)
+    if (annotations == null)
+    {
       annotations = new AnnotationPanel(av);
+    }
 
     return annotations.adjustPanelHeight();
-    }
+  }
 
-    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)
     {
-      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++)
       {
-        draw(g1, startRes, endRes, startSeq, endSeq, offset);
+        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;
       }
-      else
+
+      if (screenY <= (endRes - startRes))
       {
-        java.util.Vector regions = av.getColumnSelection().getHiddenColumns();
+        blockEnd = blockStart + (endRes - startRes) - screenY;
+        g1.translate(screenY * av.charWidth, 0);
+        draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
 
-        int screenY = 0;
-        int blockStart = startRes;
-        int blockEnd = endRes;
+        g1.translate( -screenY * av.charWidth, 0);
+      }
+    }
 
-        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;
-          }
+  //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);
 
-          blockEnd = hideStart - 1;
+    SequenceI nextSeq;
 
-          g1.translate(screenY * av.charWidth, 0);
+    /// First draw the sequences
+    /////////////////////////////
+    for (int i = startSeq; i < endSeq; i++)
+    {
+      nextSeq = av.alignment.getSequenceAt(i);
 
-          draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
+      if (nextSeq == null)
+      {
+        continue;
+      }
 
-          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);
-          }
+      sr.drawSequence(nextSeq, av.alignment.findAllGroups(nextSeq),
+                      startRes, endRes,
+                      offset + ( (i - startSeq) * av.charHeight));
 
-          g1.translate( -screenY * av.charWidth, 0);
-          screenY += blockEnd - blockStart + 1;
-          blockStart = hideEnd + 1;
-        }
+      if (av.showSequenceFeatures)
+      {
+        fr.drawSequence(g, nextSeq, startRes, endRes,
+                        offset + ( (i - startSeq) * av.charHeight));
+      }
 
-        if (screenY <= (endRes - startRes))
+      /// Highlight search Results once all sequences have been drawn
+      //////////////////////////////////////////////////////////
+      if (searchResults != null)
+      {
+        int[] visibleResults = searchResults.getResults(nextSeq, startRes,
+            endRes);
+        if (visibleResults != null)
         {
-          blockEnd = blockStart + (endRes - startRes) - screenY;
-          g1.translate(screenY * av.charWidth, 0);
-          draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
-
-          g1.translate( -screenY * av.charWidth, 0);
+          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;
+    }
 
-    //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++)
+    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++)
         {
-            nextSeq = av.alignment.getSequenceAt(i);
-
-            if(nextSeq==null)
-              continue;
+          sx = (group.getStartRes() - startRes) * av.charWidth;
+          sy = offset + ( (i - startSeq) * av.charHeight);
+          ex = ( ( (group.getEndRes() + 1) - group.getStartRes()) *
+                av.charWidth) -
+              1;
 
-            sr.drawSequence(nextSeq, av.alignment.findAllGroups(nextSeq),
-                            startRes, endRes,
-                            offset + ( (i - startSeq) * av.charHeight));
+          if (sx + ex < 0 || sx > imgWidth)
+          {
+            continue;
+          }
 
-            if (av.showSequenceFeatures)
+          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))))
             {
-                fr.drawSequence(g, nextSeq, startRes, endRes,
-                    offset + ((i - startSeq) * av.charHeight));
+              bottom = sy + av.charHeight;
             }
 
-            /// Highlight search Results once all sequences have been drawn
-            //////////////////////////////////////////////////////////
-            if (searchResults != null)
+            if (!inGroup)
             {
-              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 ( ( (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());
+              }
             }
-
-            if(av.cursorMode && cursorY==i
-               && cursorX>=startRes && cursorX<=endRes)
+          }
+          else
+          {
+            if (inGroup)
             {
-              sr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * av.charWidth,
-                            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, sx + ex, bottom);
+                bottom = -1;
+              }
+
+              inGroup = false;
             }
           }
+        }
 
-          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());
-
-     }
-   }
+        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)
   {
diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 6c1a619..b954608 100755
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -19,14 +19,14 @@
 
 package jalview.appletgui;
 
+import java.util.*;
+
 import java.awt.*;
 import java.awt.event.*;
 
+import jalview.commands.*;
 import jalview.datamodel.*;
 import jalview.schemes.*;
-import jalview.commands.*;
-
-import java.util.Vector;
 
 public class SeqPanel
     extends Panel implements MouseMotionListener, MouseListener
@@ -81,7 +81,7 @@ public class SeqPanel
 
   void endEditing()
   {
-    if (editCommand!=null && editCommand.getSize() > 0)
+    if (editCommand != null && editCommand.getSize() > 0)
     {
       ap.alignFrame.addHistoryItem(editCommand);
       av.firePropertyChange("alignment", null,
@@ -94,308 +94,341 @@ public class SeqPanel
     groupEditing = false;
     keyboardNo1 = null;
     keyboardNo2 = null;
-     editCommand = null;
-   }
-
-   void setCursorRow()
-   {
-     seqCanvas.cursorY = getKeyboardNo(keyboardNo1)-1;
-     scrollToVisible();
-   }
-
-   void setCursorColumn()
-   {
-     seqCanvas.cursorX = getKeyboardNo(keyboardNo1)-1;
-     scrollToVisible();
-   }
-
-   void setCursorRowAndColumn()
-   {
-     if(keyboardNo2==null)
-     {
-       keyboardNo2 = new StringBuffer();
-     }
-     else
-     {
-       seqCanvas.cursorX = getKeyboardNo(keyboardNo1) - 1;
-       seqCanvas.cursorY = getKeyboardNo(keyboardNo2) - 1;
-       scrollToVisible();
-     }
-   }
-
-   void setCursorPosition()
-   {
-     SequenceI sequence =
-         (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
-
-     seqCanvas.cursorX = sequence.findIndex(
-         getKeyboardNo(keyboardNo1)-1
-         );
-     scrollToVisible();
-   }
-
-   void moveCursor(int dx, int dy)
-   {
-     seqCanvas.cursorX += dx;
-     seqCanvas.cursorY += dy;
-     if (av.hasHiddenColumns && !av.colSel.isVisible(seqCanvas.cursorX))
-     {
-       int original = seqCanvas.cursorX - dx;
-       int maxWidth = av.alignment.getWidth();
-
-       while(!av.colSel.isVisible(seqCanvas.cursorX)
-             && seqCanvas.cursorX<maxWidth
-             && seqCanvas.cursorX>0)
-       {
-         seqCanvas.cursorX += dx;
-       }
-
-       if(seqCanvas.cursorX>=maxWidth
-          || !av.colSel.isVisible(seqCanvas.cursorX) )
-       {
-         seqCanvas.cursorX = original;
-       }
-      }
-     scrollToVisible();
-   }
-
-   void scrollToVisible()
-   {
-     if (seqCanvas.cursorX < 0)
-       seqCanvas.cursorX = 0;
-     else if (seqCanvas.cursorX > av.alignment.getWidth() - 1)
-       seqCanvas.cursorX = av.alignment.getWidth() - 1;
-
-     if (seqCanvas.cursorY < 0)
-       seqCanvas.cursorY = 0;
-     else if (seqCanvas.cursorY > av.alignment.getHeight() - 1)
-       seqCanvas.cursorY = av.alignment.getHeight() - 1;
-
-
-     endEditing();
-     if (av.wrapAlignment)
-     {
-       ap.scrollToWrappedVisible(seqCanvas.cursorX);
-     }
-     else
-     {
-       while (seqCanvas.cursorY < av.startSeq)
-       {
-         ap.scrollUp(true);
-       }
-       while (seqCanvas.cursorY + 1 > av.endSeq)
-       {
-         ap.scrollUp(false);
-       }
-       while (seqCanvas.cursorX < av.colSel.adjustForHiddenColumns(av.startRes))
-       {
-
-         if (!ap.scrollRight(false))
-           break;
-       }
-       while (seqCanvas.cursorX > av.colSel.adjustForHiddenColumns(av.endRes))
-       {
-         if (!ap.scrollRight(true))
-           break;
-       }
-     }
-     setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),
-                      seqCanvas.cursorX, seqCanvas.cursorY);
-
-     seqCanvas.repaint();
-   }
-
-   void setSelectionAreaAtCursor(boolean topLeft)
-   {
-     SequenceI sequence =
-         (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
-
-     if(av.getSelectionGroup()!=null)
-     {
-       SequenceGroup sg = av.selectionGroup;
-       //Find the top and bottom of this group
-       int min = av.alignment.getHeight(), max = 0;
-       for(int i=0; i<sg.getSize(); i++)
-       {
-         int index = av.alignment.findIndex( sg.getSequenceAt(i) );
-         if(index > max)
-           max = index;
-         if(index < min)
-           min = index;
-       }
-
-       max ++;
-
-       if(topLeft)
-       {
-         sg.setStartRes(seqCanvas.cursorX);
-         if(sg.getEndRes()<seqCanvas.cursorX)
-           sg.setEndRes(seqCanvas.cursorX);
-
-         min = seqCanvas.cursorY;
-       }
-       else
-       {
-         sg.setEndRes(seqCanvas.cursorX);
-         if(sg.getStartRes()>seqCanvas.cursorX)
-           sg.setStartRes(seqCanvas.cursorX);
-
-         max = seqCanvas.cursorY+1;
-       }
-
-       if(min>max)
-       {
-         // Only the user can do this
-         av.setSelectionGroup(null);
-       }
-       else
-       {
-         // Now add any sequences between min and max
-         sg.getSequences(null).removeAllElements();
-         for (int i = min; i < max; i++)
-         {
-           sg.addSequence(av.alignment.getSequenceAt(i), false);
-         }
-       }
-     }
-
-     if (av.getSelectionGroup() == null)
-     {
-       SequenceGroup sg = new SequenceGroup();
-       sg.setStartRes(seqCanvas.cursorX);
-       sg.setEndRes(seqCanvas.cursorX);
-       sg.addSequence(sequence, false);
-       av.setSelectionGroup(sg);
-     }
-
-
-     ap.repaint();
-   }
-
-   void insertGapAtCursor(boolean group)
-   {
-     groupEditing = group;
-     startseq = seqCanvas.cursorY;
-     lastres = seqCanvas.cursorX;
-     editSequence(true, seqCanvas.cursorX+getKeyboardNo(keyboardNo1));
-     endEditing();
-   }
-
-   void deleteGapAtCursor(boolean group)
-   {
-     groupEditing = group;
-     startseq = seqCanvas.cursorY;
-     lastres = seqCanvas.cursorX+getKeyboardNo(keyboardNo1);
-     editSequence(false, seqCanvas.cursorX);
-     endEditing();
-   }
-
-   void numberPressed(char value)
-   {
-     if(keyboardNo1==null)
-       keyboardNo1 = new StringBuffer();
-
-     if(keyboardNo2!=null)
-       keyboardNo2.append(value);
-     else
-       keyboardNo1.append(value);
-   }
-
-   int getKeyboardNo(StringBuffer kb)
-   {
-     if(kb==null)
-       return 1;
-     else
-       return Integer.parseInt(kb.toString());
-   }
-
-   void setStatusMessage(SequenceI sequence, int res, int seq)
-   {
-     StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
-                                          sequence.getName());
-
-     Object obj = null;
-     if (av.alignment.isNucleotide())
-     {
-       obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
-                                                  "");
-       if (obj != null)
-         text.append(" Nucleotide: ");
-     }
-     else
-     {
-       obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
-       if (obj != null)
-         text.append("  Residue: ");
-     }
-
-     if (obj != null)
-     {
-
-       if (obj != "")
-       {
-         text.append(obj + " (" + sequence.findPosition(res) +
-                     ")");
-       }
-     }
-
-     ap.alignFrame.statusBar.setText(text.toString());
-
-    }
-     public void mousePressed(MouseEvent evt)
-     {
-       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)
-       {
-         mouseWheelPressed = true;
-         return;
-       }
-
-       if (evt.isShiftDown()
-           || evt.isControlDown()
-           || evt.isAltDown())
-       {
-         if (evt.isControlDown() || evt.isAltDown())
-         {
-           groupEditing = true;
-         }
-         editingSeqs = true;
-       }
-       else
-       {
-         doMousePressedDefineMode(evt);
-         return;
-       }
-
-
-       int seq = findSeq(evt);
-       int res = findRes(evt);
-
-       if(seq<0 || res<0)
-         return;
-
-
-         if ((seq < av.getAlignment().getHeight()) &&
-                 (res < av.getAlignment().getSequenceAt(seq).getLength()))
-         {
-             startseq = seq;
-             lastres = res;
-         }
-         else
-         {
-             startseq = -1;
-             lastres = -1;
-         }
+    editCommand = null;
+  }
 
-        return;
-     }
+  void setCursorRow()
+  {
+    seqCanvas.cursorY = getKeyboardNo(keyboardNo1) - 1;
+    scrollToVisible();
+  }
+
+  void setCursorColumn()
+  {
+    seqCanvas.cursorX = getKeyboardNo(keyboardNo1) - 1;
+    scrollToVisible();
+  }
+
+  void setCursorRowAndColumn()
+  {
+    if (keyboardNo2 == null)
+    {
+      keyboardNo2 = new StringBuffer();
+    }
+    else
+    {
+      seqCanvas.cursorX = getKeyboardNo(keyboardNo1) - 1;
+      seqCanvas.cursorY = getKeyboardNo(keyboardNo2) - 1;
+      scrollToVisible();
+    }
+  }
+
+  void setCursorPosition()
+  {
+    SequenceI sequence =
+        (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
+
+    seqCanvas.cursorX = sequence.findIndex(
+        getKeyboardNo(keyboardNo1) - 1
+        );
+    scrollToVisible();
+  }
+
+  void moveCursor(int dx, int dy)
+  {
+    seqCanvas.cursorX += dx;
+    seqCanvas.cursorY += dy;
+    if (av.hasHiddenColumns && !av.colSel.isVisible(seqCanvas.cursorX))
+    {
+      int original = seqCanvas.cursorX - dx;
+      int maxWidth = av.alignment.getWidth();
+
+      while (!av.colSel.isVisible(seqCanvas.cursorX)
+             && seqCanvas.cursorX < maxWidth
+             && seqCanvas.cursorX > 0)
+      {
+        seqCanvas.cursorX += dx;
+      }
+
+      if (seqCanvas.cursorX >= maxWidth
+          || !av.colSel.isVisible(seqCanvas.cursorX))
+      {
+        seqCanvas.cursorX = original;
+      }
+    }
+    scrollToVisible();
+  }
+
+  void scrollToVisible()
+  {
+    if (seqCanvas.cursorX < 0)
+    {
+      seqCanvas.cursorX = 0;
+    }
+    else if (seqCanvas.cursorX > av.alignment.getWidth() - 1)
+    {
+      seqCanvas.cursorX = av.alignment.getWidth() - 1;
+    }
+
+    if (seqCanvas.cursorY < 0)
+    {
+      seqCanvas.cursorY = 0;
+    }
+    else if (seqCanvas.cursorY > av.alignment.getHeight() - 1)
+    {
+      seqCanvas.cursorY = av.alignment.getHeight() - 1;
+    }
+
+    endEditing();
+    if (av.wrapAlignment)
+    {
+      ap.scrollToWrappedVisible(seqCanvas.cursorX);
+    }
+    else
+    {
+      while (seqCanvas.cursorY < av.startSeq)
+      {
+        ap.scrollUp(true);
+      }
+      while (seqCanvas.cursorY + 1 > av.endSeq)
+      {
+        ap.scrollUp(false);
+      }
+      while (seqCanvas.cursorX < av.colSel.adjustForHiddenColumns(av.startRes))
+      {
+
+        if (!ap.scrollRight(false))
+        {
+          break;
+        }
+      }
+      while (seqCanvas.cursorX > av.colSel.adjustForHiddenColumns(av.endRes))
+      {
+        if (!ap.scrollRight(true))
+        {
+          break;
+        }
+      }
+    }
+    setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),
+                     seqCanvas.cursorX, seqCanvas.cursorY);
+
+    seqCanvas.repaint();
+  }
+
+  void setSelectionAreaAtCursor(boolean topLeft)
+  {
+    SequenceI sequence =
+        (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
+
+    if (av.getSelectionGroup() != null)
+    {
+      SequenceGroup sg = av.selectionGroup;
+      //Find the top and bottom of this group
+      int min = av.alignment.getHeight(), max = 0;
+      for (int i = 0; i < sg.getSize(); i++)
+      {
+        int index = av.alignment.findIndex(sg.getSequenceAt(i));
+        if (index > max)
+        {
+          max = index;
+        }
+        if (index < min)
+        {
+          min = index;
+        }
+      }
+
+      max++;
+
+      if (topLeft)
+      {
+        sg.setStartRes(seqCanvas.cursorX);
+        if (sg.getEndRes() < seqCanvas.cursorX)
+        {
+          sg.setEndRes(seqCanvas.cursorX);
+        }
 
-     public void mouseClicked(MouseEvent evt){}
+        min = seqCanvas.cursorY;
+      }
+      else
+      {
+        sg.setEndRes(seqCanvas.cursorX);
+        if (sg.getStartRes() > seqCanvas.cursorX)
+        {
+          sg.setStartRes(seqCanvas.cursorX);
+        }
 
+        max = seqCanvas.cursorY + 1;
+      }
+
+      if (min > max)
+      {
+        // Only the user can do this
+        av.setSelectionGroup(null);
+      }
+      else
+      {
+        // Now add any sequences between min and max
+        sg.getSequences(null).removeAllElements();
+        for (int i = min; i < max; i++)
+        {
+          sg.addSequence(av.alignment.getSequenceAt(i), false);
+        }
+      }
+    }
+
+    if (av.getSelectionGroup() == null)
+    {
+      SequenceGroup sg = new SequenceGroup();
+      sg.setStartRes(seqCanvas.cursorX);
+      sg.setEndRes(seqCanvas.cursorX);
+      sg.addSequence(sequence, false);
+      av.setSelectionGroup(sg);
+    }
+
+    ap.repaint();
+  }
+
+  void insertGapAtCursor(boolean group)
+  {
+    groupEditing = group;
+    startseq = seqCanvas.cursorY;
+    lastres = seqCanvas.cursorX;
+    editSequence(true, seqCanvas.cursorX + getKeyboardNo(keyboardNo1));
+    endEditing();
+  }
+
+  void deleteGapAtCursor(boolean group)
+  {
+    groupEditing = group;
+    startseq = seqCanvas.cursorY;
+    lastres = seqCanvas.cursorX + getKeyboardNo(keyboardNo1);
+    editSequence(false, seqCanvas.cursorX);
+    endEditing();
+  }
+
+  void numberPressed(char value)
+  {
+    if (keyboardNo1 == null)
+    {
+      keyboardNo1 = new StringBuffer();
+    }
+
+    if (keyboardNo2 != null)
+    {
+      keyboardNo2.append(value);
+    }
+    else
+    {
+      keyboardNo1.append(value);
+    }
+  }
+
+  int getKeyboardNo(StringBuffer kb)
+  {
+    if (kb == null)
+    {
+      return 1;
+    }
+    else
+    {
+      return Integer.parseInt(kb.toString());
+    }
+  }
+
+  void setStatusMessage(SequenceI sequence, int res, int seq)
+  {
+    StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
+                                         sequence.getName());
+
+    Object obj = null;
+    if (av.alignment.isNucleotide())
+    {
+      obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
+                                                 "");
+      if (obj != null)
+      {
+        text.append(" Nucleotide: ");
+      }
+    }
+    else
+    {
+      obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
+      if (obj != null)
+      {
+        text.append("  Residue: ");
+      }
+    }
+
+    if (obj != null)
+    {
+
+      if (obj != "")
+      {
+        text.append(obj + " (" + sequence.findPosition(res) +
+                    ")");
+      }
+    }
+
+    ap.alignFrame.statusBar.setText(text.toString());
+
+  }
+
+  public void mousePressed(MouseEvent evt)
+  {
+    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)
+    {
+      mouseWheelPressed = true;
+      return;
+    }
+
+    if (evt.isShiftDown()
+        || evt.isControlDown()
+        || evt.isAltDown())
+    {
+      if (evt.isControlDown() || evt.isAltDown())
+      {
+        groupEditing = true;
+      }
+      editingSeqs = true;
+    }
+    else
+    {
+      doMousePressedDefineMode(evt);
+      return;
+    }
+
+    int seq = findSeq(evt);
+    int res = findRes(evt);
+
+    if (seq < 0 || res < 0)
+    {
+      return;
+    }
+
+    if ( (seq < av.getAlignment().getHeight()) &&
+        (res < av.getAlignment().getSequenceAt(seq).getLength()))
+    {
+      startseq = seq;
+      lastres = res;
+    }
+    else
+    {
+      startseq = -1;
+      lastres = -1;
+    }
+
+    return;
+  }
+
+  public void mouseClicked(MouseEvent evt)
+  {}
 
   public void mouseReleased(MouseEvent evt)
   {
@@ -404,91 +437,101 @@ public class SeqPanel
 
     if (!editingSeqs)
     {
-       doMouseReleasedDefineMode(evt);
-       return;
+      doMouseReleasedDefineMode(evt);
+      return;
     }
 
-     endEditing();
-     ap.repaint();
+    endEditing();
+    ap.repaint();
   }
 
-  int startWrapBlock=-1;
-  int wrappedBlock=-1;
+  int startWrapBlock = -1;
+  int wrappedBlock = -1;
   int findRes(MouseEvent evt)
- {
-   int res = 0;
-   int x = evt.getX();
-
-  if (av.wrapAlignment)
   {
+    int res = 0;
+    int x = evt.getX();
 
-    int hgap = av.charHeight;
-    if (av.scaleAboveWrapped)
-      hgap += av.charHeight;
+    if (av.wrapAlignment)
+    {
 
-    int cHeight = av.getAlignment().getHeight() * av.charHeight
-        + hgap + seqCanvas.getAnnotationHeight();
+      int hgap = av.charHeight;
+      if (av.scaleAboveWrapped)
+      {
+        hgap += av.charHeight;
+      }
+
+      int cHeight = av.getAlignment().getHeight() * av.charHeight
+          + hgap + seqCanvas.getAnnotationHeight();
 
       int y = evt.getY();
       y -= hgap;
       x -= seqCanvas.LABEL_WEST;
 
-
       int cwidth = seqCanvas.getWrappedCanvasWidth(getSize().width);
-      if(cwidth<1)
+      if (cwidth < 1)
+      {
         return 0;
+      }
 
       wrappedBlock = y / cHeight;
       wrappedBlock += av.getStartRes() / cwidth;
 
       res = wrappedBlock * cwidth + x / av.getCharWidth();
 
-  }
-  else
-  {
+    }
+    else
+    {
       res = (x / av.getCharWidth()) + av.getStartRes();
-  }
-
-  if(av.hasHiddenColumns)
-          res = av.getColumnSelection().adjustForHiddenColumns(res);
+    }
 
-  return res;
+    if (av.hasHiddenColumns)
+    {
+      res = av.getColumnSelection().adjustForHiddenColumns(res);
+    }
 
- }
+    return res;
 
- int findSeq(MouseEvent evt)
- {
+  }
 
-   int seq = 0;
-   int y = evt.getY();
+  int findSeq(MouseEvent evt)
+  {
 
-   if (av.wrapAlignment)
-   {
-     int hgap = av.charHeight;
-     if (av.scaleAboveWrapped)
-       hgap += av.charHeight;
+    int seq = 0;
+    int y = evt.getY();
 
-     int cHeight = av.getAlignment().getHeight() * av.charHeight
-         + hgap + seqCanvas.getAnnotationHeight();
+    if (av.wrapAlignment)
+    {
+      int hgap = av.charHeight;
+      if (av.scaleAboveWrapped)
+      {
+        hgap += av.charHeight;
+      }
 
-       y -= hgap;
+      int cHeight = av.getAlignment().getHeight() * av.charHeight
+          + hgap + seqCanvas.getAnnotationHeight();
 
-     seq = Math.min( (y % cHeight) / av.getCharHeight(),
-                     av.alignment.getHeight() -1);
-     if(seq<0)
-       seq = 0;
-   }
-   else
-   {
-     seq = Math.min( (y / av.getCharHeight()) + av.getStartSeq(),
-                     av.alignment.getHeight() -1);
-     if(seq<0)
-       seq = 0;
-   }
+      y -= hgap;
 
-   return seq;
- }
+      seq = Math.min( (y % cHeight) / av.getCharHeight(),
+                     av.alignment.getHeight() - 1);
+      if (seq < 0)
+      {
+        seq = 0;
+      }
+    }
+    else
+    {
+      seq = Math.min( (y / av.getCharHeight()) + av.getStartSeq(),
+                     av.alignment.getHeight() - 1);
+      if (seq < 0)
+      {
+        seq = 0;
+      }
+    }
 
+    return seq;
+  }
 
   public void doMousePressed(MouseEvent evt)
   {
@@ -520,37 +563,45 @@ public class SeqPanel
     int res = findRes(evt);
     int seq = findSeq(evt);
 
-    if (seq >= av.getAlignment().getHeight() || seq<0 || res<0)
+    if (seq >= av.getAlignment().getHeight() || seq < 0 || res < 0)
     {
-      if(tooltip!=null)
+      if (tooltip != null)
+      {
         tooltip.setTip("");
+      }
       return;
     }
 
     SequenceI sequence = av.getAlignment().getSequenceAt(seq);
     if (res > sequence.getLength())
     {
-      if(tooltip!=null)
+      if (tooltip != null)
+      {
         tooltip.setTip("");
+      }
       return;
     }
 
     StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
-            sequence.getName());
+                                         sequence.getName());
 
     Object obj = null;
     if (av.alignment.isNucleotide())
     {
       obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
-          "");
-      if(obj!=null)
+                                                 "");
+      if (obj != null)
+      {
         text.append(" Nucleotide: ");
+      }
     }
     else
     {
       obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
-      if(obj!=null)
+      if (obj != null)
+      {
         text.append("  Residue: ");
+      }
     }
 
     if (obj != null)
@@ -561,7 +612,7 @@ public class SeqPanel
       }
     }
 
-    if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence)
+    if (seqCanvas.pdbCanvas != null && sequence == seqCanvas.pdbCanvas.sequence)
     {
       seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));
     }
@@ -569,18 +620,22 @@ public class SeqPanel
     ap.alignFrame.statusBar.setText(text.toString());
 
     StringBuffer tooltipText = new StringBuffer();
-    SequenceGroup []  groups = av.alignment.findAllGroups(sequence);
-    if(groups!=null)
+    SequenceGroup[] groups = av.alignment.findAllGroups(sequence);
+    if (groups != null)
     {
-      for(int g=0; g<groups.length; g++)
+      for (int g = 0; g < groups.length; g++)
       {
-        if(groups[g].getStartRes()<=res && groups[g].getEndRes()>=res)
+        if (groups[g].getStartRes() <= res && groups[g].getEndRes() >= res)
         {
           if (!groups[g].getName().startsWith("JTreeGroup") &&
               !groups[g].getName().startsWith("JGroup"))
+          {
             tooltipText.append(groups[g].getName() + " ");
-          if(groups[g].getDescription()!=null)
+          }
+          if (groups[g].getDescription() != null)
+          {
             tooltipText.append(groups[g].getDescription());
+          }
           tooltipText.append("\n");
         }
       }
@@ -588,27 +643,32 @@ public class SeqPanel
 
     // use aa to see if the mouse pointer is on a
     if (av.showSequenceFeatures
-        && sequence.getSequenceFeatures()!=null
-        && av.featuresDisplayed!=null)
+        && sequence.getSequenceFeatures() != null
+        && av.featuresDisplayed != null)
     {
 
-      Vector allFeatures = getAllFeaturesAtRes(sequence, sequence.findPosition(res));
+      Vector allFeatures = getAllFeaturesAtRes(sequence,
+                                               sequence.findPosition(res));
 
       int index = 0;
       while (index < allFeatures.size())
       {
         SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(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.getValue("status") != null )
+        if (sf.getValue("status") != null)
         {
           String status = sf.getValue("status").toString();
-          if(status.length()>0)
+          if (status.length() > 0)
+          {
             tooltipText.append(" (" + sf.getValue("status") + ")");
+          }
         }
         tooltipText.append("\n");
 
@@ -617,16 +677,20 @@ public class SeqPanel
     }
 
     if (tooltip == null)
+    {
       tooltip = new Tooltip(tooltipText.toString(), seqCanvas);
+    }
     else
+    {
       tooltip.setTip(tooltipText.toString());
+    }
   }
 
   Vector getAllFeaturesAtRes(SequenceI seq, int res)
   {
     Vector allFeatures = new Vector();
     int index = 0;
-    if(seq.getSequenceFeatures()!=null)
+    if (seq.getSequenceFeatures() != null)
     {
       while (index < seq.getSequenceFeatures().length)
       {
@@ -668,9 +732,10 @@ public class SeqPanel
           fontSize++;
         }
 
-
-        if(fontSize<1)
+        if (fontSize < 1)
+        {
           fontSize = 1;
+        }
 
         av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
         av.charWidth = oldWidth;
@@ -686,7 +751,7 @@ public class SeqPanel
           av.charWidth++;
         }
 
-        if(av.charWidth<1)
+        if (av.charWidth < 1)
         {
           av.charWidth = 1;
         }
@@ -702,37 +767,41 @@ public class SeqPanel
       ap.repaint();
       ap.annotationPanel.image = null;
       return;
-      }
+    }
 
-      if (!editingSeqs)
-      {
-        doMouseDraggedDefineMode(evt);
-        return;
-      }
+    if (!editingSeqs)
+    {
+      doMouseDraggedDefineMode(evt);
+      return;
+    }
 
-  int res = findRes(evt);
+    int res = findRes(evt);
 
-  if (res < 0)
-  {
+    if (res < 0)
+    {
       res = 0;
-  }
+    }
 
-  if ((lastres == -1) || (lastres == res))
-  {
+    if ( (lastres == -1) || (lastres == res))
+    {
       return;
-  }
+    }
 
-  if ( (res < av.getAlignment().getWidth()) && (res < lastres))
-  {
-    // dragLeft, delete gap
-    editSequence(false, res);
-  }
-  else
-    editSequence(true, res);
+    if ( (res < av.getAlignment().getWidth()) && (res < lastres))
+    {
+      // dragLeft, delete gap
+      editSequence(false, res);
+    }
+    else
+    {
+      editSequence(true, res);
+    }
 
-  mouseDragging = true;
-  if(scrollThread!=null)
-    scrollThread.setEvent(evt);
+    mouseDragging = true;
+    if (scrollThread != null)
+    {
+      scrollThread.setEvent(evt);
+    }
 
   }
 
@@ -745,331 +814,348 @@ public class SeqPanel
 
     SequenceI seq = av.alignment.getSequenceAt(startseq);
 
-      if (!groupEditing && av.hasHiddenRows)
+    if (!groupEditing && av.hasHiddenRows)
+    {
+      if (av.hiddenRepSequences != null
+          && av.hiddenRepSequences.containsKey(seq))
       {
-        if (av.hiddenRepSequences!=null
-            && av.hiddenRepSequences.containsKey(seq))
-        {
-          sg = (SequenceGroup)av.hiddenRepSequences.get(seq);
-          groupEditing = true;
-          }
+        sg = (SequenceGroup) av.hiddenRepSequences.get(seq);
+        groupEditing = true;
       }
+    }
 
-      StringBuffer message = new StringBuffer();
-      if (groupEditing)
+    StringBuffer message = new StringBuffer();
+    if (groupEditing)
+    {
+      message.append("Edit group:");
+      if (editCommand == null)
       {
-        message.append("Edit group:");
-        if (editCommand == null)
-          editCommand = new EditCommand("Edit Group");
+        editCommand = new EditCommand("Edit Group");
       }
-      else
-       {
-         message.append("Edit sequence: " + seq.getName());
-         String label = seq.getName();
-         if(label.length()>10)
-           label = label.substring(0,10);
-         if(editCommand==null)
-           editCommand = new EditCommand("Edit "+label);
-       }
+    }
+    else
+    {
+      message.append("Edit sequence: " + seq.getName());
+      String label = seq.getName();
+      if (label.length() > 10)
+      {
+        label = label.substring(0, 10);
+      }
+      if (editCommand == null)
+      {
+        editCommand = new EditCommand("Edit " + label);
+      }
+    }
 
-     if(insertGap)
-       message.append(" insert ");
-     else
-       message.append(" delete ");
+    if (insertGap)
+    {
+      message.append(" insert ");
+    }
+    else
+    {
+      message.append(" delete ");
+    }
 
-     message.append(Math.abs(startres-lastres)+" gaps.");
-     ap.alignFrame.statusBar.setText(message.toString());
+    message.append(Math.abs(startres - lastres) + " gaps.");
+    ap.alignFrame.statusBar.setText(message.toString());
 
+    //Are we editing within a selection group?
+    if (groupEditing
+        || (sg != null && sg.getSequences(av.hiddenRepSequences).contains(seq)))
+    {
+      fixedColumns = true;
 
-      //Are we editing within a selection group?
-      if (groupEditing
-          || (sg != null && sg.getSequences(av.hiddenRepSequences).contains(seq)))
+      //sg might be null as the user may only see 1 sequence,
+      //but the sequence represents a group
+      if (sg == null)
       {
-        fixedColumns = true;
-
-        //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))
         {
-          if (av.hiddenRepSequences == null
-              || !av.hiddenRepSequences.containsKey(seq))
-          {
-            endEditing();
-            return;
-          }
-
-          sg = (SequenceGroup) av.hiddenRepSequences.get(seq);
+          endEditing();
+          return;
         }
 
-        fixedLeft = sg.getStartRes();
-        fixedRight = sg.getEndRes();
+        sg = (SequenceGroup) av.hiddenRepSequences.get(seq);
+      }
+
+      fixedLeft = sg.getStartRes();
+      fixedRight = sg.getEndRes();
+
+      if ( (startres < fixedLeft && lastres >= fixedLeft)
+          || (startres >= fixedLeft && lastres < fixedLeft)
+          || (startres > fixedRight && lastres <= fixedRight)
+          || (startres <= fixedRight && lastres > fixedRight))
+      {
+        endEditing();
+        return;
+      }
+
+      if (fixedLeft > startres)
+      {
+        fixedRight = fixedLeft - 1;
+        fixedLeft = 0;
+      }
+      else if (fixedRight < startres)
+      {
+        fixedLeft = fixedRight;
+        fixedRight = -1;
+      }
+    }
+
+    if (av.hasHiddenColumns)
+    {
+      fixedColumns = true;
+      int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
+      int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
 
-        if (   (startres < fixedLeft && lastres >= fixedLeft)
-            || (startres >= fixedLeft && lastres < fixedLeft)
-            || (startres > fixedRight && lastres <=fixedRight)
-            || (startres <= fixedRight && lastres > fixedRight))
-        {
-          endEditing();
-          return;
-        }
+      if ( (insertGap && startres > y1 && lastres < y1)
+          || (!insertGap && startres < y2 && lastres > y2))
+      {
+        endEditing();
+        return;
+      }
 
-        if (fixedLeft > startres)
+      //System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
+      //Selection spans a hidden region
+      if (fixedLeft < y1 && (fixedRight > y2 || fixedRight == -1))
+      {
+        if (startres >= y2)
         {
-          fixedRight = fixedLeft - 1;
-          fixedLeft = 0;
+          fixedLeft = y2;
         }
-        else if (fixedRight < startres)
+        else
         {
-          fixedLeft = fixedRight;
-          fixedRight = -1;
+          fixedRight = y2 - 1;
         }
       }
+    }
 
-
-      if(av.hasHiddenColumns )
+    if (groupEditing)
+    {
+      Vector vseqs = sg.getSequences(av.hiddenRepSequences);
+      int g, groupSize = vseqs.size();
+      SequenceI[] groupSeqs = new SequenceI[groupSize];
+      for (g = 0; g < groupSeqs.length; g++)
       {
-          fixedColumns = true;
-          int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
-          int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
-
-          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
-          if(fixedLeft<y1 && (fixedRight>y2 || fixedRight==-1))
-          {
-            if(startres>=y2)
-            {
-              fixedLeft = y2;
-            }
-            else
-            {
-             fixedRight = y2 - 1;
-           }
-          }
+        groupSeqs[g] = (SequenceI) vseqs.elementAt(g);
       }
 
-
-      if (groupEditing)
+      // drag to right
+      if (insertGap)
       {
-        Vector vseqs = sg.getSequences(av.hiddenRepSequences);
-        int g, groupSize = vseqs.size();
-        SequenceI[] groupSeqs = new SequenceI[groupSize];
-        for (g = 0; g < groupSeqs.length; g++)
-          groupSeqs[g] = (SequenceI) vseqs.elementAt(g);
+        //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
+            )
+        {
+          sg.setEndRes(av.alignment.getWidth() + startres - lastres);
+          fixedRight = sg.getEndRes();
+        }
 
-        // drag to right
-        if (insertGap)
+        // Is it valid with fixed columns??
+        // Find the next gap before the end
+        // of the visible region boundary
+        boolean blank = false;
+        for (fixedRight = fixedRight;
+             fixedRight > lastres;
+             fixedRight--)
         {
-            //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
-               )
-            {
-              sg.setEndRes(av.alignment.getWidth() + startres - lastres);
-              fixedRight = sg.getEndRes();
-            }
+          blank = true;
 
-          // Is it valid with fixed columns??
-          // Find the next gap before the end
-          // of the visible region boundary
-          boolean blank = false;
-          for (fixedRight = fixedRight;
-               fixedRight > lastres;
-               fixedRight--)
+          for (g = 0; g < groupSize; g++)
           {
-            blank = true;
-
-            for (g = 0; g < groupSize; g++)
+            for (int j = 0; j < startres - lastres; j++)
             {
-              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;
-                }
+                blank = false;
+                break;
               }
             }
-            if (blank)
-              break;
           }
-
-          if (!blank)
+          if (blank)
           {
-            if(sg.getSize() == av.alignment.getHeight()  )
-            {
-              if((av.hasHiddenColumns
-                  && startres<av.getColumnSelection().getHiddenBoundaryRight(startres)))
-              {
-                endEditing();
-                return;
-              }
-
-              int alWidth = av.alignment.getWidth();
-              if(av.hasHiddenRows)
-              {
-                int hwidth = av.alignment.getHiddenSequences().getWidth();
-                if(hwidth>alWidth)
-                  alWidth = hwidth;
-              }
-              //We can still insert gaps if the selectionGroup
-              //contains all the sequences
-              sg.setEndRes(sg.getEndRes()+startres-lastres);
-              fixedRight = alWidth+startres-lastres;
-            }
-            else
-            {
-              endEditing();
-              return;
-            }
+            break;
           }
         }
 
-
-        // drag to left
-        else if(!insertGap)
+        if (!blank)
         {
-          /// Are we able to delete?
-          // ie are all columns blank?
-
-          for (g = 0; g < groupSize; g++)
+          if (sg.getSize() == av.alignment.getHeight())
           {
-            for (int j = startres; j < lastres; j++)
+            if ( (av.hasHiddenColumns
+                  &&
+                  startres < av.getColumnSelection().getHiddenBoundaryRight(startres)))
             {
-              if (groupSeqs[g].getLength() <= j)
-              {
-                continue;
-              }
+              endEditing();
+              return;
+            }
 
-              if (!jalview.util.Comparison.isGap(
-                  groupSeqs[g].getCharAt(j)))
+            int alWidth = av.alignment.getWidth();
+            if (av.hasHiddenRows)
+            {
+              int hwidth = av.alignment.getHiddenSequences().getWidth();
+              if (hwidth > alWidth)
               {
-                // Not a gap, block edit not valid
-                endEditing();
-                return;
+                alWidth = hwidth;
               }
             }
+            //We can still insert gaps if the selectionGroup
+            //contains all the sequences
+            sg.setEndRes(sg.getEndRes() + startres - lastres);
+            fixedRight = alWidth + startres - lastres;
+          }
+          else
+          {
+            endEditing();
+            return;
           }
         }
+      }
+
+      // drag to left
+      else if (!insertGap)
+      {
+        /// Are we able to delete?
+        // ie are all columns blank?
 
-          if (insertGap)
+        for (g = 0; g < groupSize; g++)
+        {
+          for (int j = startres; j < lastres; j++)
           {
-            // dragging to the right
-            if (fixedColumns && fixedRight != -1)
+            if (groupSeqs[g].getLength() <= j)
             {
-              for (int j = lastres; j < startres; j++)
-              {
-                  insertChar(j, groupSeqs, fixedRight);
-              }
+              continue;
             }
-            else
+
+            if (!jalview.util.Comparison.isGap(
+                groupSeqs[g].getCharAt(j)))
             {
-              editCommand.appendEdit(EditCommand.INSERT_GAP,
-                                     groupSeqs,
-                                     startres, startres-lastres,
-                                     av.alignment,
-                                     true);
+              // Not a gap, block edit not valid
+              endEditing();
+              return;
             }
           }
-          else
-          {
-            // dragging to the left
-            if (fixedColumns && fixedRight != -1)
-            {
-              for (int j = lastres; j > startres; j--)
-              {
-                deleteChar(startres, groupSeqs, fixedRight);
-              }
-            }
-            else
-              editCommand.appendEdit(EditCommand.DELETE_GAP,
-                                     groupSeqs,
-                                     startres, lastres - startres,
-                                     av.alignment,
-                                     true);
+        }
+      }
 
+      if (insertGap)
+      {
+        // dragging to the right
+        if (fixedColumns && fixedRight != -1)
+        {
+          for (int j = lastres; j < startres; j++)
+          {
+            insertChar(j, groupSeqs, fixedRight);
           }
+        }
+        else
+        {
+          editCommand.appendEdit(EditCommand.INSERT_GAP,
+                                 groupSeqs,
+                                 startres, startres - lastres,
+                                 av.alignment,
+                                 true);
+        }
       }
-      else /////Editing a single sequence///////////
+      else
       {
-        if (insertGap)
+        // dragging to the left
+        if (fixedColumns && fixedRight != -1)
         {
-          // dragging to the right
-          if (fixedColumns && fixedRight != -1)
+          for (int j = lastres; j > startres; j--)
           {
-            for (int j = lastres; j < startres; j++)
-            {
-              insertChar(j, new SequenceI[]{seq}, fixedRight);
-            }
+            deleteChar(startres, groupSeqs, fixedRight);
           }
-          else
+        }
+        else
+        {
+          editCommand.appendEdit(EditCommand.DELETE_GAP,
+                                 groupSeqs,
+                                 startres, lastres - startres,
+                                 av.alignment,
+                                 true);
+        }
+
+      }
+    }
+    else /////Editing a single sequence///////////
+    {
+      if (insertGap)
+      {
+        // dragging to the right
+        if (fixedColumns && fixedRight != -1)
+        {
+          for (int j = lastres; j < startres; j++)
           {
-            editCommand.appendEdit(EditCommand.INSERT_GAP,
-                                   new SequenceI[]
-                                   {seq},
-                                   lastres, startres-lastres,
-                                   av.alignment,
-                                   true);
+            insertChar(j, new SequenceI[]
+                       {seq}, fixedRight);
           }
         }
         else
         {
-          // dragging to the left
-          if (fixedColumns && fixedRight != -1)
+          editCommand.appendEdit(EditCommand.INSERT_GAP,
+                                 new SequenceI[]
+                                 {seq},
+                                 lastres, startres - lastres,
+                                 av.alignment,
+                                 true);
+        }
+      }
+      else
+      {
+        // dragging to the left
+        if (fixedColumns && fixedRight != -1)
+        {
+          for (int j = lastres; j > startres; j--)
           {
-            for (int j = lastres; j > startres; j--)
+            if (!jalview.util.Comparison.isGap(seq.getCharAt(startres)))
             {
-              if (!jalview.util.Comparison.isGap(seq.getCharAt(startres)))
-              {
-                endEditing();
-                break;
-              }
-              deleteChar(startres, new SequenceI[]{seq}, fixedRight);
+              endEditing();
+              break;
             }
+            deleteChar(startres, new SequenceI[]
+                       {seq}, fixedRight);
           }
-          else
+        }
+        else
+        {
+          //could be a keyboard edit trying to delete none gaps
+          int max = 0;
+          for (int m = startres; m < lastres; m++)
           {
-            //could be a keyboard edit trying to delete none gaps
-            int max=0;
-            for(int m = startres; m<lastres; m++)
+            if (!jalview.util.Comparison.isGap(seq.getCharAt(m)))
             {
-              if(!jalview.util.Comparison.isGap(seq.getCharAt(m)))
-                break;
-              max++;
+              break;
             }
+            max++;
+          }
 
-            if (max>0)
-            {
-              editCommand.appendEdit(EditCommand.DELETE_GAP,
-                                     new SequenceI[]
-                                     {seq},
-                                     startres, max,
-                                     av.alignment,
-                                     true);
-            }
+          if (max > 0)
+          {
+            editCommand.appendEdit(EditCommand.DELETE_GAP,
+                                   new SequenceI[]
+                                   {seq},
+                                   startres, max,
+                                   av.alignment,
+                                   true);
           }
         }
       }
+    }
 
-      lastres = startres;
-      seqCanvas.repaint();
+    lastres = startres;
+    seqCanvas.repaint();
   }
 
-
-
-  void insertChar(int j, SequenceI [] seq, int fixedColumn)
+  void insertChar(int j, SequenceI[] seq, int fixedColumn)
   {
     int blankColumn = fixedColumn;
-    for(int s=0; s<seq.length; s++)
+    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
@@ -1102,7 +1188,7 @@ public class SeqPanel
 
   }
 
-  void deleteChar(int j, SequenceI [] seq, int fixedColumn)
+  void deleteChar(int j, SequenceI[] seq, int fixedColumn)
   {
 
     editCommand.appendEdit(EditCommand.DELETE_GAP,
@@ -1114,7 +1200,6 @@ public class SeqPanel
                            fixedColumn, 1, av.alignment, true);
   }
 
-
 //////////////////////////////////////////
 /////Everything below this is for defining the boundary of the rubberband
 //////////////////////////////////////////
@@ -1129,10 +1214,12 @@ public class SeqPanel
     int res = findRes(evt);
     int seq = findSeq(evt);
     oldSeq = seq;
-    startWrapBlock=wrappedBlock;
+    startWrapBlock = wrappedBlock;
 
-    if(seq==-1)
+    if (seq == -1)
+    {
       return;
+    }
 
     SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
 
@@ -1180,16 +1267,15 @@ public class SeqPanel
       av.setSelectionGroup(stretchGroup);
     }
 
-
     // DETECT RIGHT MOUSE BUTTON IN AWT
     if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK) ==
-             InputEvent.BUTTON3_MASK)
+        InputEvent.BUTTON3_MASK)
     {
       Vector allFeatures = getAllFeaturesAtRes(sequence,
                                                sequence.findPosition(res));
 
       Vector links = null;
-      if(allFeatures!=null)
+      if (allFeatures != null)
       {
         for (int i = 0; i < allFeatures.size(); i++)
         {
@@ -1219,40 +1305,40 @@ 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)
+    if (stretchGroup == null)
+    {
+      // define a new group here
+      SequenceGroup sg = new SequenceGroup();
+      sg.setStartRes(res);
+      sg.setEndRes(res);
+      sg.addSequence(sequence, false);
+      av.setSelectionGroup(sg);
+      stretchGroup = sg;
+
+      if (av.getConservationSelected())
       {
-        // define a new group here
-        SequenceGroup sg = new SequenceGroup();
-        sg.setStartRes(res);
-        sg.setEndRes(res);
-        sg.addSequence(sequence, false);
-        av.setSelectionGroup(sg);
-        stretchGroup = sg;
-
-        if (av.getConservationSelected())
-        {
-          SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),
-                                            "Background");
-        }
-        if (av.getAbovePIDThreshold())
-        {
-          SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
-                                         "Background");
-        }
-
+        SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),
+                                          "Background");
+      }
+      if (av.getAbovePIDThreshold())
+      {
+        SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
+                                       "Background");
       }
+
+    }
   }
 
   public void doMouseReleasedDefineMode(MouseEvent evt)
   {
     if (stretchGroup == null)
     {
-        return;
+      return;
     }
 
-    if(stretchGroup.cs!=null)
+    if (stretchGroup.cs != null)
     {
       if (stretchGroup.cs instanceof ClustalxColourScheme)
       {
@@ -1265,8 +1351,9 @@ public class SeqPanel
           || stretchGroup.cs instanceof PIDColourScheme
           || stretchGroup.cs.conservationApplied()
           || stretchGroup.cs.getThreshold() > 0)
+      {
         stretchGroup.recalcConservation();
-
+      }
 
       if (stretchGroup.cs.conservationApplied())
       {
@@ -1292,125 +1379,132 @@ public class SeqPanel
     int res = findRes(evt);
     int y = findSeq(evt);
 
-    if(wrappedBlock!=startWrapBlock)
+    if (wrappedBlock != startWrapBlock)
+    {
       return;
+    }
 
-     if (stretchGroup == null)
-     {
-          return;
-     }
+    if (stretchGroup == null)
+    {
+      return;
+    }
+
+    mouseDragging = true;
 
-     mouseDragging = true;
+    if (y > av.alignment.getHeight())
+    {
+      y = av.alignment.getHeight() - 1;
+    }
 
+    if (res >= av.alignment.getWidth())
+    {
+      res = av.alignment.getWidth() - 1;
+    }
 
-      if(y > av.alignment.getHeight())
-      {
-        y = av.alignment.getHeight() -1;
-      }
+    if (stretchGroup.getEndRes() == res)
+    {
+      // Edit end res position of selected group
+      changeEndRes = true;
+    }
+    else if (stretchGroup.getStartRes() == res)
+    {
+      // Edit start res position of selected group
+      changeStartRes = true;
+    }
 
-      if(res>=av.alignment.getWidth())
-        res = av.alignment.getWidth()-1;
+    if (res < 0)
+    {
+      res = 0;
+    }
 
-      if (stretchGroup.getEndRes() == res)
+    if (changeEndRes)
+    {
+      if (res > (stretchGroup.getStartRes() - 1))
       {
-          // Edit end res position of selected group
-          changeEndRes = true;
+        stretchGroup.setEndRes(res);
       }
-      else if (stretchGroup.getStartRes() == res)
+    }
+    else if (changeStartRes)
+    {
+      if (res < (stretchGroup.getEndRes() + 1))
       {
-          // Edit start res position of selected group
-          changeStartRes = true;
+        stretchGroup.setStartRes(res);
       }
+    }
 
-      if (res < 0)
-      {
-          res = 0;
-      }
+    int dragDirection = 0;
 
-      if (changeEndRes)
-      {
-          if (res > (stretchGroup.getStartRes() - 1))
-          {
-              stretchGroup.setEndRes(res);
-          }
-      }
-      else if (changeStartRes)
-      {
-          if (res < (stretchGroup.getEndRes() + 1))
-          {
-              stretchGroup.setStartRes(res);
-          }
-      }
+    if (y > oldSeq)
+    {
+      dragDirection = 1;
+    }
+    else if (y < oldSeq)
+    {
+      dragDirection = -1;
+    }
+
+    while ( (y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))
+    {
+      // This routine ensures we don't skip any sequences, as the
+      // selection is quite slow.
+      Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
 
-      int dragDirection = 0;
+      oldSeq += dragDirection;
 
-      if (y > oldSeq)
-      {
-          dragDirection = 1;
-      }
-      else if (y < oldSeq)
+      if (oldSeq < 0)
       {
-          dragDirection = -1;
+        break;
       }
 
+      Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
 
-      while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))
+      if (stretchGroup.getSequences(null).contains(nextSeq))
       {
-          // This routine ensures we don't skip any sequences, as the
-          // selection is quite slow.
-          Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
-
-          oldSeq += dragDirection;
-
-          if(oldSeq<0)
-            break;
-
-          Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
-
-          if (stretchGroup.getSequences(null).contains(nextSeq))
-          {
-              stretchGroup.deleteSequence(seq, false);
-          }
-          else
-          {
-              if (seq != null)
-              {
-                  stretchGroup.addSequence(seq, false);
-              }
+        stretchGroup.deleteSequence(seq, false);
+      }
+      else
+      {
+        if (seq != null)
+        {
+          stretchGroup.addSequence(seq, false);
+        }
 
-              stretchGroup.addSequence(nextSeq, false);
-          }
+        stretchGroup.addSequence(nextSeq, false);
       }
+    }
 
-      if(oldSeq < 0)
-        oldSeq = -1;
+    if (oldSeq < 0)
+    {
+      oldSeq = -1;
+    }
 
+    if (res > av.endRes || res < av.startRes
+        || y < av.startSeq || y > av.endSeq)
+    {
+      mouseExited(evt);
+    }
 
-      if(res>av.endRes || res<av.startRes
-          || y<av.startSeq || y>av.endSeq)
-      {
-        mouseExited(evt);
-      }
+    if (scrollThread != null)
+    {
+      scrollThread.setEvent(evt);
+    }
 
-      if (scrollThread != null)
-      {
-        scrollThread.setEvent(evt);
-      }
+    seqCanvas.repaint();
+  }
 
-      seqCanvas.repaint();
+  public void mouseEntered(MouseEvent e)
+  {
+    if (oldSeq < 0)
+    {
+      oldSeq = 0;
     }
 
-    public void mouseEntered(MouseEvent e)
+    if (scrollThread != null)
     {
-      if (oldSeq < 0)
-        oldSeq = 0;
-
-      if (scrollThread != null)
-      {
-        scrollThread.running = false;
-        scrollThread = null;
-      }
+      scrollThread.running = false;
+      scrollThread = null;
     }
+  }
 
   public void mouseExited(MouseEvent e)
   {
@@ -1419,7 +1513,7 @@ public class SeqPanel
       return;
     }
 
-    if (mouseDragging && scrollThread==null)
+    if (mouseDragging && scrollThread == null)
     {
       scrollThread = new ScrollThread();
     }
@@ -1427,9 +1521,9 @@ public class SeqPanel
 
   void scrollCanvas(MouseEvent evt)
   {
-    if(evt==null)
+    if (evt == null)
     {
-      if(scrollThread!=null)
+      if (scrollThread != null)
       {
         scrollThread.running = false;
         scrollThread = null;
@@ -1439,13 +1533,15 @@ public class SeqPanel
     else
     {
       if (scrollThread == null)
+      {
         scrollThread = new ScrollThread();
+      }
 
       mouseDragging = true;
       scrollThread.setEvent(evt);
     }
 
-    }
+  }
 
   // this class allows scrolling off the bottom of the visible alignment
   class ScrollThread
diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index 04defb7..daf971d 100755
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -47,11 +47,11 @@ public class SequenceRenderer
    */
   public void prepare(Graphics g, boolean renderGaps)
   {
-      graphics = g;
-      fm = g.getFontMetrics();
+    graphics = g;
+    fm = g.getFontMetrics();
 
-      this.renderGaps = renderGaps;
-    }
+    this.renderGaps = renderGaps;
+  }
 
   public Color getResidueBoxColour(SequenceI seq, int i)
   {
@@ -66,11 +66,11 @@ public class SequenceRenderer
     }
     else if (av.getShowBoxes())
     {
-        getBoxColour(av.globalColourScheme, seq, i);
+      getBoxColour(av.globalColourScheme, seq, i);
     }
 
     return resBoxColour;
-    }
+  }
 
   void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
   {
@@ -78,9 +78,9 @@ public class SequenceRenderer
     {
       resBoxColour = cs.findColour(seq.getCharAt(i), i);
     }
-    else if(forOverview && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
+    else if (forOverview && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
     {
-        resBoxColour = Color.lightGray;
+      resBoxColour = Color.lightGray;
     }
     else
     {
@@ -92,27 +92,29 @@ public class SequenceRenderer
   public Color findSequenceColour(SequenceI seq, int i)
   {
     allGroups = av.alignment.findAllGroups(seq);
-    drawBoxes(seq, i,i, 0);
+    drawBoxes(seq, i, i, 0);
     return resBoxColour;
   }
 
   public void drawSequence(SequenceI seq, SequenceGroup[] sg,
-                           int start, int end,  int y1)
+                           int start, int end, int y1)
   {
-    if(seq==null)
+    if (seq == null)
+    {
       return;
+    }
 
     allGroups = sg;
 
-    drawBoxes(seq, start, end,  y1);
+    drawBoxes(seq, start, end, y1);
 
-    if(av.validCharWidth)
+    if (av.validCharWidth)
     {
       drawText(seq, start, end, y1);
     }
   }
 
-  public void drawBoxes(SequenceI seq, int start, int end,  int y1)
+  public void drawBoxes(SequenceI seq, int start, int end, int y1)
   {
     int i = start;
     int length = seq.getLength();
@@ -124,7 +126,7 @@ public class SequenceRenderer
     while (i <= end)
     {
       resBoxColour = Color.white;
-      if(i < length)
+      if (i < length)
       {
         if (inCurrentSequenceGroup(i))
         {
@@ -139,7 +141,6 @@ public class SequenceRenderer
         }
       }
 
-
       if (resBoxColour != tempColour)
       {
         if (tempColour != null)
@@ -162,27 +163,30 @@ public class SequenceRenderer
       i++;
     }
 
-    graphics.fillRect(av.charWidth * (curStart - start), y1, curWidth, av.charHeight);
+    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);
+    Font boldFont = null;
+    boolean bold = false;
+    if (av.upperCasebold)
+    {
+      boldFont = new Font(av.getFont().getName(), Font.BOLD, av.charHeight);
 
-     graphics.setFont(av.getFont());
-   }
+      graphics.setFont(av.getFont());
+    }
 
-    y1 += av.charHeight - av.charHeight / 5;  // height/5 replaces pady
+    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;
+    if (end + 1 >= seq.getLength())
+    {
+      end = seq.getLength() - 1;
+    }
 
     char s = ' ';
 
@@ -235,14 +239,14 @@ public class SequenceRenderer
         fm = graphics.getFontMetrics();
         if ('A' <= s && s <= 'Z')
         {
-          if(!bold)
+          if (!bold)
           {
 
             graphics.setFont(boldFont);
           }
           bold = true;
         }
-        else if(bold)
+        else if (bold)
         {
           graphics.setFont(av.font);
           bold = false;
@@ -252,8 +256,8 @@ public class SequenceRenderer
 
       charOffset = (av.charWidth - fm.charWidth(s)) / 2;
       graphics.drawString(String.valueOf(s),
-                         charOffset + av.charWidth * (i - start),
-                        y1 );
+                          charOffset + av.charWidth * (i - start),
+                          y1);
     }
 
   }
@@ -277,7 +281,8 @@ public class SequenceRenderer
     return false;
   }
 
-  public void drawHighlightedText(SequenceI seq, int start, int end, int x1, int y1)
+  public void drawHighlightedText(SequenceI seq, int start, int end, int x1,
+                                  int y1)
   {
     int pady = av.charHeight / 5;
     int charOffset = 0;
@@ -287,7 +292,7 @@ public class SequenceRenderer
 
     char s = '~';
     // Need to find the sequence position here.
-    if(av.validCharWidth)
+    if (av.validCharWidth)
     {
       for (int i = start; i <= end; i++)
       {
@@ -323,6 +328,6 @@ public class SequenceRenderer
                           charOffset + x1,
                           (y1 + av.charHeight) - pady);
     }
-    }
+  }
 
 }
diff --git a/src/jalview/appletgui/SliderPanel.java b/src/jalview/appletgui/SliderPanel.java
index fc7c760..c87f7c2 100755
--- a/src/jalview/appletgui/SliderPanel.java
+++ b/src/jalview/appletgui/SliderPanel.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -27,8 +27,8 @@ import java.awt.event.*;
 import jalview.datamodel.*;
 import jalview.schemes.*;
 
-public class SliderPanel extends Panel
-    implements ActionListener,
+public class SliderPanel
+    extends Panel implements ActionListener,
     AdjustmentListener,
     MouseListener
 {
@@ -154,11 +154,14 @@ public class SliderPanel extends Panel
   public SliderPanel(AlignmentPanel ap, int value, boolean forConserve,
                      ColourSchemeI cs)
   {
-    try {
-        jbInit();
-    } catch (Exception e) {
-        e.printStackTrace();
-      }
+    try
+    {
+      jbInit();
+    }
+    catch (Exception e)
+    {
+      e.printStackTrace();
+    }
     this.ap = ap;
     this.cs = cs;
     forConservation = forConserve;
@@ -237,12 +240,18 @@ public class SliderPanel extends Panel
 
   public void actionPerformed(ActionEvent evt)
   {
-    if(evt.getSource()==applyButton)
+    if (evt.getSource() == applyButton)
+    {
       applyButton_actionPerformed();
-    else if(evt.getSource()==undoButton)
+    }
+    else if (evt.getSource() == undoButton)
+    {
       undoButton_actionPerformed();
-    else if(evt.getSource()==valueField)
+    }
+    else if (evt.getSource() == valueField)
+    {
       valueField_actionPerformed();
+    }
   }
 
   public void adjustmentValueChanged(AdjustmentEvent evt)
@@ -251,7 +260,6 @@ public class SliderPanel extends Panel
     valueChanged(slider.getValue());
   }
 
-
   public void valueField_actionPerformed()
   {
     try
@@ -289,63 +297,70 @@ public class SliderPanel extends Panel
   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);
+  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)
   {
     if (ap.overviewPanel != null)
+    {
       ap.overviewPanel.updateOverviewImage();
+    }
   }
+
   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 6766330..90f2e97 100755
--- a/src/jalview/appletgui/Tooltip.java
+++ b/src/jalview/appletgui/Tooltip.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -19,194 +19,206 @@
 
 package jalview.appletgui;
 
-import java.awt.*;
 import java.applet.*;
-import java.awt.event.*;
 import java.util.*;
 
-public class Tooltip extends Canvas implements MouseListener,
+import java.awt.*;
+import java.awt.event.*;
+
+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;
-
-        Image linkImage;
-
-        FontMetrics fm;
-
-        public Tooltip(String tip, Component owner)
-        {
-          this.owner = owner;
-          owner.addMouseListener(this);
-          owner.addMouseMotionListener(this);
-          setBackground(new Color(255, 255, 220));
-          setTip(tip);
-          java.net.URL url = getClass().getResource("/images/link.gif");
-          if (url != null)
-          {
-            linkImage = java.awt.Toolkit.getDefaultToolkit().getImage(url);
-          }
-        }
-
-        public void paint(Graphics g)
-        {
-          int w = getSize().width;
-          int h = getSize().height;
-
-          g.drawRect(0, 0, w - 1, h - 1);
-          int lindex, x;
-          for (int i = 0; i < tip.length; i++)
-          {
-            x = 3;
-            lindex = tip[i].indexOf("%LINK%");
-            if (lindex != -1)
-            {
-              if (lindex > 0)
-              {
-                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);
-              }
-            }
-            else
-            {
-              g.drawString(tip[i], 3, (i + 1) * fontHeight - 3);
-            }
-          }
-        }
-
-        synchronized void setTip(String tip)
-        {
-          if(tip==null)
-          {
-            setTip("");
-            return;
-          }
-
-          if(lastTip.equals(tip))
-            return;
-
-          lastTip = tip;
-          setPosition = true;
-
-          fm = getFontMetrics(owner.getFont());
-          fontHeight = fm.getHeight();
-
-          int longestLine = 0;
-          StringTokenizer st = new StringTokenizer(tip, "\n");
-          this.tip = new String[st.countTokens()];
-          int index = 0;
-          while(st.hasMoreElements())
-          {
-            this.tip[index] = st.nextToken();
-            if(fm.stringWidth(this.tip[index])>longestLine)
-              longestLine = fm.stringWidth(this.tip[index]);
-            index ++;
-          }
-
-          setSize(longestLine + HORIZONTAL_ENLARGE,
-                  fontHeight*this.tip.length);
-
-          repaint();
-
-        }
-
-        void setTipLocation(MouseEvent evt)
-        {
-          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);
-          }
-        }
-
-
-        private void removeToolTip() {
-                if (shown) {
-                        mainContainer.remove(0);
-                        mainContainer.setLayout(mainLayout);
-                        mainContainer.validate();
-                }
-                shown = false;
-        }
-
-        private void findMainContainer() {
-                Container parent = owner.getParent();
-                while (true) {
-                        if ((parent instanceof Applet) || (parent instanceof Frame)) {
-                                mainContainer = parent;
-                                break;
-                        } else {
-                                parent = parent.getParent();
-                        }
-                }
-                mainLayout = mainContainer.getLayout();
-        }
-
-        public void mouseEntered(MouseEvent me)
+  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;
+
+  Image linkImage;
+
+  FontMetrics fm;
+
+  public Tooltip(String tip, Component owner)
+  {
+    this.owner = owner;
+    owner.addMouseListener(this);
+    owner.addMouseMotionListener(this);
+    setBackground(new Color(255, 255, 220));
+    setTip(tip);
+    java.net.URL url = getClass().getResource("/images/link.gif");
+    if (url != null)
+    {
+      linkImage = java.awt.Toolkit.getDefaultToolkit().getImage(url);
+    }
+  }
+
+  public void paint(Graphics g)
+  {
+    int w = getSize().width;
+    int h = getSize().height;
+
+    g.drawRect(0, 0, w - 1, h - 1);
+    int lindex, x;
+    for (int i = 0; i < tip.length; i++)
+    {
+      x = 3;
+      lindex = tip[i].indexOf("%LINK%");
+      if (lindex != -1)
+      {
+        if (lindex > 0)
         {
-          setTipLocation(me);
+          g.drawString(tip[i].substring(0, lindex), 3, (i + 1) * fontHeight - 3);
+          x += fm.stringWidth(tip[i].substring(0, lindex) + 3);
         }
-
-        public void mouseExited(MouseEvent me)
-        {
-          removeToolTip();
-        }
-
-        public void mousePressed(MouseEvent me)
-        {
-          removeToolTip();
-        }
-
-        public void mouseReleased(MouseEvent me)
-        {}
-
-        public void mouseClicked(MouseEvent me)
-        {}
-
-        public void mouseMoved(MouseEvent me)
+        g.drawImage(linkImage, x, i * fontHeight + 1, this);
+        if (lindex + 6 < tip[i].length())
         {
-         if(!shown)
-          {
-            findMainContainer();
-            mainContainer.setLayout(null);
-            mainContainer.add(this, 0);
-            mainContainer.validate();
-            shown = true;
-            setTipLocation(me);
-          }
-          else if (setPosition)
-          {
-            setTipLocation(me);
-            setPosition = false;
-          }
+          g.drawString(tip[i].substring(lindex + 6),
+                       x + linkImage.getWidth(this),
+                       (i + 1) * fontHeight - 3);
         }
-
-        public void mouseDragged(MouseEvent me)
-        {}
+      }
+      else
+      {
+        g.drawString(tip[i], 3, (i + 1) * fontHeight - 3);
+      }
+    }
+  }
+
+  synchronized void setTip(String tip)
+  {
+    if (tip == null)
+    {
+      setTip("");
+      return;
+    }
+
+    if (lastTip.equals(tip))
+    {
+      return;
+    }
+
+    lastTip = tip;
+    setPosition = true;
+
+    fm = getFontMetrics(owner.getFont());
+    fontHeight = fm.getHeight();
+
+    int longestLine = 0;
+    StringTokenizer st = new StringTokenizer(tip, "\n");
+    this.tip = new String[st.countTokens()];
+    int index = 0;
+    while (st.hasMoreElements())
+    {
+      this.tip[index] = st.nextToken();
+      if (fm.stringWidth(this.tip[index]) > longestLine)
+      {
+        longestLine = fm.stringWidth(this.tip[index]);
+      }
+      index++;
+    }
+
+    setSize(longestLine + HORIZONTAL_ENLARGE,
+            fontHeight * this.tip.length);
+
+    repaint();
+
+  }
+
+  void setTipLocation(MouseEvent evt)
+  {
+    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);
+    }
+  }
+
+  private void removeToolTip()
+  {
+    if (shown)
+    {
+      mainContainer.remove(0);
+      mainContainer.setLayout(mainLayout);
+      mainContainer.validate();
+    }
+    shown = false;
+  }
+
+  private void findMainContainer()
+  {
+    Container parent = owner.getParent();
+    while (true)
+    {
+      if ( (parent instanceof Applet) || (parent instanceof Frame))
+      {
+        mainContainer = parent;
+        break;
+      }
+      else
+      {
+        parent = parent.getParent();
+      }
+    }
+    mainLayout = mainContainer.getLayout();
+  }
+
+  public void mouseEntered(MouseEvent me)
+  {
+    setTipLocation(me);
+  }
+
+  public void mouseExited(MouseEvent me)
+  {
+    removeToolTip();
+  }
+
+  public void mousePressed(MouseEvent me)
+  {
+    removeToolTip();
+  }
+
+  public void mouseReleased(MouseEvent me)
+  {}
+
+  public void mouseClicked(MouseEvent me)
+  {}
+
+  public void mouseMoved(MouseEvent me)
+  {
+    if (!shown)
+    {
+      findMainContainer();
+      mainContainer.setLayout(null);
+      mainContainer.add(this, 0);
+      mainContainer.validate();
+      shown = true;
+      setTipLocation(me);
+    }
+    else if (setPosition)
+    {
+      setTipLocation(me);
+      setPosition = false;
+    }
+  }
+
+  public void mouseDragged(MouseEvent me)
+  {}
 }
diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java
index 5f707d5..c38b1a5 100755
--- a/src/jalview/appletgui/TreeCanvas.java
+++ b/src/jalview/appletgui/TreeCanvas.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -55,7 +55,6 @@ public class TreeCanvas
 
   SequenceNode highlightNode;
 
-
   public TreeCanvas(AlignViewport av, ScrollPane scroller)
   {
     this.av = av;
@@ -77,7 +76,7 @@ public class TreeCanvas
       av.setSelectionGroup(selected);
     }
 
-    selected.setEndRes(av.alignment.getWidth()-1);
+    selected.setEndRes(av.alignment.getWidth() - 1);
     selected.addOrRemove(sequence, true);
   }
 
@@ -168,7 +167,7 @@ public class TreeCanvas
       }
       if (!nodeLabel.equals(""))
       {
-        g.drawString(nodeLabel, xstart+2, ypos - 2);
+        g.drawString(nodeLabel, xstart + 2, ypos - 2);
       }
 
       String name = (markPlaceholders && node.isPlaceholder()) ?
@@ -212,9 +211,13 @@ public class TreeCanvas
       // Draw horizontal line
       g.drawLine(xstart, ypos, xend, ypos);
       if (node == highlightNode)
+      {
         g.fillRect(xend - 3, ypos - 3, 6, 6);
+      }
       else
+      {
         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;
@@ -227,7 +230,7 @@ public class TreeCanvas
 
       if (showDistances && node.dist > 0)
       {
-        g.drawString(new Format("%-.2f").form(node.dist), xstart+2, ypos - 2);
+        g.drawString(new Format("%-.2f").form(node.dist), xstart + 2, ypos - 2);
       }
 
     }
@@ -337,7 +340,7 @@ public class TreeCanvas
 
       if (node.element() instanceof SequenceI)
       {
-        av.setSequenceColour((SequenceI) node.element(), c);
+        av.setSequenceColour( (SequenceI) node.element(), c);
       }
     }
     else
@@ -355,8 +358,10 @@ public class TreeCanvas
 
   public void paint(Graphics g)
   {
-    if(tree==null)
+    if (tree == null)
+    {
       return;
+    }
 
     if (nameHash.size() == 0)
     {
@@ -365,20 +370,19 @@ public class TreeCanvas
 
     int width = scrollPane.getSize().width;
     int height = scrollPane.getSize().height;
-    if(!fitToWindow)
+    if (!fitToWindow)
     {
       height = g.getFontMetrics(font).getHeight() * nameHash.size();
     }
 
-    if(getSize().width>width)
+    if (getSize().width > width)
     {
-      setSize(new Dimension(width,height));
+      setSize(new Dimension(width, height));
       scrollPane.validate();
       return;
     }
 
-    setSize(new Dimension(width,height));
-
+    setSize(new Dimension(width, height));
 
     g.setFont(font);
 
@@ -386,10 +390,9 @@ public class TreeCanvas
 
   }
 
-
   public void draw(Graphics g, int width, int height)
   {
-    offy = font.getSize()+10;
+    offy = font.getSize() + 10;
 
     g.setColor(Color.white);
     g.fillRect(0, 0, width, height);
@@ -468,7 +471,6 @@ public class TreeCanvas
   public void mouseDragged(MouseEvent ect)
   {}
 
-
   public void mouseMoved(MouseEvent evt)
   {
     av.setCurrentTree(tree);
@@ -506,7 +508,7 @@ public class TreeCanvas
       repaint();
       return;
     }
-    else if ( !(ob instanceof SequenceNode))
+    else if (! (ob instanceof SequenceNode))
     {
       // Find threshold
 
@@ -521,7 +523,7 @@ public class TreeCanvas
 
         av.setSelectionGroup(null);
         av.alignment.deleteAllGroups();
-        av.sequenceColours=null;
+        av.sequenceColours = null;
 
         colourGroups();
 
@@ -536,71 +538,76 @@ public class TreeCanvas
   void colourGroups()
   {
     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();
-            if(!sequences.contains(s1))
-              sequences.addElement(s1);
-          }
+      Vector sequences = new Vector();
+      for (int j = 0; j < l.size(); j++)
+      {
+        SequenceI s1 = (SequenceI) ( (SequenceNode) l.elementAt(j)).element();
+        if (!sequences.contains(s1))
+        {
+          sequences.addElement(s1);
+        }
+      }
 
-          ColourSchemeI cs = null;
+      ColourSchemeI cs = null;
 
-          if (av.getGlobalColourScheme() != null)
-          {
-            if (av.getGlobalColourScheme() instanceof UserColourScheme)
-            {
-              cs = new UserColourScheme(
-                  ( (UserColourScheme) av.getGlobalColourScheme()).getColours());
-
-            }
-            else
-              cs = ColourSchemeProperty.getColour(sequences,
-                                                  av.alignment.getWidth(),
-                                                  ColourSchemeProperty.getColourName(
-                                                      av.getGlobalColourScheme()));
-
-              cs.setThreshold(av.getGlobalColourScheme().getThreshold(),
-                                                   av.getIgnoreGapsConsensus());
-          }
+      if (av.getGlobalColourScheme() != null)
+      {
+        if (av.getGlobalColourScheme() instanceof UserColourScheme)
+        {
+          cs = new UserColourScheme(
+              ( (UserColourScheme) av.getGlobalColourScheme()).getColours());
+
+        }
+        else
+        {
+          cs = ColourSchemeProperty.getColour(sequences,
+                                              av.alignment.getWidth(),
+                                              ColourSchemeProperty.
+                                              getColourName(
+                                                  av.getGlobalColourScheme()));
+        }
 
-          SequenceGroup sg = new SequenceGroup(sequences, "",
-                                               cs, true, true,
-                                               false, 0, av.alignment.getWidth()-1);
+        cs.setThreshold(av.getGlobalColourScheme().getThreshold(),
+                        av.getIgnoreGapsConsensus());
+      }
 
-          sg.setName("JTreeGroup:"+sg.hashCode());
+      SequenceGroup sg = new SequenceGroup(sequences, "",
+                                           cs, true, true,
+                                           false, 0,
+                                           av.alignment.getWidth() - 1);
 
+      sg.setName("JTreeGroup:" + sg.hashCode());
 
-          if (  av.getGlobalColourScheme()!=null
-             && av.getGlobalColourScheme().conservationApplied())
-            {
-            Conservation c = new Conservation("Group",
-                                              ResidueProperties.propHash, 3,
-                                              sg.getSequences(null),
-                                              sg.getStartRes(),
-                                              sg.getEndRes());
+      if (av.getGlobalColourScheme() != null
+          && av.getGlobalColourScheme().conservationApplied())
+      {
+        Conservation c = new Conservation("Group",
+                                          ResidueProperties.propHash, 3,
+                                          sg.getSequences(null),
+                                          sg.getStartRes(),
+                                          sg.getEndRes());
 
-            c.calculate();
-            c.verdict(false, av.ConsPercGaps);
-            cs.setConservation(c);
+        c.calculate();
+        c.verdict(false, av.ConsPercGaps);
+        cs.setConservation(c);
 
-            sg.cs = cs;
+        sg.cs = cs;
 
-          }
+      }
 
-          av.alignment.addGroup(sg);
+      av.alignment.addGroup(sg);
 
-        }
+    }
 
   }
 
diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java
index 103c96b..6bb96f1 100755
--- a/src/jalview/appletgui/TreePanel.java
+++ b/src/jalview/appletgui/TreePanel.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -19,16 +19,15 @@
 
 package jalview.appletgui;
 
-import java.util.*;
-
-import java.awt.event.*;
 import java.awt.*;
+import java.awt.event.*;
 
 import jalview.analysis.*;
 import jalview.datamodel.*;
 import jalview.io.*;
 
-public class TreePanel extends Frame implements ActionListener, ItemListener
+public class TreePanel
+    extends Frame implements ActionListener, ItemListener
 {
   SequenceI[] seq;
   String type;
@@ -96,7 +95,6 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
     initTreePanel(av, type, pwtype, newtree);
   }
 
-
   void initTreePanel(AlignViewport av,
                      String type,
                      String pwtype,
@@ -110,7 +108,6 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
     treeCanvas = new TreeCanvas(av, scrollPane);
     scrollPane.add(treeCanvas);
 
-
     TreeLoader tl = new TreeLoader(newTree);
     tl.start();
 
@@ -122,7 +119,7 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
     // 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)
+    if (tree.seqData != null)
     {
       Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(av.
           getGapCharacter());
@@ -139,13 +136,16 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
       }
     }
     else
+    {
       System.out.println("Original Tree Data not available");
+    }
   }
 
-  class TreeLoader extends Thread
+  class TreeLoader
+      extends Thread
   {
     NewickFile newtree;
-    jalview.datamodel.AlignmentView odata=null;
+    jalview.datamodel.AlignmentView odata = null;
 
     public TreeLoader(NewickFile newtree)
     {
@@ -154,40 +154,44 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
 
     public void run()
     {
-      if(newtree!=null)
+      if (newtree != null)
       {
         if (odata == null)
+        {
           tree = new NJTree(av.alignment.getSequencesArray(),
                             newtree);
+        }
         else
+        {
           tree = new NJTree(av.alignment.getSequencesArray(), odata, newtree);
+        }
 
+      }
+      else
+      {
+        int start, end;
+        SequenceI[] seqs;
+        AlignmentView seqStrings = av.getAlignmentView(av.getSelectionGroup() != null);
+        if (av.getSelectionGroup() == null)
+        {
+          start = 0;
+          end = av.alignment.getWidth();
+          seqs = av.alignment.getSequencesArray();
         }
         else
         {
-          int start, end;
-          SequenceI [] seqs;
-          AlignmentView seqStrings = av.getAlignmentView(av.getSelectionGroup()!=null);
-          if(av.getSelectionGroup()==null)
-          {
-            start = 0;
-            end = av.alignment.getWidth();
-            seqs = av.alignment.getSequencesArray();
-          }
-          else
-          {
-            start = av.getSelectionGroup().getStartRes();
-            end = av.getSelectionGroup().getEndRes()+1;
-            seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
-          }
-
-          tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
+          start = av.getSelectionGroup().getStartRes();
+          end = av.getSelectionGroup().getEndRes() + 1;
+          seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
         }
 
+        tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
+      }
+
       tree.reCount(tree.getTopNode());
       tree.findHeight(tree.getTopNode());
       treeCanvas.setTree(tree);
-      if(newtree!=null)
+      if (newtree != null)
       {
         distanceMenu.setState(newtree.HasDistances());
         bootstrapMenu.setState(newtree.HasBootstrap());
@@ -195,7 +199,6 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
         treeCanvas.setShowDistances(newtree.HasDistances());
       }
 
-
       treeCanvas.repaint();
 
       av.setCurrentTree(tree);
@@ -205,32 +208,45 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
 
   public void actionPerformed(ActionEvent evt)
   {
-    if(evt.getSource()==newickOutput)
+    if (evt.getSource() == newickOutput)
+    {
       newickOutput_actionPerformed();
-    else if(evt.getSource()==fontSize)
+    }
+    else if (evt.getSource() == fontSize)
+    {
       fontSize_actionPerformed();
-    else if(evt.getSource()==inputData)
+    }
+    else if (evt.getSource() == inputData)
+    {
       showOriginalData();
+    }
   }
 
   public void itemStateChanged(ItemEvent evt)
   {
-    if(evt.getSource()==fitToWindow)
+    if (evt.getSource() == fitToWindow)
+    {
       treeCanvas.fitToWindow = fitToWindow.getState();
+    }
 
-    else if(evt.getSource()==distanceMenu)
+    else if (evt.getSource() == distanceMenu)
+    {
       treeCanvas.setShowDistances(distanceMenu.getState());
+    }
 
-    else if(evt.getSource()==bootstrapMenu)
+    else if (evt.getSource() == bootstrapMenu)
+    {
       treeCanvas.setShowBootstrap(bootstrapMenu.getState());
+    }
 
-    else if(evt.getSource()==placeholdersMenu)
+    else if (evt.getSource() == placeholdersMenu)
+    {
       treeCanvas.setMarkPlaceholders(placeholdersMenu.getState());
+    }
 
     treeCanvas.repaint();
   }
 
-
   public void newickOutput_actionPerformed()
   {
     jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
@@ -255,15 +271,14 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
 
   protected void fontSize_actionPerformed()
   {
-     if( treeCanvas==null )
-        return;
+    if (treeCanvas == null)
+    {
+      return;
+    }
 
     new FontChooser(this);
   }
 
-
-
-
   BorderLayout borderLayout1 = new BorderLayout();
   protected ScrollPane scrollPane = new ScrollPane();
   MenuBar jMenuBar1 = new MenuBar();
@@ -277,35 +292,37 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
   MenuItem newickOutput = new MenuItem();
   MenuItem inputData = new MenuItem();
 
-  private void jbInit() throws Exception {
-      setLayout(borderLayout1);
-      this.setBackground(Color.white);
-      this.setFont(new java.awt.Font("Verdana", 0, 12));
-      jMenu2.setLabel("View");
-      fontSize.setLabel("Font...");
-      fontSize.addActionListener(this);
-      bootstrapMenu.setLabel("Show Bootstrap Values");
-      bootstrapMenu.addItemListener(this);
-      distanceMenu.setLabel("Show Distances");
-      distanceMenu.addItemListener(this);
-      placeholdersMenu.setLabel("Mark Unassociated Leaves");
-      placeholdersMenu.addItemListener(this);
-      fitToWindow.setState(true);
-      fitToWindow.setLabel("Fit To Window");
-      fitToWindow.addItemListener(this);
-      fileMenu.setLabel("File");
-      newickOutput.setLabel("Newick Format");
-      newickOutput.addActionListener(this);
+  private void jbInit()
+      throws Exception
+  {
+    setLayout(borderLayout1);
+    this.setBackground(Color.white);
+    this.setFont(new java.awt.Font("Verdana", 0, 12));
+    jMenu2.setLabel("View");
+    fontSize.setLabel("Font...");
+    fontSize.addActionListener(this);
+    bootstrapMenu.setLabel("Show Bootstrap Values");
+    bootstrapMenu.addItemListener(this);
+    distanceMenu.setLabel("Show Distances");
+    distanceMenu.addItemListener(this);
+    placeholdersMenu.setLabel("Mark Unassociated Leaves");
+    placeholdersMenu.addItemListener(this);
+    fitToWindow.setState(true);
+    fitToWindow.setLabel("Fit To Window");
+    fitToWindow.addItemListener(this);
+    fileMenu.setLabel("File");
+    newickOutput.setLabel("Newick Format");
+    newickOutput.addActionListener(this);
     inputData.setLabel("Input Data...");
 
     add(scrollPane, BorderLayout.CENTER);
-      jMenuBar1.add(fileMenu);
-      jMenuBar1.add(jMenu2);
-      jMenu2.add(fitToWindow);
-      jMenu2.add(fontSize);
-      jMenu2.add(distanceMenu);
-      jMenu2.add(bootstrapMenu);
-      jMenu2.add(placeholdersMenu);
+    jMenuBar1.add(fileMenu);
+    jMenuBar1.add(jMenu2);
+    jMenu2.add(fitToWindow);
+    jMenu2.add(fontSize);
+    jMenu2.add(distanceMenu);
+    jMenu2.add(bootstrapMenu);
+    jMenu2.add(placeholdersMenu);
     fileMenu.add(newickOutput);
     fileMenu.add(inputData);
     inputData.addActionListener(this);
diff --git a/src/jalview/appletgui/UserDefinedColours.java b/src/jalview/appletgui/UserDefinedColours.java
index b9c0950..af08b75 100755
--- a/src/jalview/appletgui/UserDefinedColours.java
+++ b/src/jalview/appletgui/UserDefinedColours.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -87,35 +87,53 @@ public class UserDefinedColours
     setTargetColour(colour);
 
     okcancelPanel.setBounds(new Rectangle(0, 113, 400, 35));
-    frame.setTitle("User Defined Colours - "+label);
+    frame.setTitle("User Defined Colours - " + label);
     frame.setSize(420, 200);
   }
 
   public void actionPerformed(ActionEvent evt)
   {
-    if(evt.getSource()==okButton)
-     okButton_actionPerformed();
-   else if(evt.getSource()==applyButton)
+    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();
-}
+    }
+    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();
-}
+    if (evt.getSource() == rScroller)
+    {
+      rScroller_adjustmentValueChanged();
+    }
+    else if (evt.getSource() == gScroller)
+    {
+      gScroller_adjustmentValueChanged();
+    }
+    else if (evt.getSource() == bScroller)
+    {
+      bScroller_adjustmentValueChanged();
+    }
+  }
 
   void init()
   {
@@ -149,6 +167,7 @@ public class UserDefinedColours
 
     validate();
   }
+
   protected void rText_actionPerformed()
   {
     try
@@ -279,22 +298,27 @@ public class UserDefinedColours
   {
     if (caller != null)
     {
-      if(caller instanceof FeatureSettings)
-        ((FeatureSettings)caller).setUserColour
-            (originalLabel, new Color(R,G,B));
-      else if(caller instanceof AnnotationColourChooser)
+      if (caller instanceof FeatureSettings)
+      {
+        ( (FeatureSettings) caller).setUserColour
+            (originalLabel, new Color(R, G, B));
+      }
+      else if (caller instanceof AnnotationColourChooser)
       {
         if (originalLabel.equals("Min Colour"))
+        {
           ( (AnnotationColourChooser) caller).minColour_actionPerformed
               (new Color(R, G, B));
+        }
         else
+        {
           ( (AnnotationColourChooser) caller).maxColour_actionPerformed
               (new Color(R, G, B));
+        }
       }
       return;
     }
 
-
     Color[] newColours = new Color[24];
     for (int i = 0; i < 24; i++)
     {
@@ -303,10 +327,12 @@ public class UserDefinedColours
     }
 
     UserColourScheme ucs = new UserColourScheme(newColours);
-    if(ap!=null)
+    if (ap != null)
+    {
       ucs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
+    }
 
-    if(ap!=null)
+    if (ap != null)
     {
       if (seqGroup != null)
       {
@@ -319,29 +345,34 @@ public class UserDefinedColours
       ap.seqPanel.seqCanvas.img = null;
       ap.repaint();
     }
-    else if(pdbcanvas!=null)
+    else if (pdbcanvas != null)
     {
       pdbcanvas.pdb.setColours(ucs);
       pdbcanvas.updateSeqColours();
     }
   }
 
-
   protected void cancelButton_actionPerformed()
   {
     if (caller != null)
     {
-      if(caller instanceof FeatureSettings)
-        ((FeatureSettings)caller).setUserColour
+      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);
+        }
       }
       frame.setVisible(false);
       return;
@@ -356,7 +387,7 @@ public class UserDefinedColours
 
     UserColourScheme ucs = new UserColourScheme(newColours);
 
-   if(ap!=null)
+    if (ap != null)
     {
       if (seqGroup != null)
       {
@@ -368,7 +399,7 @@ public class UserDefinedColours
       }
       ap.repaint();
     }
-    else if(pdbcanvas!=null)
+    else if (pdbcanvas != null)
     {
       pdbcanvas.pdb.setColours(ucs);
     }
@@ -376,7 +407,6 @@ public class UserDefinedColours
     frame.setVisible(false);
   }
 
-
   protected Panel buttonPanel = new Panel();
   protected GridLayout gridLayout = new GridLayout();
   Panel okcancelPanel = new Panel();
@@ -394,82 +424,84 @@ public class UserDefinedColours
   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);
-}
+  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 0927272..72fec6c 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -19,14 +19,9 @@
 package jalview.bin;
 
 import java.io.*;
-
 import java.util.*;
 
-import org.apache.log4j.Logger;
-import org.apache.log4j.SimpleLayout;
-import org.apache.log4j.Level;
-import org.apache.log4j.ConsoleAppender;
-
+import org.apache.log4j.*;
 
 /**
  * Stores and retrieves Jalview Application Properties
@@ -51,278 +46,293 @@ public class Cache
    */
   public static Logger log;
 
-    /** Jalview Properties */
-    public static Properties applicationProperties = new Properties();
+  /** Jalview Properties */
+  public static Properties applicationProperties = new Properties();
 
-    /** Default file is  ~/.jalview_properties */
-    static String propertiesFile;
+  /** Default file is  ~/.jalview_properties */
+  static String propertiesFile;
 
-    public static void initLogger()
+  public static void initLogger()
+  {
+    try
+    {
+      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())));
+      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())));
+      ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),
+                                               "System.err");
+      ap.setName("JalviewLogger");
+
+      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)
     {
-      try
-      {
-        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())));
-        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())));
-        ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),
-                                                 "System.err");
-        ap.setName("JalviewLogger");
-
-        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)
-      {
       System.err.println("Problems initializing the log4j system\n");
-      }
     }
+  }
 
-
-    /** Called when Jalview is started */
-    public static void loadProperties(String propsFile)
+  /** Called when Jalview is started */
+  public static void loadProperties(String propsFile)
+  {
+    propertiesFile = propsFile;
+    if (propsFile == null)
     {
-        propertiesFile = propsFile;
-        if (propsFile == null)
-        {
-          propertiesFile = System.getProperty("user.home") +File.separatorChar+".jalview_properties";
-        }
-
-        try
-        {
-            FileInputStream fis = new FileInputStream(propertiesFile);
-            applicationProperties.load(fis);
-            applicationProperties.remove("LATEST_VERSION");
-            applicationProperties.remove("VERSION");
-            fis.close();
-        }
-        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.setProperty("http.proxyPort", getDefault("PROXY_PORT", null));
-      }
+      propertiesFile = System.getProperty("user.home") + File.separatorChar +
+          ".jalview_properties";
+    }
 
-        // FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar
-        // MUST FOLLOW READING OF LOCAL PROPERTIES FILE AS THE
-        // VERSION MAY HAVE CHANGED SINCE LAST USING JALVIEW
-         try
-         {
-             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)
-         {
-           System.out.println("Error reading build details: "+ex);
-           applicationProperties.remove("VERSION");
-        }
+    try
+    {
+      FileInputStream fis = new FileInputStream(propertiesFile);
+      applicationProperties.load(fis);
+      applicationProperties.remove("LATEST_VERSION");
+      applicationProperties.remove("VERSION");
+      fis.close();
+    }
+    catch (Exception ex)
+    {
+      System.out.println("Error reading properties file: " + ex);
+    }
 
-        String jnlpVersion = System.getProperty("jalview.version");
-        String codeVersion = getProperty("VERSION");
+    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.setProperty("http.proxyPort", getDefault("PROXY_PORT", null));
+    }
 
+    // FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar
+    // MUST FOLLOW READING OF LOCAL PROPERTIES FILE AS THE
+    // VERSION MAY HAVE CHANGED SINCE LAST USING JALVIEW
+    try
+    {
+      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)
+    {
+      System.out.println("Error reading build details: " + ex);
+      applicationProperties.remove("VERSION");
+    }
 
-        if(codeVersion==null)
-        {
-          // THIS SHOULD ONLY BE THE CASE WHEN TESTING!!
-          codeVersion = "Test";
-          jnlpVersion = "Test";
-        }
+    String jnlpVersion = System.getProperty("jalview.version");
+    String codeVersion = getProperty("VERSION");
 
+    if (codeVersion == null)
+    {
+      // THIS SHOULD ONLY BE THE CASE WHEN TESTING!!
+      codeVersion = "Test";
+      jnlpVersion = "Test";
+    }
 
-        System.out.println("Jalview Version: "+codeVersion);
+    System.out.println("Jalview Version: " + codeVersion);
 
+    // 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")))
+    {
 
-        // 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")))
+      class VersionChecker
+          extends Thread
+      {
+        public void run()
         {
-
-          class VersionChecker
-              extends Thread
+          String jnlpVersion = null;
+          try
           {
-            public void run()
+            java.net.URL url = new java.net.URL(
+                "http://www.jalview.org/webstart/jalview.jnlp");
+            BufferedReader in = new BufferedReader(new InputStreamReader(url.
+                openStream()));
+            String line = null;
+            while ( (line = in.readLine()) != null)
             {
-              String jnlpVersion = null;
-              try
+              if (line.indexOf("jalview.version") == -1)
               {
-                java.net.URL url = new java.net.URL(
-                    "http://www.jalview.org/webstart/jalview.jnlp");
-                BufferedReader in = new BufferedReader(new InputStreamReader(url.
-                    openStream()));
-                String line = null;
-                while ( (line = in.readLine()) != null)
-                {
-                  if (line.indexOf("jalview.version") == -1)
-                    continue;
-
-                  line = line.substring(line.indexOf("value=") + 7);
-                  line = line.substring(0, line.lastIndexOf("\""));
-                  jnlpVersion = line;
-                  break;
-                }
-              }
-              catch (Exception ex)
-              {
-                System.out.println(ex);
-                jnlpVersion = getProperty("VERSION");
+                continue;
               }
 
-              setProperty("LATEST_VERSION", jnlpVersion);
+              line = line.substring(line.indexOf("value=") + 7);
+              line = line.substring(0, line.lastIndexOf("\""));
+              jnlpVersion = line;
+              break;
             }
           }
+          catch (Exception ex)
+          {
+            System.out.println(ex);
+            jnlpVersion = getProperty("VERSION");
+          }
 
-          VersionChecker vc = new VersionChecker();
-          vc.start();
+          setProperty("LATEST_VERSION", jnlpVersion);
         }
-        else
-        {
-          if(jnlpVersion!=null)
-            setProperty("LATEST_VERSION", jnlpVersion);
-          else
-          applicationProperties.remove("LATEST_VERSION");
-        }
-
-        setProperty("VERSION", codeVersion);
+      }
 
-        //LOAD USERDEFINED COLOURS
-        jalview.gui.UserDefinedColours.initUserColourSchemes( getProperty("USER_DEFINED_COLOURS"));
-        jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER", false);
+      VersionChecker vc = new VersionChecker();
+      vc.start();
     }
+    else
+    {
+      if (jnlpVersion != null)
+      {
+        setProperty("LATEST_VERSION", jnlpVersion);
+      }
+      else
+      {
+        applicationProperties.remove("LATEST_VERSION");
+      }
+    }
+
+    setProperty("VERSION", codeVersion);
+
+    //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
+   *
+   * @return Property value
+   */
+  public static String getProperty(String key)
+  {
+    return applicationProperties.getProperty(key);
+  }
 
+  /** These methods are used when checking if the saved preference
+   * is different to the default setting
+   */
 
-    /**
-     * 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)
+  public static boolean getDefault(String property, boolean def)
+  {
+    String string = getProperty(property);
+    if (string != null)
     {
-        return applicationProperties.getProperty(key);
+      def = Boolean.valueOf(string).booleanValue();
     }
 
+    return def;
+  }
 
-    /** These methods are used when checking if the saved preference
-     * is different to the default setting
-     */
-
-    public static boolean getDefault(String property, boolean def)
+  /** These methods are used when checking if the saved preference
+   * is different to the default setting
+   */
+  public static String getDefault(String property, String def)
+  {
+    String string = getProperty(property);
+    if (string != null)
     {
-      String string = getProperty(property);
-      if (string != null)
-      {
-        def = Boolean.valueOf(string).booleanValue();
-      }
-
-      return def;
+      return string;
     }
 
-    /** These methods are used when checking if the saved preference
-    * is different to the default setting
-    */
-    public static String getDefault(String property, String def)
-    {
-      String string = getProperty(property);
-      if (string != null)
-      {
-        return string;
-      }
+    return def;
+  }
 
-      return def;
+  /**
+   * Stores property in the file "HOME_DIR/.jalview_properties"
+   *
+   * @param key Name of object
+   * @param obj String value of property
+   *
+   * @return String value of property
+   */
+  public static String setProperty(String key, String obj)
+  {
+    try
+    {
+      FileOutputStream out = new FileOutputStream(propertiesFile);
+      applicationProperties.setProperty(key, obj);
+      applicationProperties.store(out, "---JalviewX Properties File---");
+      out.close();
     }
+    catch (Exception ex)
+    {
+      System.out.println("Error setting property: " + key + " " + obj + "\n" +
+                         ex);
+    }
+    return obj;
+  }
 
-
-    /**
-     * Stores property in the file "HOME_DIR/.jalview_properties"
-     *
-     * @param key Name of object
-     * @param obj String value of property
-     *
-     * @return String value of property
-     */
-    public static String setProperty(String key, String obj)
+  public static void saveProperties()
+  {
+    try
     {
-        try
-        {
-            FileOutputStream out = new FileOutputStream(propertiesFile);
-            applicationProperties.setProperty(key, obj);
-            applicationProperties.store(out, "---JalviewX Properties File---");
-            out.close();
-        }
-        catch (Exception ex)
-        {   System.out.println("Error setting property: "+key+" "+obj+"\n"+ex);   }
-        return obj;
+      FileOutputStream out = new FileOutputStream(propertiesFile);
+      applicationProperties.store(out, "---JalviewX Properties File---");
+      out.close();
     }
+    catch (Exception ex)
+    {
+      System.out.println("Error saving properties: " + ex);
+    }
+  }
 
-    public static void saveProperties()
+  /**
+   * 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()
+  {
+    if (vamsasJarsArePresent == -1)
     {
-        try
+      try
+      {
+        if (jalview.jbgui.GDesktop.class.getClassLoader().loadClass(
+            "uk.ac.vamsas.client.VorbaId") != null)
         {
-            FileOutputStream out = new FileOutputStream(propertiesFile);
-            applicationProperties.store(out, "---JalviewX Properties File---");
-            out.close();
-        }
-        catch (Exception ex)
-        {  System.out.println("Error saving properties: "+ex);  }
-    }
-    /**
-     * 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() {
-      if (vamsasJarsArePresent==-1) {
-        try {
-          if (jalview.jbgui.GDesktop.class.getClassLoader().loadClass("uk.ac.vamsas.client.VorbaId")!=null) {
-            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.addAppender(log.getAppender("JalviewLogger"));
-            // Tell the user that debug is enabled
-            lvclient.debug("Jalview Vamsas Client Debugging Output Follows.");
-          }
-        } catch (Exception e) {
-          vamsasJarsArePresent=0;
-          jalview.bin.Cache.log.debug("Vamsas Classes are not present");
+          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.addAppender(log.getAppender("JalviewLogger"));
+          // Tell the user that debug is enabled
+          lvclient.debug("Jalview Vamsas Client Debugging Output Follows.");
         }
       }
-      return (vamsasJarsArePresent>0);
+      catch (Exception e)
+      {
+        vamsasJarsArePresent = 0;
+        jalview.bin.Cache.log.debug("Vamsas Classes are not present");
+      }
     }
+    return (vamsasJarsArePresent > 0);
+  }
 
 }
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 6079790..3c6fc39 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,12 +18,11 @@
  */
 package jalview.bin;
 
-import jalview.gui.*;
+import java.util.*;
 
 import javax.swing.*;
 
-import java.util.Vector;
-
+import jalview.gui.*;
 
 /**
  * Main class for Jalview Application
@@ -36,326 +35,341 @@ import java.util.Vector;
 public class Jalview
 {
 
-    /**
-     * main class for Jalview application
-     *
-     * @param args open <em>filename</em>
-     */
-    public static void main(String[] args)
+  /**
+   * main class for Jalview application
+   *
+   * @param args open <em>filename</em>
+   */
+  public static void main(String[] args)
+  {
+    System.out.println("Java version: " + System.getProperty("java.version"));
+    System.out.println(System.getProperty("os.arch") + " "
+                       + System.getProperty("os.name") + " "
+                       + System.getProperty("os.version"));
+
+    ArgsParser aparser = new ArgsParser(args);
+    boolean headless = false;
+
+    if (aparser.contains("help") || aparser.contains("h"))
     {
-      System.out.println("Java version: "+System.getProperty("java.version"));
-      System.out.println(System.getProperty("os.arch")+" "
-                         +System.getProperty("os.name")+" "
-                         +System.getProperty("os.version"));
+      System.out.println(
+          "Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
+          + "-nodisplay\tRun Jalview without User Interface.\n"
+          +
+          "-props FILE\tUse the given Jalview properties file instead of users default.\n"
+          +
+          "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
+          +
+          "-features FILE\tUse the given file to mark features on the alignment.\n"
+          + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
+          + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
+          + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
+          + "-msf FILE\tCreate alignment file FILE in MSF format.\n"
+          + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
+          + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
+          + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
+          + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
+          + "-png FILE\tCreate PNG image FILE from alignment.\n"
+          +
+          "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
+          + "-eps FILE\tCreate EPS file FILE from alignment."
+          + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires."
+          + "\n\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
+      System.exit(0);
+    }
 
+    Cache.loadProperties(aparser.getValue("props")); // must do this before anything else!
 
-      ArgsParser aparser = new ArgsParser(args);
-      boolean headless = false;
+    if (aparser.contains("nodisplay"))
+    {
+      System.setProperty("java.awt.headless", "true");
+    }
+    if (System.getProperty("java.awt.headless") != null
+        && System.getProperty("java.awt.headless").equals("true"))
+    {
+      headless = true;
+    }
+
+    try
+    {
+      Cache.initLogger();
+    }
+    catch (java.lang.NoClassDefFoundError error)
+    {
+      error.printStackTrace();
+      System.out.println(
+          "\nEssential logging libraries not found."
+          + "\nUse: java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview");
+      System.exit(0);
+    }
 
-      if( aparser.contains("help") || aparser.contains("h") )
+    Desktop desktop = null;
+
+    try
+    {
+      UIManager.setLookAndFeel(
+          UIManager.getSystemLookAndFeelClassName()
+          //        UIManager.getCrossPlatformLookAndFeelClassName()
+          //"com.sun.java.swing.plaf.gtk.GTKLookAndFeel"
+          //"javax.swing.plaf.metal.MetalLookAndFeel"
+          //"com.sun.java.swing.plaf.windows.WindowsLookAndFeel"
+          //"com.sun.java.swing.plaf.motif.MotifLookAndFeel"
+
+          );
+    }
+    catch (Exception ex)
+    {}
+    if (!headless)
+    {
+      desktop = new Desktop();
+      desktop.setVisible(true);
+      desktop.discoverer.start();
+      String url = aparser.getValue("questionnaire");
+      if (url != null)
       {
-        System.out.println("Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
-                           +"-nodisplay\tRun Jalview without User Interface.\n"
-                           +"-props FILE\tUse the given Jalview properties file instead of users default.\n"
-                           +"-annotations FILE\tAdd precalculated annotations to the alignment.\n"
-                           +"-features FILE\tUse the given file to mark features on the alignment.\n"
-                           +"-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
-                           +"-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
-                           +"-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
-                           +"-msf FILE\tCreate alignment file FILE in MSF format.\n"
-                           +"-pileup FILE\tCreate alignment file FILE in Pileup format\n"
-                           +"-pir FILE\tCreate alignment file FILE in PIR format.\n"
-                           +"-blc FILE\tCreate alignment file FILE in BLC format.\n"
-                           +"-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
-                           +"-png FILE\tCreate PNG image FILE from alignment.\n"
-                           +"-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
-                           +"-eps FILE\tCreate EPS file FILE from alignment."
-                           +"-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires."
-            +"\n\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
-        System.exit(0);
-          }
+        // Start the desktop questionnaire prompter with the specified questionnaire
+        Cache.log.debug("Starting questionnaire url at " + url);
+        desktop.checkForQuestionnaire(url);
+      }
+      else
+      {
+        if (Cache.getProperty("NOQUESTIONNAIRES") == null)
+        {
+          // Start the desktop questionnaire prompter with the specified questionnaire
+          // String defurl = "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl"; //
+          String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl";
+          Cache.log.debug("Starting questionnaire with default url: " + defurl);
+          desktop.checkForQuestionnaire(defurl);
 
-          Cache.loadProperties(aparser.getValue("props")); // must do this before anything else!
+        }
+      }
 
-          if (aparser.contains("nodisplay"))
-          {
-            System.setProperty("java.awt.headless", "true");
-          }
-          if (System.getProperty("java.awt.headless") != null
-              && System.getProperty("java.awt.headless").equals("true"))
-          {
-            headless = true;
-          }
+    }
 
-          try
-          {
-            Cache.initLogger();
-          }
-          catch (java.lang.NoClassDefFoundError error)
+    String file = null, protocol = null, format = null, data = null;
+    jalview.io.FileLoader fileLoader = new jalview.io.FileLoader();
+
+    file = aparser.getValue("open");
+
+    if (file == null && desktop == null)
+    {
+      System.out.println("No files to open!");
+      System.exit(1);
+    }
+
+    if (file != null)
+    {
+      System.out.println("Opening file: " + file);
+
+      if (!file.startsWith("http://"))
+      {
+        if (! (new java.io.File(file)).exists())
+        {
+          System.out.println("Can't find " + file);
+          if (headless)
           {
-            error.printStackTrace();
-            System.out.println(
-                "\nEssential logging libraries not found."
-                +"\nUse: java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview");
-            System.exit(0);
+            System.exit(1);
           }
+        }
+      }
+
+      protocol = "File";
+
+      if (file.indexOf("http:") > -1 || file.indexOf("file:") > -1)
+      {
+        protocol = "URL";
+      }
+
+      if (file.endsWith(".jar"))
+      {
+        format = "Jalview";
+      }
+      else
+      {
+        format = new jalview.io.IdentifyFile().Identify(file, protocol);
+      }
+
+      AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol, format);
 
-        Desktop desktop = null;
+      if (af == null)
+      {
+        System.out.println("error");
+        return;
+      }
+
+      data = aparser.getValue("colour");
+      if (data != null)
+      {
+        data.replaceAll("%20", " ");
 
+        jalview.schemes.ColourSchemeI cs =
+            jalview.schemes.ColourSchemeProperty.getColour(af.getViewport().
+            getAlignment(), data);
 
-        try
+        if (cs == null)
         {
-          UIManager.setLookAndFeel(
-              UIManager.getSystemLookAndFeelClassName()
-              //        UIManager.getCrossPlatformLookAndFeelClassName()
-      //"com.sun.java.swing.plaf.gtk.GTKLookAndFeel"
-      //"javax.swing.plaf.metal.MetalLookAndFeel"
-      //"com.sun.java.swing.plaf.windows.WindowsLookAndFeel"
-      //"com.sun.java.swing.plaf.motif.MotifLookAndFeel"
-
-              );
+          jalview.schemes.UserColourScheme ucs
+              = new jalview.schemes.UserColourScheme("white");
+          ucs.parseAppletParameter(data);
+          cs = ucs;
         }
-        catch (Exception ex)
-        {}
-          if (!headless)
-          {
-            desktop = new Desktop();
-            desktop.setVisible(true);
-            desktop.discoverer.start();
-            String url = aparser.getValue("questionnaire");
-            if (url!=null) {
-                // Start the desktop questionnaire prompter with the specified questionnaire
-                Cache.log.debug("Starting questionnaire url at "+url);
-                desktop.checkForQuestionnaire(url);
-            } else {
-                if (Cache.getProperty("NOQUESTIONNAIRES")==null) {
-                    // Start the desktop questionnaire prompter with the specified questionnaire
-                    // String defurl = "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl"; // 
-                    String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl";
-                    Cache.log.debug("Starting questionnaire with default url: "+defurl);
-                    desktop.checkForQuestionnaire(defurl);
-                        
-                }
-            }
 
-          }
+        System.out.println("colour is " + data);
+        af.changeColour(cs);
+      }
 
-         String file = null, protocol = null, format = null, data=null;
-         jalview.io.FileLoader fileLoader = new jalview.io.FileLoader();
+      // Must maintain ability to use the groups flag
+      data = aparser.getValue("groups");
+      if (data != null)
+      {
+        af.parseFeaturesFile(data, protocol);
+        System.out.println("Added " + data);
+      }
+      data = aparser.getValue("features");
+      if (data != null)
+      {
+        af.parseFeaturesFile(data, protocol);
+        System.out.println("Added " + data);
+      }
 
-          file = aparser.getValue("open");
+      data = aparser.getValue("annotations");
+      if (data != null)
+      {
+        af.loadJalviewDataFile(data);
+        System.out.println("Added " + data);
+      }
 
-          if (file == null && desktop==null)
-          {
-            System.out.println("No files to open!");
-            System.exit(1);
-          }
+      String imageName = "unnamed.png";
+      while (aparser.getSize() > 1)
+      {
+        format = aparser.nextValue();
+        file = aparser.nextValue();
 
-          if(file!=null)
-          {
-            System.out.println("Opening file: " + file);
-
-            if (!file.startsWith("http://"))
-            {
-              if (! (new java.io.File(file)).exists())
-              {
-                System.out.println("Can't find " + file);
-                if(headless)
-                  System.exit(1);
-              }
-            }
-
-            protocol = "File";
-
-            if (file.indexOf("http:") > -1 || file.indexOf("file:") >-1)
-            {
-              protocol = "URL";
-            }
-
-
-
-            if (file.endsWith(".jar"))
-              format = "Jalview";
-            else
-              format = new jalview.io.IdentifyFile().Identify(file, protocol);
-
-
-
-            AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol, format);
-
-            if(af==null)
-            {
-              System.out.println("error");
-              return;
-            }
-
-            data = aparser.getValue("colour");
-            if(data!=null)
-            {
-              data.replaceAll("%20", " ");
-
-              jalview.schemes.ColourSchemeI cs =
-                  jalview.schemes.ColourSchemeProperty.getColour(af.getViewport().
-                  getAlignment(), data);
-
-              if(cs == null)
-              {
-                jalview.schemes.UserColourScheme ucs
-                    = new jalview.schemes.UserColourScheme("white");
-                ucs.parseAppletParameter(data);
-                cs = ucs;
-              }
-
-              System.out.println("colour is " + data);
-              af.changeColour( cs );
-            }
-
-
-            // Must maintain ability to use the groups flag
-            data = aparser.getValue("groups");
-            if (data != null)
-            {
-              af.parseFeaturesFile(data, protocol);
-              System.out.println("Added "+data);
-            }
-            data = aparser.getValue("features");
-            if (data != null)
-            {
-              af.parseFeaturesFile(data, protocol);
-              System.out.println("Added "+data);
-            }
-
-            data = aparser.getValue("annotations");
-            if (data != null)
-            {
-              af.loadJalviewDataFile(data);
-              System.out.println("Added "+data);
-            }
-
-
-            String imageName = "unnamed.png";
-            while (aparser.getSize() > 1)
-            {
-              format = aparser.nextValue();
-              file = aparser.nextValue();
-
-              if (format.equalsIgnoreCase("png"))
-              {
-                af.createPNG(new java.io.File(file));
-                imageName = (new java.io.File(file)).getName();
-                System.out.println("Creating PNG image: " + file);
-                continue;
-              }
-              else if (format.equalsIgnoreCase("imgMap"))
-              {
-                af.createImageMap(new java.io.File(file), imageName);
-                System.out.println("Creating image map: " + file);
-                continue;
-              }
-              else if (format.equalsIgnoreCase("eps"))
-              {
-                System.out.println("Creating EPS file: " + file);
-                af.createEPS(new java.io.File(file));
-                continue;
-              }
-
-              if (af.saveAlignment(file, format))
-                System.out.println("Written alignment in " + format +
-                                   " format to " + file);
-              else
-                System.out.println("Error writing file " + file + " in " + format +
-                                   " format!!");
-
-            }
-
-            while (aparser.getSize() > 0)
-            {
-              System.out.println("Unknown arg: " + aparser.nextValue());
-            }
-          }
+        if (format.equalsIgnoreCase("png"))
+        {
+          af.createPNG(new java.io.File(file));
+          imageName = (new java.io.File(file)).getName();
+          System.out.println("Creating PNG image: " + file);
+          continue;
+        }
+        else if (format.equalsIgnoreCase("imgMap"))
+        {
+          af.createImageMap(new java.io.File(file), imageName);
+          System.out.println("Creating image map: " + file);
+          continue;
+        }
+        else if (format.equalsIgnoreCase("eps"))
+        {
+          System.out.println("Creating EPS file: " + file);
+          af.createEPS(new java.io.File(file));
+          continue;
+        }
 
-        // We'll only open the default file if the desktop is visible.
-        // And the user
-        //////////////////////
-          if (
-              !headless
-          && file==null
-          && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true)
-                    )
-          {
+        if (af.saveAlignment(file, format))
+        {
+          System.out.println("Written alignment in " + format +
+                             " format to " + file);
+        }
+        else
+        {
+          System.out.println("Error writing file " + file + " in " + format +
+                             " format!!");
+        }
+
+      }
+
+      while (aparser.getSize() > 0)
+      {
+        System.out.println("Unknown arg: " + aparser.nextValue());
+      }
+    }
+
+    // We'll only open the default file if the desktop is visible.
+    // And the user
+    //////////////////////
+    if (
+        !headless
+        && file == null
+        && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true)
+        )
+    {
 
-            file = jalview.bin.Cache.getDefault("STARTUP_FILE",
-                                                "http://www.jalview.org/examples/exampleFile.jar");
+      file = jalview.bin.Cache.getDefault("STARTUP_FILE",
+                                          "http://www.jalview.org/examples/exampleFile.jar");
 
-            protocol = "File";
+      protocol = "File";
 
-            if (file.indexOf("http:") > -1)
-            {
-              protocol = "URL";
-            }
+      if (file.indexOf("http:") > -1)
+      {
+        protocol = "URL";
+      }
 
-            if (file.endsWith(".jar"))
-            {
-              format = "Jalview";
-            }
-            else
-            {
-              format = new jalview.io.IdentifyFile().Identify(file, protocol);
-            }
+      if (file.endsWith(".jar"))
+      {
+        format = "Jalview";
+      }
+      else
+      {
+        format = new jalview.io.IdentifyFile().Identify(file, protocol);
+      }
 
-            fileLoader.LoadFile(file, protocol, format);
+      fileLoader.LoadFile(file, protocol, format);
 
-          }
     }
+  }
 }
 
- class ArgsParser
- {
-   Vector vargs = null;
-   public ArgsParser(String [] args)
-   {
-     vargs = new Vector();
-     for (int i = 0; i < args.length; i++)
-     {
-       String arg = args[i].trim();
-       if (arg.charAt(0) == '-')
-         arg = arg.substring(1);
-       vargs.addElement(arg);
-     }
-   }
-
-   public String getValue(String arg)
-   {
-     int index = vargs.indexOf(arg);
-     String ret = null;
-     if (index != -1)
-     {
-       ret = vargs.elementAt(index + 1).toString();
-       vargs.removeElementAt(index);
-       vargs.removeElementAt(index);
-     }
-     return ret;
-   }
-
-   public boolean contains(String arg)
-   {
-     if(vargs.contains(arg))
-     {
-       vargs.removeElement(arg);
-       return true;
-     }
-     else
-       return false;
-   }
-
-   public String nextValue()
-   {
-     return  vargs.remove(0).toString();
-   }
-
-   public int getSize()
-   {
-     return vargs.size();
-   }
-
- }
+class ArgsParser
+{
+  Vector vargs = null;
+  public ArgsParser(String[] args)
+  {
+    vargs = new Vector();
+    for (int i = 0; i < args.length; i++)
+    {
+      String arg = args[i].trim();
+      if (arg.charAt(0) == '-')
+      {
+        arg = arg.substring(1);
+      }
+      vargs.addElement(arg);
+    }
+  }
+
+  public String getValue(String arg)
+  {
+    int index = vargs.indexOf(arg);
+    String ret = null;
+    if (index != -1)
+    {
+      ret = vargs.elementAt(index + 1).toString();
+      vargs.removeElementAt(index);
+      vargs.removeElementAt(index);
+    }
+    return ret;
+  }
+
+  public boolean contains(String arg)
+  {
+    if (vargs.contains(arg))
+    {
+      vargs.removeElement(arg);
+      return true;
+    }
+    else
+    {
+      return false;
+    }
+  }
+
+  public String nextValue()
+  {
+    return vargs.remove(0).toString();
+  }
+
+  public int getSize()
+  {
+    return vargs.size();
+  }
+
+}
diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 89c0167..e6bb685 100755
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -1,35 +1,31 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 jalview.bin;
 
-import jalview.appletgui.AlignFrame;
-
-import jalview.datamodel.*;
-
-import jalview.io.*;
-
 import java.applet.*;
 
 import java.awt.*;
 import java.awt.event.*;
-import jalview.appletgui.FeatureSettings;
 
+import jalview.appletgui.*;
+import jalview.datamodel.*;
+import jalview.io.*;
 
 /**
  * Jalview Applet. Runs in Java 1.18 runtime
@@ -37,7 +33,8 @@ import jalview.appletgui.FeatureSettings;
  * @author $author$
  * @version $Revision$
  */
-public class JalviewLite extends Applet
+public class JalviewLite
+    extends Applet
 {
 
   ///////////////////////////////////////////
@@ -45,477 +42,516 @@ public class JalviewLite extends Applet
   //externally, eg via javascript in HTML page
 
   public String getSelectedSequences()
+  {
+    StringBuffer result = new StringBuffer("");
+
+    if (initialAlignFrame.viewport.getSelectionGroup() != null)
     {
-      StringBuffer result = new StringBuffer("");
+      SequenceI[] seqs = initialAlignFrame.viewport.getSelectionGroup().
+          getSequencesInOrder(
+              initialAlignFrame.viewport.getAlignment());
 
-      if(initialAlignFrame.viewport.getSelectionGroup()!=null)
+      for (int i = 0; i < seqs.length; i++)
       {
-        SequenceI[] seqs = initialAlignFrame.viewport.getSelectionGroup().
-            getSequencesInOrder(
-                initialAlignFrame.viewport.getAlignment());
-
-        for (int i = 0; i < seqs.length; i++)
-          result.append(seqs[i].getName() + "¬");
+        result.append(seqs[i].getName() + "¬");
       }
+    }
+
+    return result.toString();
+  }
+
+  public String getAlignment(String format)
+  {
+    return getAlignment(format, "true");
+  }
 
-      return result.toString();
+  public String getAlignment(String format, String suffix)
+  {
+    try
+    {
+      boolean seqlimits = suffix.equalsIgnoreCase("true");
+
+      String reply = new AppletFormatAdapter().formatSequences(format,
+          currentAlignFrame.viewport.getAlignment(), seqlimits);
+      return reply;
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+      return "Error retrieving alignment in " + format + " format. ";
     }
+  }
 
-    public String getAlignment(String format)
+  public void loadAnnotation(String annotation)
+  {
+    if (new AnnotationFile().readAnnotationFile(
+        currentAlignFrame.getAlignViewport().getAlignment(), annotation,
+        AppletFormatAdapter.PASTE))
+    {
+      currentAlignFrame.alignPanel.fontChanged();
+      currentAlignFrame.alignPanel.setScrollValues(0, 0);
+    }
+    else
     {
-      return getAlignment(format, "true");
+      currentAlignFrame.parseFeaturesFile(annotation, AppletFormatAdapter.PASTE);
     }
+  }
+
+  public String getFeatures(String format)
+  {
+    return currentAlignFrame.outputFeatures(false, format);
+  }
+
+  public String getAnnotation()
+  {
+    return currentAlignFrame.outputAnnotations(false);
+  }
+
+  public void loadAlignment(String text, String title)
+  {
+    Alignment al = null;
+    String format = new IdentifyFile().Identify(text, AppletFormatAdapter.PASTE);
+    try
+    {
+      al = new AppletFormatAdapter().readFile(text,
+                                              AppletFormatAdapter.PASTE,
+                                              format);
+      if (al.getHeight() > 0)
+      {
+        new AlignFrame(al, this, title, false);
+      }
+    }
+    catch (java.io.IOException ex)
+    {
+      ex.printStackTrace();
+    }
+  }
+
+  ////////////////////////////////////////////////
+  ////////////////////////////////////////////////
+
+
 
-    public String getAlignment(String format, String suffix)
+  static int lastFrameX = 200;
+  static int lastFrameY = 200;
+  boolean fileFound = true;
+  String file = "No file";
+  Button launcher = new Button("Start Jalview");
+
+  //The currentAlignFrame is static, it will change
+  //if and when the user selects a new window
+  public static AlignFrame currentAlignFrame;
+
+  //This is the first frame to be displayed, and does not change
+  AlignFrame initialAlignFrame;
+
+  boolean embedded = false;
+
+  /**
+   * init method for Jalview Applet
+   */
+  public void init()
+  {
+    int r = 255;
+    int g = 255;
+    int b = 255;
+    String param = getParameter("RGB");
+
+    if (param != null)
     {
       try
       {
-        boolean seqlimits = suffix.equalsIgnoreCase("true");
-
-        String reply = new AppletFormatAdapter().formatSequences(format,
-            currentAlignFrame.viewport.getAlignment(), seqlimits);
-        return reply;
+        r = Integer.parseInt(param.substring(0, 2), 16);
+        g = Integer.parseInt(param.substring(2, 4), 16);
+        b = Integer.parseInt(param.substring(4, 6), 16);
       }
       catch (Exception ex)
       {
-        ex.printStackTrace();
-        return "Error retrieving alignment in " + format + " format. ";
+        r = 255;
+        g = 255;
+        b = 255;
       }
     }
 
-    public void loadAnnotation(String annotation)
+    param = getParameter("label");
+    if (param != null)
+    {
+      launcher.setLabel(param);
+    }
+
+    this.setBackground(new Color(r, g, b));
+
+    file = getParameter("file");
+
+    if (file == null)
     {
-      if (new AnnotationFile().readAnnotationFile(
-          currentAlignFrame.getAlignViewport().getAlignment(), annotation,
-          AppletFormatAdapter.PASTE))
+      //Maybe the sequences are added as parameters
+      StringBuffer data = new StringBuffer("PASTE");
+      int i = 1;
+      while ( (file = getParameter("sequence" + i)) != null)
       {
-        currentAlignFrame.alignPanel.fontChanged();
-        currentAlignFrame.alignPanel.setScrollValues(0, 0);
+        data.append(file.toString() + "\n");
+        i++;
       }
-      else
+      if (data.length() > 5)
       {
-        currentAlignFrame.parseFeaturesFile(annotation, AppletFormatAdapter.PASTE);
+        file = data.toString();
       }
     }
 
-    public String getFeatures(String format)
+    final JalviewLite applet = this;
+    if (getParameter("embedded") != null
+        && getParameter("embedded").equalsIgnoreCase("true"))
     {
-      return currentAlignFrame.outputFeatures(false, format);
+      embedded = true;
+      LoadingThread loader = new LoadingThread(file, applet);
+      loader.start();
     }
-
-    public String getAnnotation()
+    else if (file != null)
     {
-      return currentAlignFrame.outputAnnotations(false);
-    }
+      add(launcher);
 
-    public void loadAlignment(String text, String title)
-    {
-        Alignment al = null;
-        String format = new IdentifyFile().Identify(text, AppletFormatAdapter.PASTE);
-        try{
-          al = new AppletFormatAdapter().readFile(text,
-                                                  AppletFormatAdapter.PASTE,
-                                                  format);
-          if (al.getHeight() > 0)
-            new AlignFrame(al, this, title, false);
-        }catch(java.io.IOException ex)
+      launcher.addActionListener(new java.awt.event.ActionListener()
+      {
+        public void actionPerformed(ActionEvent e)
         {
-          ex.printStackTrace();
+          LoadingThread loader = new LoadingThread(file,
+              applet);
+          loader.start();
         }
-   }
-
-    ////////////////////////////////////////////////
-    ////////////////////////////////////////////////
-
-
-
-    static int lastFrameX = 200;
-    static int lastFrameY = 200;
-    boolean fileFound = true;
-    String file = "No file";
-    Button launcher = new Button("Start Jalview");
-
-    //The currentAlignFrame is static, it will change
-    //if and when the user selects a new window
-    public static AlignFrame currentAlignFrame;
-
-    //This is the first frame to be displayed, and does not change
-    AlignFrame initialAlignFrame;
+      });
+    }
+    else
+    {
+      file = "NO FILE";
+      fileFound = false;
+    }
+  }
 
-    boolean embedded = false;
+  public static void main(String[] args)
+  {
+    if (args.length != 1)
+    {
+      System.out.println("\nUsage: java -jar jalviewApplet.jar fileName\n");
+      System.exit(1);
+    }
 
+    String format = new jalview.io.IdentifyFile().Identify(args[0],
+        AppletFormatAdapter.FILE);
 
-    /**
-     * init method for Jalview Applet
-     */
-    public void init()
+    Alignment al = null;
+    try
     {
-        int r = 255;
-        int g = 255;
-        int b = 255;
-        String param = getParameter("RGB");
-
-        if (param != null)
+      al = new AppletFormatAdapter().readFile(args[0], AppletFormatAdapter.FILE,
+                                              format);
+    }
+    catch (java.io.IOException ex)
+    {
+      ex.printStackTrace();
+    }
+    if ( (al != null) && (al.getHeight() > 0))
+    {
+      AlignFrame af = new AlignFrame(al, null, args[0], false);
+      af.statusBar.setText("Successfully loaded file " + args[0]);
+    }
+  }
+
+  /**
+   * Initialises and displays a new java.awt.Frame
+   *
+   * @param frame java.awt.Frame to be displayed
+   * @param title title of new frame
+   * @param width width if new frame
+   * @param height height of new frame
+   */
+  public static void addFrame(final Frame frame, String title, int width,
+                              int height)
+  {
+    frame.setLocation(lastFrameX, lastFrameY);
+    lastFrameX += 40;
+    lastFrameY += 40;
+    frame.setSize(width, height);
+    frame.setTitle(title);
+    frame.addWindowListener(new WindowAdapter()
+    {
+      public void windowClosing(WindowEvent e)
+      {
+        if (frame instanceof AlignFrame)
         {
-            try
-            {
-                r = Integer.parseInt(param.substring(0, 2), 16);
-                g = Integer.parseInt(param.substring(2, 4), 16);
-                b = Integer.parseInt(param.substring(4, 6), 16);
-            }
-            catch (Exception ex)
-            {
-                r = 255;
-                g = 255;
-                b = 255;
-            }
+          ( (AlignFrame) frame).closeMenuItem_actionPerformed();
         }
-
-        param = getParameter("label");
-        if(param != null)
-          launcher.setLabel(param);
-
-        this.setBackground(new Color(r, g, b));
-
-        file = getParameter("file");
-
-        if(file==null)
+        if (currentAlignFrame == frame)
         {
-          //Maybe the sequences are added as parameters
-          StringBuffer data = new StringBuffer("PASTE");
-          int i=1;
-          while( (file=getParameter("sequence"+i))!=null)
-          {
-            data.append(file.toString()+"\n");
-            i++;
-          }
-          if(data.length()>5)
-            file = data.toString();
+          currentAlignFrame = null;
         }
+        lastFrameX -= 40;
+        lastFrameY -= 40;
+        frame.setMenuBar(null);
+        frame.dispose();
+      }
 
-        final JalviewLite applet = this;
-        if(getParameter("embedded")!=null
-           && getParameter("embedded").equalsIgnoreCase("true"))
-        {
-          embedded = true;
-          LoadingThread loader = new LoadingThread(file, applet);
-          loader.start();
-        }
-        else if (file != null)
-        {
-            add(launcher);
-
-            launcher.addActionListener(new java.awt.event.ActionListener()
-                {
-                    public void actionPerformed(ActionEvent e)
-                    {
-                        LoadingThread loader = new LoadingThread(file,
-                            applet);
-                        loader.start();
-                      }
-                });
-        }
-        else
+      public void windowActivated(WindowEvent e)
+      {
+        if (frame instanceof AlignFrame)
         {
-            file = "NO FILE";
-            fileFound = false;
+          currentAlignFrame = (AlignFrame) frame;
         }
+      }
+
+    });
+    frame.setVisible(true);
+  }
+
+  /**
+   * This paints the background surrounding the "Launch Jalview button"
+   * <br>
+   * <br>If file given in parameter not found, displays error message
+   *
+   * @param g graphics context
+   */
+  public void paint(Graphics g)
+  {
+    if (!fileFound)
+    {
+      g.setColor(new Color(200, 200, 200));
+      g.setColor(Color.cyan);
+      g.fillRect(0, 0, getSize().width, getSize().height);
+      g.setColor(Color.red);
+      g.drawString("Jalview can't open file", 5, 15);
+      g.drawString("\"" + file + "\"", 5, 30);
     }
+    else if (embedded)
+    {
+      g.setColor(Color.black);
+      g.setFont(new Font("Arial", Font.BOLD, 24));
+      g.drawString("Jalview Applet", 50, this.getSize().height / 2 - 30);
+      g.drawString("Loading Data...", 50, this.getSize().height / 2);
+    }
+
+  }
 
+  class LoadingThread
+      extends Thread
+  {
+    String file;
+    String protocol;
+    String format;
+    JalviewLite applet;
 
-    public static void main(String [] args)
+    public LoadingThread(String _file,
+                         JalviewLite _applet)
     {
-      if(args.length!=1)
+      file = _file;
+      if (file.startsWith("PASTE"))
       {
-        System.out.println("\nUsage: java -jar jalviewApplet.jar fileName\n");
-        System.exit(1);
+        file = file.substring(5);
+        protocol = AppletFormatAdapter.PASTE;
       }
-
-      String format = new jalview.io.IdentifyFile().Identify(args[0],AppletFormatAdapter.FILE);
-
-     Alignment al = null;
-     try{
-       al = new AppletFormatAdapter().readFile(args[0], AppletFormatAdapter.FILE, format);
-     }catch(java.io.IOException ex)
-     {
-       ex.printStackTrace();
-     }
-      if ( (al != null) && (al.getHeight() > 0))
+      else if (inArchive(file))
       {
-        AlignFrame af = new AlignFrame(al, null, args[0], false);
-        af.statusBar.setText("Successfully loaded file " + args[0]);
+        protocol = AppletFormatAdapter.CLASSLOADER;
       }
+      else
+      {
+        file = addProtocol(file);
+        protocol = AppletFormatAdapter.URL;
+      }
+      format = new jalview.io.IdentifyFile().Identify(file, protocol);
+      applet = _applet;
     }
 
-
-    /**
-     * Initialises and displays a new java.awt.Frame
-     *
-     * @param frame java.awt.Frame to be displayed
-     * @param title title of new frame
-     * @param width width if new frame
-     * @param height height of new frame
-     */
-    public static void addFrame(final Frame frame, String title, int width,
-        int height)
+    public void run()
     {
-        frame.setLocation(lastFrameX, lastFrameY);
-        lastFrameX += 40;
-        lastFrameY += 40;
-        frame.setSize(width, height);
-        frame.setTitle(title);
-        frame.addWindowListener(new WindowAdapter()
-            {
-                public void windowClosing(WindowEvent e)
-                {
-                  if(frame instanceof AlignFrame)
-                    ((AlignFrame)frame).closeMenuItem_actionPerformed();
-                    if(currentAlignFrame == frame)
-                    {
-                      currentAlignFrame = null;
-                    }
-                    lastFrameX -=40;
-                    lastFrameY -=40;
-                    frame.setMenuBar(null);
-                    frame.dispose();
-                }
-                public void windowActivated(WindowEvent e)
-                {
-                  if(frame instanceof AlignFrame)
-                    currentAlignFrame = (AlignFrame)frame;
-                }
-
-            });
-        frame.setVisible(true);
-    }
-
-
+      Alignment al = null;
+      try
+      {
+        al = new AppletFormatAdapter().readFile(file, protocol,
+                                                format);
+      }
+      catch (java.io.IOException ex)
+      {
+        ex.printStackTrace();
+      }
+      if ( (al != null) && (al.getHeight() > 0))
+      {
+        currentAlignFrame = new AlignFrame(al,
+                                           applet,
+                                           file,
+                                           embedded);
 
-    /**
-     * This paints the background surrounding the "Launch Jalview button"
-     * <br>
-     * <br>If file given in parameter not found, displays error message
-     *
-     * @param g graphics context
-     */
-    public void paint(Graphics g)
-    {
-        if (!fileFound)
+        if (protocol == jalview.io.AppletFormatAdapter.PASTE)
         {
-            g.setColor(new Color(200, 200, 200));
-            g.setColor(Color.cyan);
-            g.fillRect(0, 0, getSize().width, getSize().height);
-            g.setColor(Color.red);
-            g.drawString("Jalview can't open file", 5, 15);
-            g.drawString("\"" + file + "\"", 5, 30);
-        }
-        else if(embedded)
-        {
-          g.setColor(Color.black);
-          g.setFont(new Font("Arial", Font.BOLD, 24));
-          g.drawString("Jalview Applet", 50, this.getSize().height/2 -30);
-          g.drawString("Loading Data...", 50, this.getSize().height/2);
+          currentAlignFrame.setTitle("Sequences from " + getDocumentBase());
         }
 
+        initialAlignFrame = currentAlignFrame;
 
-    }
+        currentAlignFrame.statusBar.setText("Successfully loaded file " + file);
 
-    class LoadingThread extends Thread
-    {
-        String file;
-        String protocol;
-        String format;
-        JalviewLite applet;
+        String treeFile = applet.getParameter("tree");
+        if (treeFile == null)
+        {
+          treeFile = applet.getParameter("treeFile");
+        }
 
-        public LoadingThread(String _file,
-                             JalviewLite _applet)
+        if (treeFile != null)
         {
-            file = _file;
-            if(file.startsWith("PASTE"))
+          try
+          {
+            if (inArchive(treeFile))
             {
-              file = file.substring(5);
-              protocol = AppletFormatAdapter.PASTE;
-            }
-            else if(inArchive(file))
               protocol = AppletFormatAdapter.CLASSLOADER;
+            }
             else
             {
-              file = addProtocol(file);
               protocol = AppletFormatAdapter.URL;
+              treeFile = addProtocol(treeFile);
             }
-            format = new jalview.io.IdentifyFile().Identify(file, protocol);
-            applet = _applet;
-        }
 
-        public void run()
-        {
-            Alignment al = null;
-            try{
-              al = new AppletFormatAdapter().readFile(file, protocol,
-                  format);
-            }catch(java.io.IOException ex)
+            jalview.io.NewickFile fin = new jalview.io.NewickFile(treeFile,
+                protocol);
+
+            fin.parse();
+
+            if (fin.getTree() != null)
             {
-              ex.printStackTrace();
+              currentAlignFrame.loadTree(fin, treeFile);
             }
-            if ((al != null) && (al.getHeight() > 0))
+          }
+          catch (Exception ex)
+          {
+            ex.printStackTrace();
+          }
+        }
+
+        String param = getParameter("features");
+        if (param != null)
+        {
+          if (!inArchive(param))
+          {
+            param = addProtocol(param);
+          }
+
+          currentAlignFrame.parseFeaturesFile(param, protocol);
+        }
+
+        param = getParameter("showFeatureSettings");
+        if (param != null && param.equalsIgnoreCase("true"))
+        {
+          currentAlignFrame.viewport.showSequenceFeatures(true);
+          new FeatureSettings(currentAlignFrame.alignPanel);
+        }
+
+        param = getParameter("annotations");
+        if (param != null)
+        {
+          if (!inArchive(param))
+          {
+            param = addProtocol(param);
+          }
+
+          new AnnotationFile().readAnnotationFile(
+              currentAlignFrame.viewport.getAlignment(),
+              param,
+              protocol);
+
+          currentAlignFrame.alignPanel.fontChanged();
+          currentAlignFrame.alignPanel.setScrollValues(0, 0);
+
+        }
+
+        param = getParameter("jnetfile");
+        if (param != null)
+        {
+          try
+          {
+            if (inArchive(param))
             {
-              currentAlignFrame = new AlignFrame(al,
-                                                 applet,
-                                                 file,
-                                                 embedded);
-
-              if(protocol==jalview.io.AppletFormatAdapter.PASTE)
-                currentAlignFrame.setTitle("Sequences from "+getDocumentBase());
-
-              initialAlignFrame = currentAlignFrame;
-
-              currentAlignFrame.statusBar.setText("Successfully loaded file " + file);
-
-
-                String treeFile = applet.getParameter("tree");
-                if(treeFile==null)
-                  treeFile = applet.getParameter("treeFile");
-
-                if (treeFile != null)
-                {
-                  try
-                  {
-                    if(inArchive(treeFile))
-                      protocol = AppletFormatAdapter.CLASSLOADER;
-                    else
-                    {
-                      protocol = AppletFormatAdapter.URL;
-                      treeFile = addProtocol(treeFile);
-                    }
-
-                    jalview.io.NewickFile fin = new jalview.io.NewickFile(treeFile, protocol);
-
-                    fin.parse();
-
-                    if (fin.getTree() != null)
-                    {
-                      currentAlignFrame.loadTree(fin, treeFile);
-                    }
-                  }
-                  catch (Exception ex)
-                  {
-                    ex.printStackTrace();
-                  }
-              }
-
-              String param = getParameter("features");
-              if (param != null)
-              {
-                if( !inArchive(param) )
-                  param = addProtocol( param );
-
-                currentAlignFrame.parseFeaturesFile(param, protocol);
-              }
-
-              param = getParameter("showFeatureSettings");
-              if(param !=null && param.equalsIgnoreCase("true"))
-              {
-                currentAlignFrame.viewport.showSequenceFeatures(true);
-                new FeatureSettings(currentAlignFrame.alignPanel);
-              }
-
-             param = getParameter("annotations");
-             if (param != null)
-             {
-               if( !inArchive(param) )
-                  param = addProtocol( param );
-
-               new AnnotationFile().readAnnotationFile(
-                   currentAlignFrame.viewport.getAlignment(),
-                   param,
-                   protocol);
-
-               currentAlignFrame.alignPanel.fontChanged();
-               currentAlignFrame.alignPanel.setScrollValues(0,0);
-
-             }
-
-             param = getParameter("jnetfile");
-             if (param != null)
-             {
-               try
-               {
-                 if (inArchive(param))
-                   protocol = AppletFormatAdapter.CLASSLOADER;
-                 else
-                 {
-                   protocol = AppletFormatAdapter.URL;
-                   param = addProtocol(param);
-                 }
-
-                 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
-                     param, protocol);
-                 new JnetAnnotationMaker().add_annotation(predictions,
-                     currentAlignFrame.viewport.getAlignment(),
-                     0,false); // do not add sequence profile from concise output
-                 currentAlignFrame.alignPanel.fontChanged();
-                 currentAlignFrame.alignPanel.setScrollValues(0, 0);
-               } catch (Exception ex) {
-                 ex.printStackTrace();
-               }
-             }
-
-
-                param = getParameter("PDBFILE");
-                if(param!=null)
-                {
-                  if( inArchive(param) )
-                    protocol = AppletFormatAdapter.CLASSLOADER;
-                  else
-                  {
-                    protocol = AppletFormatAdapter.URL;
-                    param = addProtocol(param);
-                  }
-
-                  String sequence = applet.getParameter("PDBSEQ");
-
-                  if(sequence!=null)
-                  {
-                    new MCview.AppletPDBViewer(param, protocol,
-                                               (Sequence)currentAlignFrame.getAlignViewport().getAlignment().findName(sequence),
-                                               currentAlignFrame.getSeqcanvas());
-                  }
-
-                }
+              protocol = AppletFormatAdapter.CLASSLOADER;
             }
             else
             {
-                fileFound = false;
-                remove(launcher);
-                repaint();
+              protocol = AppletFormatAdapter.URL;
+              param = addProtocol(param);
             }
-        }
 
-        /**
-         * Discovers whether the given file is in the Applet Archive
-         * @param file String
-         * @return boolean
-         */
-        boolean inArchive(String file)
-        {
-          //This might throw a security exception in certain browsers
-          //Netscape Communicator for instance.
-          try{
-            return (getClass().getResourceAsStream("/" + file) != null);
-          }catch(Exception ex)
+            jalview.io.JPredFile predictions = new jalview.io.JPredFile(
+                param, protocol);
+            new JnetAnnotationMaker().add_annotation(predictions,
+                currentAlignFrame.viewport.getAlignment(),
+                0, false); // do not add sequence profile from concise output
+            currentAlignFrame.alignPanel.fontChanged();
+            currentAlignFrame.alignPanel.setScrollValues(0, 0);
+          }
+          catch (Exception ex)
           {
-            System.out.println("Exception checking resources: "+file+" "+ex);
-            return false;
+            ex.printStackTrace();
           }
         }
 
-        String addProtocol(String file)
+        param = getParameter("PDBFILE");
+        if (param != null)
         {
-          if (file.indexOf("://") == -1)
-             file = getCodeBase() + file;
+          if (inArchive(param))
+          {
+            protocol = AppletFormatAdapter.CLASSLOADER;
+          }
+          else
+          {
+            protocol = AppletFormatAdapter.URL;
+            param = addProtocol(param);
+          }
+
+          String sequence = applet.getParameter("PDBSEQ");
+
+          if (sequence != null)
+          {
+            new MCview.AppletPDBViewer(param, protocol,
+                                       (Sequence) currentAlignFrame.
+                                       getAlignViewport().getAlignment().
+                                       findName(sequence),
+                                       currentAlignFrame.getSeqcanvas());
+          }
 
-          return file;
         }
+      }
+      else
+      {
+        fileFound = false;
+        remove(launcher);
+        repaint();
+      }
+    }
+
+    /**
+     * Discovers whether the given file is in the Applet Archive
+     * @param file String
+     * @return boolean
+     */
+    boolean inArchive(String file)
+    {
+      //This might throw a security exception in certain browsers
+      //Netscape Communicator for instance.
+      try
+      {
+        return (getClass().getResourceAsStream("/" + file) != null);
+      }
+      catch (Exception ex)
+      {
+        System.out.println("Exception checking resources: " + file + " " + ex);
+        return false;
+      }
+    }
+
+    String addProtocol(String file)
+    {
+      if (file.indexOf("://") == -1)
+      {
+        file = getCodeBase() + file;
+      }
 
+      return file;
     }
+
+  }
 }
diff --git a/src/jalview/commands/ChangeCaseCommand.java b/src/jalview/commands/ChangeCaseCommand.java
index 00d9000..d34552d 100644
--- a/src/jalview/commands/ChangeCaseCommand.java
+++ b/src/jalview/commands/ChangeCaseCommand.java
@@ -1,6 +1,6 @@
-  /*
+/*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -20,18 +20,19 @@ 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;
+  SequenceI[] seqs;
+  int[][] regions;
   public ChangeCaseCommand(String description,
                            SequenceI[] seqs,
-                           int [][] regions,
+                           int[][] regions,
                            int caseChange)
   {
     this.description = description;
@@ -75,9 +76,13 @@ public class ChangeCaseCommand implements CommandI
         StringBuffer newSeq = new StringBuffer();
 
         if (regions[r][1] > sequence.length())
+        {
           end = sequence.length();
+        }
         else
+        {
           end = regions[r][1];
+        }
 
         if (start > 0)
         {
@@ -86,11 +91,15 @@ public class ChangeCaseCommand implements CommandI
 
         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))
+        {
           newSeq.append(sequence.substring(start, end).toLowerCase());
+        }
 
         else //TOGGLE CASE
         {
@@ -112,7 +121,9 @@ public class ChangeCaseCommand implements CommandI
         }
 
         if (end < sequence.length())
+        {
           newSeq.append(sequence.substring(end));
+        }
 
         seqs[s].setSequence(newSeq.toString());
       }
diff --git a/src/jalview/commands/CommandI.java b/src/jalview/commands/CommandI.java
index e12a4c7..d97a6bb 100644
--- a/src/jalview/commands/CommandI.java
+++ b/src/jalview/commands/CommandI.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -20,11 +20,11 @@ package jalview.commands;
 
 public interface CommandI
 {
-    public void doCommand();
+  public void doCommand();
 
-    public void undoCommand();
+  public void undoCommand();
 
-    public String getDescription();
+  public String getDescription();
 
-    public int getSize();
+  public int getSize();
 }
diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index d9f51e0..d0a2e03 100644
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,9 +18,9 @@
  */
 package jalview.commands;
 
-import jalview.datamodel.*;
+import java.util.*;
 
-import java.util.Hashtable;
+import jalview.datamodel.*;
 
 /**
  *
@@ -37,7 +37,8 @@ import java.util.Hashtable;
  * @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;
@@ -56,22 +57,23 @@ public class EditCommand implements CommandI
     this.description = description;
   }
 
-  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)};
-     }
-
-     performEdit(0);
-  }
+  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)};
+    }
 
+    performEdit(0);
+  }
 
   final public String getDescription()
   {
@@ -80,7 +82,7 @@ public class EditCommand implements CommandI
 
   public int getSize()
   {
-    return edits==null?0:edits.length;
+    return edits == null ? 0 : edits.length;
   }
 
   final public AlignmentI getAlignment()
@@ -88,16 +90,15 @@ public class EditCommand implements CommandI
     return edits[0].al;
   }
 
-
   final public void appendEdit(int command,
-                         SequenceI[] seqs,
-                         int position,
-                         int number,
-                         AlignmentI al,
-                         boolean performEdit)
+                               SequenceI[] seqs,
+                               int position,
+                               int number,
+                               AlignmentI al,
+                               boolean performEdit)
   {
     Edit edit = new Edit(command, seqs, position, number, al.getGapCharacter());
-    if(al.getHeight()==seqs.length)
+    if (al.getHeight() == seqs.length)
     {
       edit.al = al;
       edit.fullAlignmentHeight = true;
@@ -111,10 +112,16 @@ public class EditCommand implements CommandI
       edits[edits.length - 1] = edit;
     }
     else
-      edits = new Edit[] {  edit  };
+    {
+      edits = new Edit[]
+          {
+          edit};
+    }
 
     if (performEdit)
+    {
       performEdit(edits.length - 1);
+    }
   }
 
   final void performEdit(int commandIndex)
@@ -122,19 +129,19 @@ public class EditCommand implements CommandI
     int eSize = edits.length;
     for (int e = commandIndex; e < eSize; e++)
     {
-      if (edits[e].command==INSERT_GAP)
+      if (edits[e].command == INSERT_GAP)
       {
         insertGap(edits[e]);
       }
-      else if (edits[e].command==DELETE_GAP)
+      else if (edits[e].command == DELETE_GAP)
       {
         deleteGap(edits[e]);
       }
-      else if(edits[e].command==CUT)
+      else if (edits[e].command == CUT)
       {
         cut(edits[e]);
       }
-      else if(edits[e].command==PASTE)
+      else if (edits[e].command == PASTE)
       {
         paste(edits[e]);
       }
@@ -149,21 +156,21 @@ public class EditCommand implements CommandI
   final public void undoCommand()
   {
     int e = 0, eSize = edits.length;
-    for (e = eSize-1; e > -1; e--)
+    for (e = eSize - 1; e > -1; e--)
     {
-      if (edits[e].command==INSERT_GAP)
+      if (edits[e].command == INSERT_GAP)
       {
         deleteGap(edits[e]);
       }
-      else if (edits[e].command==DELETE_GAP)
+      else if (edits[e].command == DELETE_GAP)
       {
         insertGap(edits[e]);
       }
-      else if (edits[e].command==CUT)
+      else if (edits[e].command == CUT)
       {
         paste(edits[e]);
       }
-      else if (edits[e].command==PASTE)
+      else if (edits[e].command == PASTE)
       {
         cut(edits[e]);
       }
@@ -172,11 +179,11 @@ public class EditCommand implements CommandI
 
   final void insertGap(Edit command)
   {
-    for(int s=0; s<command.seqs.length; s++)
+    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);
@@ -186,7 +193,8 @@ public class EditCommand implements CommandI
   {
     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);
@@ -194,19 +202,20 @@ public class EditCommand implements CommandI
 
   void cut(Edit command)
   {
-    command.string = new char [command.seqs.length][];
+    command.string = new char[command.seqs.length][];
 
-    for(int i=0; i<command.seqs.length; i++)
+    for (int i = 0; i < command.seqs.length; i++)
     {
-      if(command.seqs[i].getLength()>command.position)
+      if (command.seqs[i].getLength() > command.position)
       {
         command.string[i] = command.seqs[i].getSequence(command.position,
             command.position + command.number);
 
-        if(command.seqs[i].getDatasetSequence()!=null
-        || command.seqs[i].getSequenceFeatures()!=null)
+        if (command.seqs[i].getDatasetSequence() != null
+            || command.seqs[i].getSequenceFeatures() != null)
         {
-          for (int s = command.position; s < command.position + command.number; s++)
+          for (int s = command.position; s < command.position + command.number;
+               s++)
           {
             if (jalview.schemes.ResidueProperties
                 .aaIndex[command.seqs[i].getCharAt(s)] != 23)
@@ -214,7 +223,7 @@ public class EditCommand implements CommandI
               adjustFeatures(command, i,
                              command.seqs[i].findPosition(command.position),
                              command.seqs[i].findPosition(command.position +
-                                                          command.number),
+                  command.number),
                              false);
               break;
             }
@@ -224,7 +233,7 @@ public class EditCommand implements CommandI
                                     command.position + command.number);
       }
 
-      if(command.seqs[i].getLength()<1)
+      if (command.seqs[i].getLength() < 1)
       {
         command.al.deleteSequence(command.seqs[i]);
       }
@@ -237,31 +246,35 @@ public class EditCommand implements CommandI
   {
     StringBuffer tmp;
     boolean newDSNeeded;
-    int start=0, end=0;
+    int start = 0, end = 0;
 
-    for(int i=0; i<command.seqs.length; i++)
+    for (int i = 0; i < command.seqs.length; i++)
     {
       newDSNeeded = false;
-      if(command.seqs[i].getLength()<1)
+      if (command.seqs[i].getLength() < 1)
       {
         // ie this sequence was deleted, we need to
         // read it to the alignment
         if (command.alIndex[i] < command.al.getHeight())
+        {
           command.al.getSequences().insertElementAt(command.seqs[i],
               command.alIndex[i]);
+        }
         else
+        {
           command.al.addSequence(command.seqs[i]);
+        }
       }
       tmp = new StringBuffer();
       tmp.append(command.seqs[i].getSequence());
 
-      if(command.string!=null && command.string[i]!=null)
+      if (command.string != null && command.string[i] != null)
       {
-        if(command.position>=tmp.length())
+        if (command.position >= tmp.length())
         {
           //This occurs if padding is on, and residues
           //are removed from end of alignment
-          int length = command.position-tmp.length();
+          int length = command.position - tmp.length();
           while (length > 0)
           {
             tmp.append(command.gapChar);
@@ -272,21 +285,22 @@ public class EditCommand implements CommandI
 
         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)
           {
             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);
             break;
           }
         }
         command.string[i] = null;
       }
 
-
       command.seqs[i].setSequence(tmp.toString());
 
-      if(newDSNeeded)
+      if (newDSNeeded)
       {
         if (command.seqs[i].getDatasetSequence() != null)
         {
@@ -305,17 +319,15 @@ public class EditCommand implements CommandI
       }
     }
 
-
     adjustAnnotations(command, true);
 
     command.string = null;
   }
 
-
   final void adjustAnnotations(Edit command, boolean insert)
   {
 
-    AlignmentAnnotation [] annotations = null;
+    AlignmentAnnotation[] annotations = null;
 
     if (command.fullAlignmentHeight)
     {
@@ -324,196 +336,220 @@ public class EditCommand implements CommandI
     else
     {
       int aSize = 0;
-      AlignmentAnnotation [] tmp;
-      for(int s=0; s<command.seqs.length; s++)
+      AlignmentAnnotation[] tmp;
+      for (int s = 0; s < command.seqs.length; s++)
       {
-        if(command.seqs[s].getAnnotation()==null)
+        if (command.seqs[s].getAnnotation() == null)
+        {
           continue;
+        }
 
         if (aSize == 0)
-            annotations = command.seqs[s].getAnnotation();
+        {
+          annotations = command.seqs[s].getAnnotation();
+        }
         else
         {
           tmp = new AlignmentAnnotation
               [aSize + command.seqs[s].getAnnotation().length];
 
-          System.arraycopy(annotations,0,tmp,0,aSize);
+          System.arraycopy(annotations, 0, tmp, 0, aSize);
 
           System.arraycopy(command.seqs[s].getAnnotation(),
-              0,tmp,aSize,command.seqs[s].getAnnotation().length);
+                           0, tmp, aSize,
+                           command.seqs[s].getAnnotation().length);
 
           annotations = tmp;
         }
 
-
         aSize = annotations.length;
       }
     }
 
-    if(annotations==null)
+    if (annotations == null)
+    {
       return;
+    }
 
+    if (!insert)
+    {
+      command.deletedAnnotations = new Hashtable();
+    }
 
-      if(!insert)
-        command.deletedAnnotations = new Hashtable();
-
-      int aSize;
-      Annotation [] temp;
-      for (int a = 0; a < annotations.length; a++)
+    int aSize;
+    Annotation[] temp;
+    for (int a = 0; a < annotations.length; a++)
+    {
+      if (annotations[a].autoCalculated)
       {
-        if(annotations[a].autoCalculated)
-        {
-          continue;
-        }
+        continue;
+      }
 
-        int tSize = 0;
+      int tSize = 0;
 
-        aSize = annotations[a].annotations.length;
-        if(insert)
-          temp = new Annotation[aSize + command.number];
-        else
+      aSize = annotations[a].annotations.length;
+      if (insert)
+      {
+        temp = new Annotation[aSize + command.number];
+      }
+      else
+      {
+        if (command.position < aSize)
         {
-          if(command.position<aSize)
+          if (command.position + command.number > aSize)
           {
-            if(command.position+command.number>aSize)
-              tSize = aSize;
-            else
-             {
-                tSize = aSize - command.number + command.position;
-             }
+            tSize = aSize;
           }
           else
-            tSize = aSize;
-
-          if(tSize<0)
           {
-            tSize = aSize;
+            tSize = aSize - command.number + command.position;
           }
-          temp = new Annotation[tSize];
+        }
+        else
+        {
+          tSize = aSize;
+        }
 
+        if (tSize < 0)
+        {
+          tSize = aSize;
         }
+        temp = new Annotation[tSize];
+
+      }
 
-        if(insert)
+      if (insert)
+      {
+        if (command.position < annotations[a].annotations.length)
         {
-          if(command.position < annotations[a].annotations.length)
+          System.arraycopy(annotations[a].annotations,
+                           0, temp, 0, command.position);
+
+          if (command.deletedAnnotations != null
+              &&
+              command.deletedAnnotations.containsKey(annotations[a].
+              annotationId))
           {
-            System.arraycopy(annotations[a].annotations,
-                             0, temp, 0, command.position);
+            Annotation[] restore = (Annotation[])
+                command.deletedAnnotations.get(annotations[a].annotationId);
 
-            if (command.deletedAnnotations != null
-                &&
-                command.deletedAnnotations.containsKey(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);
+        }
+        else
+        {
+          if (command.deletedAnnotations != null
+              &&
+              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,
-                             command.position, temp,
-                             command.position + command.number,
-                             aSize - command.position);
+                             0, temp, 0,
+                             annotations[a].annotations.length);
+            System.arraycopy(restore, 0, temp,
+                             annotations[a].annotations.length, restore.length);
           }
           else
           {
-            if (command.deletedAnnotations != null
-                           &&
-                           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);
-              System.arraycopy(restore,0,temp,annotations[a].annotations.length,restore.length);
-            }
-            else
-              temp = annotations[a].annotations;
+            temp = annotations[a].annotations;
           }
         }
+      }
+      else
+      {
+        if (tSize != aSize || command.position < 2)
+        {
+          System.arraycopy(annotations[a].annotations,
+                           0, temp, 0, command.position);
+
+          Annotation[] deleted = new Annotation[command.number];
+          System.arraycopy(annotations[a].annotations,
+                           command.position, deleted, 0, command.number);
+
+          command.deletedAnnotations.put(annotations[a].annotationId,
+                                         deleted);
+
+          System.arraycopy(annotations[a].annotations,
+                           command.position + command.number,
+                           temp, command.position,
+                           aSize - command.position - command.number);
+        }
         else
         {
-          if(tSize!=aSize || command.position<2)
-          {
-            System.arraycopy(annotations[a].annotations,
-                             0, temp, 0, command.position);
+          int dSize = aSize - command.position;
 
+          if (dSize > 0)
+          {
             Annotation[] deleted = new Annotation[command.number];
             System.arraycopy(annotations[a].annotations,
-                             command.position, deleted, 0, command.number);
+                             command.position, deleted, 0, dSize);
 
             command.deletedAnnotations.put(annotations[a].annotationId,
                                            deleted);
 
+            tSize = Math.min(annotations[a].annotations.length,
+                             command.position);
+            temp = new Annotation[tSize];
             System.arraycopy(annotations[a].annotations,
-                             command.position + command.number,
-                             temp, command.position,
-                             aSize - command.position - command.number);
+                             0, temp, 0, tSize);
           }
           else
           {
-            int dSize = aSize - command.position;
-
-            if(dSize>0)
-            {
-              Annotation[] deleted = new Annotation[command.number];
-              System.arraycopy(annotations[a].annotations,
-                               command.position, deleted, 0, dSize);
-
-              command.deletedAnnotations.put(annotations[a].annotationId,
-                                             deleted);
-
-              tSize = Math.min(annotations[a].annotations.length, command.position);
-              temp = new Annotation[tSize];
-              System.arraycopy(annotations[a].annotations,
-                  0, temp, 0, tSize);
-            }
-            else
-              temp = annotations[a].annotations;
+            temp = annotations[a].annotations;
           }
         }
+      }
 
-        annotations[a].annotations = temp;
-     }
+      annotations[a].annotations = temp;
+    }
   }
 
-  final void adjustFeatures(Edit command, int index, int i, int j, boolean insert)
+  final void adjustFeatures(Edit command, int index, int i, int j,
+                            boolean insert)
   {
     SequenceI seq = command.seqs[index];
     SequenceI sequence = seq.getDatasetSequence();
-    if(sequence==null)
+    if (sequence == null)
+    {
       sequence = seq;
+    }
 
-    if(insert)
+    if (insert)
     {
       if (command.editedFeatures != null
           && command.editedFeatures.containsKey(seq))
+      {
         sequence.setSequenceFeatures(
             (SequenceFeature[]) command.editedFeatures.get(seq)
             );
+      }
 
       return;
     }
 
+    SequenceFeature[] sf = sequence.getSequenceFeatures();
 
-    SequenceFeature [] sf = sequence.getSequenceFeatures();
-
-
-    if(sf==null)
+    if (sf == null)
     {
       return;
     }
 
-    SequenceFeature [] oldsf = new SequenceFeature[sf.length];
+    SequenceFeature[] oldsf = new SequenceFeature[sf.length];
 
     int cSize = j - i;
 
@@ -524,7 +560,9 @@ public class EditCommand implements CommandI
       oldsf[s] = copy;
 
       if (sf[s].getEnd() < i)
+      {
         continue;
+      }
 
       if (sf[s].getBegin() > j)
       {
@@ -534,25 +572,32 @@ public class EditCommand implements CommandI
       }
 
       if (sf[s].getBegin() >= i)
+      {
         sf[s].setBegin(i);
+      }
 
       if (sf[s].getEnd() < j)
+      {
         sf[s].setEnd(j - 1);
+      }
 
       sf[s].setEnd(sf[s].getEnd() - (cSize));
 
       if (sf[s].getBegin() > sf[s].getEnd())
+      {
         sequence.deleteFeature(sf[s]);
+      }
     }
 
     if (command.editedFeatures == null)
+    {
       command.editedFeatures = new Hashtable();
+    }
 
     command.editedFeatures.put(seq, oldsf);
 
   }
 
-
   class Edit
   {
     boolean fullAlignmentHeight = false;
@@ -560,9 +605,9 @@ public class EditCommand implements CommandI
     Hashtable editedFeatures;
     AlignmentI al;
     int command;
-    char [][] string;
+    char[][] string;
     SequenceI[] seqs;
-    int [] alIndex;
+    int[] alIndex;
     int position, number;
     char gapChar;
 
@@ -579,7 +624,6 @@ public class EditCommand implements CommandI
       this.gapChar = gapChar;
     }
 
-
     Edit(int command,
          SequenceI[] seqs,
          int position,
@@ -594,12 +638,12 @@ public class EditCommand implements CommandI
       this.al = al;
 
       alIndex = new int[seqs.length];
-      for(int i=0; i<seqs.length; i++)
+      for (int i = 0; i < seqs.length; i++)
       {
         alIndex[i] = al.findIndex(seqs[i]);
       }
 
-      fullAlignmentHeight = (al.getHeight()==seqs.length);
+      fullAlignmentHeight = (al.getHeight() == seqs.length);
     }
   }
 
diff --git a/src/jalview/commands/OrderCommand.java b/src/jalview/commands/OrderCommand.java
index e7d257c..57097c0 100644
--- a/src/jalview/commands/OrderCommand.java
+++ b/src/jalview/commands/OrderCommand.java
@@ -1,6 +1,6 @@
-  /*
+/*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,45 +18,45 @@
  */
 package jalview.commands;
 
+import jalview.analysis.*;
 import jalview.datamodel.*;
 
-import jalview.analysis.AlignmentSorter;
-
-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)
-    {
-      this.description = description;
-      this.seqs = seqs;
-      this.seqs2 = al.getSequencesArray();
-      this.al = al;
-      doCommand();
-    }
-
-    public String getDescription()
-    {
-      return description;
-    }
-
-    public int getSize()
-    {
-      return 1;
-    }
-
-    public void doCommand()
-    {
-      AlignmentSorter.setOrder(al, seqs2);
-    }
-
-    public void undoCommand()
-    {
-      AlignmentSorter.setOrder(al, seqs);
-    }
+  String description;
+  SequenceI[] seqs;
+  SequenceI[] seqs2;
+  AlignmentI al;
+
+  public OrderCommand(String description,
+                      SequenceI[] seqs,
+                      AlignmentI al)
+  {
+    this.description = description;
+    this.seqs = seqs;
+    this.seqs2 = al.getSequencesArray();
+    this.al = al;
+    doCommand();
+  }
+
+  public String getDescription()
+  {
+    return description;
+  }
+
+  public int getSize()
+  {
+    return 1;
+  }
+
+  public void doCommand()
+  {
+    AlignmentSorter.setOrder(al, seqs2);
+  }
+
+  public void undoCommand()
+  {
+    AlignmentSorter.setOrder(al, seqs);
+  }
 }
diff --git a/src/jalview/commands/RemoveGapColCommand.java b/src/jalview/commands/RemoveGapColCommand.java
index d3aebdb..1e9b832 100644
--- a/src/jalview/commands/RemoveGapColCommand.java
+++ b/src/jalview/commands/RemoveGapColCommand.java
@@ -1,7 +1,8 @@
 package jalview.commands;
-  /*
+
+/*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -20,7 +21,8 @@ package jalview.commands;
 
 import jalview.datamodel.*;
 
-public class RemoveGapColCommand  extends EditCommand
+public class RemoveGapColCommand
+    extends EditCommand
 {
   int columnsDeleted;
   public RemoveGapColCommand(String description,
@@ -32,7 +34,7 @@ public class RemoveGapColCommand  extends EditCommand
     int j, jSize = seqs.length;
 
     int startCol = -1, endCol = -1;
-    columnsDeleted=0;
+    columnsDeleted = 0;
 
     edits = new Edit[0];
 
@@ -48,7 +50,9 @@ public class RemoveGapColCommand  extends EditCommand
           if (!jalview.util.Comparison.isGap(seqs[j].getCharAt(i)))
           {
             if (delete)
+            {
               endCol = i;
+            }
 
             delete = false;
             break;
@@ -77,19 +81,18 @@ public class RemoveGapColCommand  extends EditCommand
 
     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);
+                      startCol - columnsDeleted,
+                      end - startCol + 1,
+                      al,
+                      false);
 
-      columnsDeleted += (end - startCol +1);
+      columnsDeleted += (end - startCol + 1);
     }
 
-
     performEdit(0);
   }
 
diff --git a/src/jalview/commands/RemoveGapsCommand.java b/src/jalview/commands/RemoveGapsCommand.java
index f6413a7..ccc8008 100644
--- a/src/jalview/commands/RemoveGapsCommand.java
+++ b/src/jalview/commands/RemoveGapsCommand.java
@@ -1,7 +1,8 @@
 package jalview.commands;
-  /*
+
+/*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -20,29 +21,34 @@ package jalview.commands;
 
 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;
-    for(int i=0; i<seqs.length; i++)
-      if(seqs[i].getLength()>width)
+    for (int i = 0; i < seqs.length; i++)
+    {
+      if (seqs[i].getLength() > width)
+      {
         width = seqs[i].getLength();
+      }
+    }
 
     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);
   }
 
-  void findGaps(SequenceI [] seqs, int start, int end, AlignmentI al)
+  void findGaps(SequenceI[] seqs, int start, int end, AlignmentI al)
   {
 
     int startCol = -1, endCol = -1;
@@ -53,30 +59,30 @@ public class RemoveGapsCommand  extends EditCommand
     edits = new Edit[0];
 
     boolean delete = true;
-    char [] sequence;
+    char[] sequence;
 
-    for(int s=0; s<seqs.length; s++)
+    for (int s = 0; s < seqs.length; s++)
     {
       deletedCols = 0;
       startCol = -1;
       endCol = -1;
-      sequence = seqs[s].getSequence(start, end+1);
+      sequence = seqs[s].getSequence(start, end + 1);
 
       jSize = sequence.length;
-      for (j=0; j<jSize; j++)
+      for (j = 0; j < jSize; j++)
       {
         delete = true;
 
-
         if (!jalview.util.Comparison.isGap(sequence[j]))
         {
           if (delete)
+          {
             endCol = j;
+          }
 
           delete = false;
         }
 
-
         if (delete && startCol == -1)
         {
           startCol = j;
@@ -84,7 +90,8 @@ public class RemoveGapsCommand  extends EditCommand
 
         if (!delete && startCol > -1)
         {
-          this.appendEdit(DELETE_GAP, new SequenceI[]{seqs[s]},
+          this.appendEdit(DELETE_GAP, new SequenceI[]
+                          {seqs[s]},
                           start + startCol - deletedCols,
                           endCol - startCol,
                           al,
@@ -97,7 +104,8 @@ public class RemoveGapsCommand  extends EditCommand
       }
       if (delete && startCol > -1)
       {
-        this.appendEdit(DELETE_GAP, new SequenceI[]{seqs[s]},
+        this.appendEdit(DELETE_GAP, new SequenceI[]
+                        {seqs[s]},
                         start + startCol - deletedCols,
                         jSize - startCol,
                         al,
diff --git a/src/jalview/commands/TrimRegionCommand.java b/src/jalview/commands/TrimRegionCommand.java
index 37518bc..4c1dea0 100644
--- a/src/jalview/commands/TrimRegionCommand.java
+++ b/src/jalview/commands/TrimRegionCommand.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,9 +18,10 @@
  */
 package jalview.commands;
 
-import jalview.util.ShiftList;
+import java.util.*;
+
 import jalview.datamodel.*;
-import java.util.Vector;
+import jalview.util.*;
 
 public class TrimRegionCommand
     extends EditCommand
@@ -30,7 +31,7 @@ public class TrimRegionCommand
 
   public ColumnSelection colSel = null;
 
-  int [] start;
+  int[] start;
 
   ShiftList shiftList;
 
@@ -41,45 +42,52 @@ public class TrimRegionCommand
   int columnsDeleted;
 
   public TrimRegionCommand(String description,
-                     String command,
-                     SequenceI[] seqs,
-                     int column,
-                     AlignmentI al,
-                     ColumnSelection colSel,
-                     SequenceGroup selectedRegion)
+                           String command,
+                           SequenceI[] seqs,
+                           int column,
+                           AlignmentI al,
+                           ColumnSelection colSel,
+                           SequenceGroup selectedRegion)
   {
     this.description = description;
     this.selectionGroup = selectedRegion;
     this.colSel = colSel;
     if (command.equalsIgnoreCase(TRIM_LEFT))
     {
-      if(column==0)
+      if (column == 0)
+      {
         return;
+      }
 
       columnsDeleted = column;
 
-      edits = new Edit[] { new Edit(CUT, seqs, 0, column, al)};
+      edits = new Edit[]
+          {
+          new Edit(CUT, seqs, 0, column, al)};
     }
     else if (command.equalsIgnoreCase(TRIM_RIGHT))
     {
-      int width = al.getWidth()-column-1;
-      if(width<2)
+      int width = al.getWidth() - column - 1;
+      if (width < 2)
       {
         return;
       }
 
-      columnsDeleted = width-1;
+      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
     int i, isize = edits[0].seqs.length;
     start = new int[isize];
-    for(i=0; i<isize; i++)
+    for (i = 0; i < isize; i++)
+    {
       start[i] = edits[0].seqs[i].getStart();
+    }
 
     performEdit(0);
   }
@@ -89,7 +97,7 @@ public class TrimRegionCommand
     int column, j, jSize = command.seqs.length;
     for (j = 0; j < jSize; j++)
     {
-      if(command.position==0)
+      if (command.position == 0)
       {
         //This is a TRIM_LEFT command
         column = command.seqs[j].findPosition(command.number);
@@ -98,7 +106,7 @@ public class TrimRegionCommand
       else
       {
         //This is a TRIM_RIGHT command
-        column = command.seqs[j].findPosition(command.position)-1;
+        column = command.seqs[j].findPosition(command.position) - 1;
         command.seqs[j].setEnd(column);
       }
     }
@@ -108,14 +116,19 @@ public class TrimRegionCommand
     if (command.position == 0)
     {
       deletedHiddenColumns = colSel.compensateForEdit(0, command.number);
-      if(selectionGroup!=null)
+      if (selectionGroup != null)
+      {
         selectionGroup.adjustForRemoveLeft(command.number);
+      }
     }
     else
     {
-      deletedHiddenColumns = colSel.compensateForEdit(command.position, command.number);
-      if(selectionGroup!=null)
+      deletedHiddenColumns = colSel.compensateForEdit(command.position,
+          command.number);
+      if (selectionGroup != null)
+      {
         selectionGroup.adjustForRemoveRight(command.position);
+      }
     }
   }
 
@@ -125,14 +138,14 @@ public class TrimRegionCommand
     int column, j, jSize = command.seqs.length;
     for (j = 0; j < jSize; j++)
     {
-      if(command.position==0)
+      if (command.position == 0)
       {
         command.seqs[j].setStart(start[j]);
       }
       else
       {
         column = command.seqs[j]
-            .findPosition(command.number+command.position)-1;
+            .findPosition(command.number + command.position) - 1;
         command.seqs[j].setEnd(column);
       }
     }
@@ -140,8 +153,10 @@ public class TrimRegionCommand
     if (command.position == 0)
     {
       colSel.compensateForEdit(0, -command.number);
-      if(selectionGroup!=null)
-        selectionGroup.adjustForRemoveLeft(-command.number);
+      if (selectionGroup != null)
+      {
+        selectionGroup.adjustForRemoveLeft( -command.number);
+      }
     }
 
     if (deletedHiddenColumns != null)
diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 8b159a6..e8787f4 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,640 +18,667 @@
  */
 package jalview.datamodel;
 
-import jalview.analysis.*;
-
 import java.util.*;
 
+import jalview.analysis.*;
+
 /** 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;
+  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!! */
-    public AlignmentAnnotation[] annotations;
-
-    HiddenSequences hiddenSequences = new HiddenSequences(this);
-
-    private void initAlignment(SequenceI[] seqs) {
-      int i=0;
-
-      if( jalview.util.Comparison.isNucleotide(seqs))
-        type = NUCLEOTIDE;
-      else
-        type = PROTEIN;
+  /** DOCUMENT ME!! */
+  public AlignmentAnnotation[] annotations;
 
-      sequences = new Vector();
+  HiddenSequences hiddenSequences = new HiddenSequences(this);
 
-      for (i = 0; i < seqs.length; i++)
-      {
-        sequences.addElement(seqs[i]);
-      }
+  private void initAlignment(SequenceI[] seqs)
+  {
+    int i = 0;
 
-    }
-    /** Make an alignment from an array of Sequences.
-     *
-     * @param sequences
-     */
-    public Alignment(SequenceI[] seqs)
+    if (jalview.util.Comparison.isNucleotide(seqs))
     {
-      initAlignment(seqs);
+      type = NUCLEOTIDE;
     }
-    /**
-     * Make a new alignment from an array of SeqCigars
-     * @param seqs SeqCigar[]
-     */
-    public Alignment(SeqCigar[] alseqs) {
-      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
-     */
-    public static AlignmentI createAlignment(CigarArray compactAlignment) {
-      throw new Error("Alignment(CigarArray) not yet implemented");
-      // this(compactAlignment.refCigars);
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Vector getSequences()
+    else
     {
-        return sequences;
+      type = PROTEIN;
     }
 
-    public SequenceI [] getSequencesArray()
-    {
-      SequenceI [] reply = new SequenceI[sequences.size()];
-      for(int i=0; i<sequences.size(); i++)
-      {
-        reply[i] = (SequenceI)sequences.elementAt(i);
-      }
-      return reply;
-    }
+    sequences = new Vector();
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public SequenceI getSequenceAt(int i)
+    for (i = 0; i < seqs.length; i++)
     {
-        if (i < sequences.size())
-        {
-            return (SequenceI) sequences.elementAt(i);
-        }
-
-        return null;
+      sequences.addElement(seqs[i]);
     }
 
-    /** Adds a sequence to the alignment.  Recalculates maxLength and size.
-     *
-     * @param snew
-     */
-    public void addSequence(SequenceI snew)
-    {
-      if(dataset!=null)
-      {
-        if(snew.getDatasetSequence()!=null)
-        {
-          getDataset().addSequence(snew.getDatasetSequence());
-        }
-        else
-        {
-          Sequence ds = new Sequence(snew.getName(),
-                                     AlignSeq.extractGaps("-. ",
-              snew.getSequenceAsString()),
-                                     snew.getStart(),
-                                     snew.getEnd());
-
-          snew.setDatasetSequence(ds);
-          getDataset().addSequence(ds);
-        }
-      }
-      sequences.addElement(snew);
+  }
 
-      hiddenSequences.adjustHeightSequenceAdded();
-    }
+  /** Make an alignment from an array of Sequences.
+   *
+   * @param sequences
+   */
+  public Alignment(SequenceI[] seqs)
+  {
+    initAlignment(seqs);
+  }
 
+  /**
+   * Make a new alignment from an array of SeqCigars
+   * @param seqs SeqCigar[]
+   */
+  public Alignment(SeqCigar[] alseqs)
+  {
+    SequenceI[] seqs = SeqCigar.createAlignmentSequences(alseqs, gapCharacter,
+        new ColumnSelection(), null);
+    initAlignment(seqs);
+  }
 
-    /** Adds a sequence to the alignment.  Recalculates maxLength and size.
-     *
-     * @param snew
-     */
-    public void setSequenceAt(int i, SequenceI snew)
-    {
-        SequenceI oldseq = getSequenceAt(i);
-        deleteSequence(oldseq);
+  /**
+   * 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)
+  {
+    throw new Error("Alignment(CigarArray) not yet implemented");
+    // this(compactAlignment.refCigars);
+  }
 
-        sequences.setElementAt(snew, i);
-    }
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Vector getSequences()
+  {
+    return sequences;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Vector getGroups()
+  public SequenceI[] getSequencesArray()
+  {
+    SequenceI[] reply = new SequenceI[sequences.size()];
+    for (int i = 0; i < sequences.size(); i++)
     {
-        return groups;
+      reply[i] = (SequenceI) sequences.elementAt(i);
     }
+    return reply;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param s DOCUMENT ME!
-     */
-    public void deleteSequence(SequenceI s)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param i DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public SequenceI getSequenceAt(int i)
+  {
+    if (i < sequences.size())
     {
-      deleteSequence(findIndex(s));
+      return (SequenceI) sequences.elementAt(i);
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     */
-    public void deleteSequence(int i)
+    return null;
+  }
+
+  /** Adds a sequence to the alignment.  Recalculates maxLength and size.
+   *
+   * @param snew
+   */
+  public void addSequence(SequenceI snew)
+  {
+    if (dataset != null)
     {
-      if(i>-1 && i<getHeight())
+      if (snew.getDatasetSequence() != null)
+      {
+        getDataset().addSequence(snew.getDatasetSequence());
+      }
+      else
       {
-        sequences.removeElementAt(i);
-        hiddenSequences.adjustHeightSequenceDeleted(i);
+        Sequence ds = new Sequence(snew.getName(),
+                                   AlignSeq.extractGaps("-. ",
+            snew.getSequenceAsString()),
+                                   snew.getStart(),
+                                   snew.getEnd());
+
+        snew.setDatasetSequence(ds);
+        getDataset().addSequence(ds);
       }
     }
+    sequences.addElement(snew);
 
+    hiddenSequences.adjustHeightSequenceAdded();
+  }
 
-    /**    */
-    public SequenceGroup findGroup(SequenceI s)
-    {
-        for (int i = 0; i < this.groups.size(); i++)
-        {
-            SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
+  /** Adds a sequence to the alignment.  Recalculates maxLength and size.
+   *
+   * @param snew
+   */
+  public void setSequenceAt(int i, SequenceI snew)
+  {
+    SequenceI oldseq = getSequenceAt(i);
+    deleteSequence(oldseq);
 
-            if (sg.getSequences(null).contains(s))
-            {
-                return sg;
-            }
-        }
+    sequences.setElementAt(snew, i);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Vector getGroups()
+  {
+    return groups;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param s DOCUMENT ME!
+   */
+  public void deleteSequence(SequenceI s)
+  {
+    deleteSequence(findIndex(s));
+  }
 
-        return null;
+  /**
+   * DOCUMENT ME!
+   *
+   * @param i DOCUMENT ME!
+   */
+  public void deleteSequence(int i)
+  {
+    if (i > -1 && i < getHeight())
+    {
+      sequences.removeElementAt(i);
+      hiddenSequences.adjustHeightSequenceDeleted(i);
     }
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param s DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public SequenceGroup[] findAllGroups(SequenceI s)
+  /**    */
+  public SequenceGroup findGroup(SequenceI s)
+  {
+    for (int i = 0; i < this.groups.size(); i++)
     {
-        Vector temp = new Vector();
+      SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
 
-        int gSize = groups.size();
-        for (int i = 0; i < gSize; i++)
-        {
-            SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
-            if(sg==null || sg.getSequences(null)==null)
-            {
-              this.deleteGroup(sg);
-              gSize--;
-              continue;
-            }
-
-            if (sg.getSequences(null).contains(s))
-            {
-                temp.addElement(sg);
-            }
-        }
+      if (sg.getSequences(null).contains(s))
+      {
+        return sg;
+      }
+    }
 
-        SequenceGroup[] ret = new SequenceGroup[temp.size()];
+    return null;
+  }
 
-        for (int i = 0; i < temp.size(); i++)
-        {
-            ret[i] = (SequenceGroup) temp.elementAt(i);
-        }
+  /**
+   * DOCUMENT ME!
+   *
+   * @param s DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public SequenceGroup[] findAllGroups(SequenceI s)
+  {
+    Vector temp = new Vector();
 
-        return ret;
+    int gSize = groups.size();
+    for (int i = 0; i < gSize; i++)
+    {
+      SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
+      if (sg == null || sg.getSequences(null) == null)
+      {
+        this.deleteGroup(sg);
+        gSize--;
+        continue;
+      }
+
+      if (sg.getSequences(null).contains(s))
+      {
+        temp.addElement(sg);
+      }
     }
 
+    SequenceGroup[] ret = new SequenceGroup[temp.size()];
 
+    for (int i = 0; i < temp.size(); i++)
+    {
+      ret[i] = (SequenceGroup) temp.elementAt(i);
+    }
+
+    return ret;
+  }
 
-    /**    */
-    public void addGroup(SequenceGroup sg)
+  /**    */
+  public void addGroup(SequenceGroup sg)
+  {
+    if (!groups.contains(sg))
     {
-        if (!groups.contains(sg))
+      if (hiddenSequences.getSize() > 0)
+      {
+        int i, iSize = sg.getSize();
+        for (i = 0; i < iSize; i++)
         {
-          if(hiddenSequences.getSize()>0)
+          if (!sequences.contains(sg.getSequenceAt(i)))
           {
-            int i, iSize = sg.getSize();
-            for (i = 0; i < iSize; i++)
-            {
-              if (!sequences.contains(sg.getSequenceAt(i)))
-              {
-                sg.deleteSequence(sg.getSequenceAt(i), false);
-                iSize--;
-                i--;
-              }
-            }
-
-            if (sg.getSize() < 1)
-              return;
+            sg.deleteSequence(sg.getSequenceAt(i), false);
+            iSize--;
+            i--;
           }
+        }
 
-          groups.addElement(sg);
+        if (sg.getSize() < 1)
+        {
+          return;
         }
-    }
+      }
 
-    /**
-     * DOCUMENT ME!
-     */
-    public void deleteAllGroups()
-    {
-        groups.removeAllElements();
+      groups.addElement(sg);
     }
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void deleteAllGroups()
+  {
+    groups.removeAllElements();
+  }
 
-    /**    */
-    public void deleteGroup(SequenceGroup g)
+  /**    */
+  public void deleteGroup(SequenceGroup g)
+  {
+    if (groups.contains(g))
     {
-        if (groups.contains(g))
-        {
-            groups.removeElement(g);
-        }
+      groups.removeElement(g);
     }
+  }
+
+  /**    */
+  public SequenceI findName(String name)
+  {
+    int i = 0;
 
-    /**    */
-    public SequenceI findName(String name)
+    while (i < sequences.size())
     {
-        int i = 0;
+      if (getSequenceAt(i).getName().equals(name))
+      {
+        return getSequenceAt(i);
+      }
 
-        while (i < sequences.size())
-        {
-            if (getSequenceAt(i).getName().equals(name))
-            {
-                return getSequenceAt(i);
-            }
+      i++;
+    }
 
-            i++;
-        }
+    return null;
+  }
 
-        return null;
-    }
+  public SequenceI[] findSequenceMatch(String name)
+  {
+    Vector matches = new Vector();
+    int i = 0;
 
-    public SequenceI [] findSequenceMatch(String name)
+    while (i < sequences.size())
     {
-      Vector matches = new Vector();
-      int i = 0;
-
-      while (i < sequences.size())
+      if (getSequenceAt(i).getName().equals(name))
       {
-          if (getSequenceAt(i).getName().equals(name))
-          {
-              matches.addElement(getSequenceAt(i));
-          }
-          i++;
+        matches.addElement(getSequenceAt(i));
       }
+      i++;
+    }
 
-      SequenceI [] result = new SequenceI[matches.size()];
-      for(i=0; i<result.length; i++)
-        result[i] = (SequenceI)matches.elementAt(i);
+    SequenceI[] result = new SequenceI[matches.size()];
+    for (i = 0; i < result.length; i++)
+    {
+      result[i] = (SequenceI) matches.elementAt(i);
+    }
 
-      return result;
+    return result;
 
-    }
+  }
 
+  /**    */
+  public int findIndex(SequenceI s)
+  {
+    int i = 0;
 
-    /**    */
-    public int findIndex(SequenceI s)
+    while (i < sequences.size())
     {
-        int i = 0;
+      if (s == getSequenceAt(i))
+      {
+        return i;
+      }
 
-        while (i < sequences.size())
-        {
-            if (s == getSequenceAt(i))
-            {
-                return i;
-            }
+      i++;
+    }
 
-            i++;
-        }
+    return -1;
+  }
 
-        return -1;
-    }
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public int getHeight()
+  {
+    return sequences.size();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public int getWidth()
+  {
+    int maxLength = -1;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getHeight()
+    for (int i = 0; i < sequences.size(); i++)
     {
-        return sequences.size();
+      if (getSequenceAt(i).getLength() > maxLength)
+      {
+        maxLength = getSequenceAt(i).getLength();
+      }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getWidth()
-    {
-        int maxLength = -1;
+    return maxLength;
+  }
 
-        for (int i = 0; i < sequences.size(); i++)
-        {
-            if (getSequenceAt(i).getLength() > maxLength)
-            {
-                maxLength = getSequenceAt(i).getLength();
-            }
-        }
+  /**
+   * DOCUMENT ME!
+   *
+   * @param gc DOCUMENT ME!
+   */
+  public void setGapCharacter(char gc)
+  {
+    gapCharacter = gc;
 
-        return maxLength;
+    for (int i = 0; i < sequences.size(); i++)
+    {
+      Sequence seq = (Sequence) sequences.elementAt(i);
+      seq.setSequence(seq.getSequenceAsString()
+                      .replace('.', gc)
+                      .replace('-', gc)
+                      .replace(' ', gc)
+          );
     }
+  }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public char getGapCharacter()
+  {
+    return gapCharacter;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param gc DOCUMENT ME!
-     */
-    public void setGapCharacter(char gc)
-    {
-        gapCharacter = gc;
-
-        for (int i = 0; i < sequences.size(); i++)
-        {
-            Sequence seq = (Sequence) sequences.elementAt(i);
-            seq.setSequence(seq.getSequenceAsString()
-                            .replace('.', gc)
-                            .replace('-', gc)
-                            .replace(' ', gc)
-                );
-        }
-    }
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public boolean isAligned()
+  {
+    int width = getWidth();
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public char getGapCharacter()
+    for (int i = 0; i < sequences.size(); i++)
     {
-        return gapCharacter;
+      if (getSequenceAt(i).getLength() != width)
+      {
+        return false;
+      }
     }
 
+    return true;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean isAligned()
-    {
-        int width = getWidth();
-
-        for (int i = 0; i < sequences.size(); i++)
-        {
-            if (getSequenceAt(i).getLength() != width)
-            {
-                return false;
-            }
-        }
+  /**
+   * DOCUMENT ME!
+   *
+   * @param aa DOCUMENT ME!
+   */
+  public void deleteAnnotation(AlignmentAnnotation aa)
+  {
+    int aSize = 1;
 
-        return true;
+    if (annotations != null)
+    {
+      aSize = annotations.length;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param aa DOCUMENT ME!
-     */
-    public void deleteAnnotation(AlignmentAnnotation aa)
+    if (aSize < 1)
     {
-        int aSize = 1;
-
-        if (annotations != null)
-        {
-            aSize = annotations.length;
-        }
-
-        if(aSize<1)
-          return;
-
-        AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize - 1];
+      return;
+    }
 
-        int tIndex = 0;
+    AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize - 1];
 
-        for (int i = 0; i < aSize; i++)
-        {
-            if (annotations[i] == aa)
-            {
-                continue;
-            }
+    int tIndex = 0;
 
-            temp[tIndex] = annotations[i];
-            tIndex++;
-        }
+    for (int i = 0; i < aSize; i++)
+    {
+      if (annotations[i] == aa)
+      {
+        continue;
+      }
 
-        annotations = temp;
+      temp[tIndex] = annotations[i];
+      tIndex++;
     }
 
+    annotations = temp;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param aa DOCUMENT ME!
-     */
-    public void addAnnotation(AlignmentAnnotation aa)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param aa DOCUMENT ME!
+   */
+  public void addAnnotation(AlignmentAnnotation aa)
+  {
+    int aSize = 1;
+    if (annotations != null)
     {
-        int aSize = 1;
-        if (annotations != null)
-        {
-            aSize = annotations.length + 1;
-        }
-
-        AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];
+      aSize = annotations.length + 1;
+    }
 
-        temp[aSize-1] = aa;
+    AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];
 
-        int i = 0;
+    temp[aSize - 1] = aa;
 
-        if (aSize > 1)
-        {
-            for (i = 0; i < (aSize-1); i++)
-            {
-                temp[i] = annotations[i];
-            }
-        }
+    int i = 0;
 
-        annotations = temp;
+    if (aSize > 1)
+    {
+      for (i = 0; i < (aSize - 1); i++)
+      {
+        temp[i] = annotations[i];
+      }
     }
 
-    public void setAnnotationIndex(AlignmentAnnotation aa, int index)
+    annotations = temp;
+  }
+
+  public void setAnnotationIndex(AlignmentAnnotation aa, int index)
+  {
+    if (aa == null || annotations == null || annotations.length - 1 < index)
     {
-      if(aa==null || annotations==null || annotations.length-1<index)
-        return;
+      return;
+    }
 
-      int aSize = annotations.length;
-      AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];
+    int aSize = annotations.length;
+    AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];
 
-      temp[index] = aa;
+    temp[index] = aa;
 
-      for (int i = 0; i < aSize; i++)
+    for (int i = 0; i < aSize; i++)
+    {
+      if (i == index)
       {
-        if(i==index)
-          continue;
-
-        if(i<index)
-          temp[i] = annotations[i];
-        else
-          temp[i] = annotations[i-1];
+        continue;
       }
 
-        annotations = temp;
+      if (i < index)
+      {
+        temp[i] = annotations[i];
+      }
+      else
+      {
+        temp[i] = annotations[i - 1];
+      }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public AlignmentAnnotation[] getAlignmentAnnotation()
+    annotations = temp;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public AlignmentAnnotation[] getAlignmentAnnotation()
+  {
+    return annotations;
+  }
+
+  public void setNucleotide(boolean b)
+  {
+    if (b)
     {
-        return annotations;
+      type = NUCLEOTIDE;
     }
-
-    public void setNucleotide(boolean b)
+    else
     {
-      if(b)
-        type = NUCLEOTIDE;
-      else
-        type = PROTEIN;
+      type = PROTEIN;
     }
+  }
 
-    public boolean isNucleotide()
+  public boolean isNucleotide()
+  {
+    if (type == NUCLEOTIDE)
     {
-      if(type==NUCLEOTIDE)
-        return true;
-      else
-        return false;
+      return true;
     }
-
-    public void setDataset(Alignment data)
+    else
     {
-      if(dataset==null && data==null)
+      return false;
+    }
+  }
+
+  public void setDataset(Alignment data)
+  {
+    if (dataset == null && data == null)
+    {
+      // Create a new dataset for this alignment.
+      // Can only be done once, if dataset is not null
+      // This will not be performed
+      Sequence[] seqs = new Sequence[getHeight()];
+      SequenceI currentSeq;
+      for (int i = 0; i < getHeight(); i++)
       {
-        // Create a new dataset for this alignment.
-        // Can only be done once, if dataset is not null
-        // This will not be performed
-        Sequence[] seqs = new Sequence[getHeight()];
-        SequenceI currentSeq;
-        for (int i = 0; i < getHeight(); i++)
+        currentSeq = getSequenceAt(i);
+        if (currentSeq.getDatasetSequence() != null)
         {
-          currentSeq = getSequenceAt(i);
-          if(currentSeq.getDatasetSequence()!=null)
-          {
-            seqs[i] = (Sequence)currentSeq.getDatasetSequence();
-          }
-          else
-          {
-            seqs[i] = new Sequence(currentSeq.getName(),
-                                   AlignSeq.extractGaps(
-                                       jalview.util.Comparison.GapChars,
-                                       currentSeq.getSequenceAsString()
-                                   ),
-                                   currentSeq.getStart(),
-                                   currentSeq.getEnd());
-            seqs[i].sequenceFeatures = currentSeq.getSequenceFeatures();
-            seqs[i].setDescription(currentSeq.getDescription());
-            getSequenceAt(i).setSequenceFeatures(null);
-            getSequenceAt(i).setDatasetSequence(seqs[i]);
-          }
+          seqs[i] = (Sequence) currentSeq.getDatasetSequence();
+        }
+        else
+        {
+          seqs[i] = new Sequence(currentSeq.getName(),
+                                 AlignSeq.extractGaps(
+                                     jalview.util.Comparison.GapChars,
+                                     currentSeq.getSequenceAsString()
+                                 ),
+                                 currentSeq.getStart(),
+                                 currentSeq.getEnd());
+          seqs[i].sequenceFeatures = currentSeq.getSequenceFeatures();
+          seqs[i].setDescription(currentSeq.getDescription());
+          getSequenceAt(i).setSequenceFeatures(null);
+          getSequenceAt(i).setDatasetSequence(seqs[i]);
         }
-
-        dataset = new Alignment(seqs);
-      }
-      else if(dataset==null && data!=null)
-      {
-        dataset = data;
       }
-    }
 
-    public Alignment getDataset()
+      dataset = new Alignment(seqs);
+    }
+    else if (dataset == null && data != null)
     {
-      return dataset;
+      dataset = data;
     }
+  }
 
-    public boolean padGaps()
-    {
-      boolean modified=false;
+  public Alignment getDataset()
+  {
+    return dataset;
+  }
+
+  public boolean padGaps()
+  {
+    boolean modified = false;
 
-      //Remove excess gaps from the end of alignment
-      int maxLength = -1;
+    //Remove excess gaps from the end of alignment
+    int maxLength = -1;
 
-      SequenceI current;
-      for (int i = 0; i < sequences.size(); i++)
+    SequenceI current;
+    for (int i = 0; i < sequences.size(); i++)
+    {
+      current = getSequenceAt(i);
+      for (int j = current.getLength(); j > maxLength; j--)
       {
-        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;
-          }
+          maxLength = j;
+          break;
         }
       }
+    }
 
-      maxLength++;
+    maxLength++;
 
-      int cLength;
-      for (int i = 0; i < sequences.size();
-           i++)
-      {
-        current = getSequenceAt(i);
-        cLength = current.getLength();
+    int cLength;
+    for (int i = 0; i < sequences.size();
+         i++)
+    {
+      current = getSequenceAt(i);
+      cLength = current.getLength();
 
-        if (cLength < maxLength)
-        {
-          current.insertCharAt(cLength,
-                              maxLength-cLength, gapCharacter);
-          modified=true;
-        }
-        else if(current.getLength() > maxLength)
-        {
-          current.deleteChars(maxLength, current.getLength());
-        }
+      if (cLength < maxLength)
+      {
+        current.insertCharAt(cLength,
+                             maxLength - cLength, gapCharacter);
+        modified = true;
+      }
+      else if (current.getLength() > maxLength)
+      {
+        current.deleteChars(maxLength, current.getLength());
       }
-      return modified;
     }
+    return modified;
+  }
 
-    public HiddenSequences getHiddenSequences()
-    {
-      return hiddenSequences;
-    }
+  public HiddenSequences getHiddenSequences()
+  {
+    return hiddenSequences;
+  }
 
   public CigarArray getCompactAlignment()
   {
     SeqCigar alseqs[] = new SeqCigar[sequences.size()];
-    for (int i=0; i<sequences.size(); i++) {
-      alseqs[i] = new SeqCigar((SequenceI) sequences.elementAt(i));
+    for (int i = 0; i < sequences.size(); i++)
+    {
+      alseqs[i] = new SeqCigar( (SequenceI) sequences.elementAt(i));
     }
     CigarArray cal = new CigarArray(alseqs);
     cal.addOperation(CigarArray.M, getWidth());
diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 66ea733..c675a75 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -1,24 +1,23 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 jalview.datamodel;
 
-
 /**
  * DOCUMENT ME!
  *
@@ -33,320 +32,334 @@ public class AlignmentAnnotation
 
   public String annotationId;
 
-    public SequenceI sequenceRef;
+  public SequenceI sequenceRef;
 
-    /** DOCUMENT ME!! */
-    public String label;
+  /** DOCUMENT ME!! */
+  public String label;
 
-    /** DOCUMENT ME!! */
-    public String description;
+  /** DOCUMENT ME!! */
+  public String description;
 
-    /** DOCUMENT ME!! */
-    public Annotation[] annotations;
+  /** DOCUMENT ME!! */
+  public Annotation[] annotations;
 
-    public java.util.Hashtable sequenceMapping;
+  public java.util.Hashtable sequenceMapping;
 
-    /** DOCUMENT ME!! */
-    public float graphMin;
+  /** DOCUMENT ME!! */
+  public float graphMin;
 
-    /** DOCUMENT ME!! */
-    public float graphMax;
+  /** DOCUMENT ME!! */
+  public float graphMax;
 
-    public GraphLine threshold;
+  public GraphLine threshold;
 
-    // Graphical hints and tips
+  // Graphical hints and tips
 
-    /** DOCUMENT ME!! */
-    public boolean editable = false;
+  /** DOCUMENT ME!! */
+  public boolean editable = false;
 
-    /** DOCUMENT ME!! */
-    public boolean hasIcons; //
+  /** DOCUMENT ME!! */
+  public boolean hasIcons; //
 
-    /** DOCUMENT ME!! */
-    public boolean hasText;
+  /** DOCUMENT ME!! */
+  public boolean hasText;
 
-    /** DOCUMENT ME!! */
-    public boolean visible = true;
+  /** DOCUMENT ME!! */
+  public boolean visible = true;
 
-    public int graphGroup = -1;
+  public int graphGroup = -1;
 
-    /** DOCUMENT ME!! */
-    public int height = 0;
+  /** DOCUMENT ME!! */
+  public int height = 0;
 
-    public int graph = 0;
+  public int graph = 0;
 
-    public int graphHeight = 40;
+  public int graphHeight = 40;
 
-    public static final int NO_GRAPH = 0;
+  public static final int NO_GRAPH = 0;
 
-    public static final int BAR_GRAPH = 1;
+  public static final int BAR_GRAPH = 1;
 
-    public static final int LINE_GRAPH = 2;
+  public static final int LINE_GRAPH = 2;
 
-    public static int getGraphValueFromString(String string)
+  public static int getGraphValueFromString(String string)
+  {
+    if (string.equalsIgnoreCase("BAR_GRAPH"))
     {
-      if(string.equalsIgnoreCase("BAR_GRAPH"))
-        return BAR_GRAPH;
-      else if(string.equalsIgnoreCase("LINE_GRAPH"))
-        return LINE_GRAPH;
-      else
-        return NO_GRAPH;
+      return BAR_GRAPH;
     }
-
-    /**
-     * Creates a new AlignmentAnnotation object.
-     *
-     * @param label DOCUMENT ME!
-     * @param description DOCUMENT ME!
-     * @param annotations DOCUMENT ME!
-     */
-    public AlignmentAnnotation(String label, String description,
-        Annotation[] annotations)
+    else if (string.equalsIgnoreCase("LINE_GRAPH"))
     {
-        // always editable?
-        editable = true;
-        this.label = label;
-        this.description = description;
-        this.annotations = annotations;
-
-       areLabelsSecondaryStructure();
+      return LINE_GRAPH;
     }
-
-    void areLabelsSecondaryStructure()
+    else
     {
-      boolean nonSSLabel = false;
-      for (int i = 0; i < annotations.length; i++)
+      return NO_GRAPH;
+    }
+  }
+
+  /**
+   * Creates a new AlignmentAnnotation object.
+   *
+   * @param label DOCUMENT ME!
+   * @param description DOCUMENT ME!
+   * @param annotations DOCUMENT ME!
+   */
+  public AlignmentAnnotation(String label, String description,
+                             Annotation[] annotations)
+  {
+    // always editable?
+    editable = true;
+    this.label = label;
+    this.description = description;
+    this.annotations = annotations;
+
+    areLabelsSecondaryStructure();
+  }
+
+  void areLabelsSecondaryStructure()
+  {
+    boolean nonSSLabel = false;
+    for (int i = 0; i < annotations.length; i++)
+    {
+      if (annotations[i] == null)
       {
-        if(annotations[i]==null)
-          continue;
+        continue;
+      }
 
-        if (annotations[i].secondaryStructure == 'H' ||
-            annotations[i].secondaryStructure == 'E')
-        {
-          hasIcons = true;
-        }
+      if (annotations[i].secondaryStructure == 'H' ||
+          annotations[i].secondaryStructure == 'E')
+      {
+        hasIcons = true;
+      }
 
-        if (annotations[i].displayCharacter.length()==1
-            && !annotations[i].displayCharacter.equals("H")
-            && !annotations[i].displayCharacter.equals("E")
-            && !annotations[i].displayCharacter.equals("-")
-            && !annotations[i].displayCharacter.equals("."))
+      if (annotations[i].displayCharacter.length() == 1
+          && !annotations[i].displayCharacter.equals("H")
+          && !annotations[i].displayCharacter.equals("E")
+          && !annotations[i].displayCharacter.equals("-")
+          && !annotations[i].displayCharacter.equals("."))
+      {
+        if (jalview.schemes.ResidueProperties.aaIndex
+            [annotations[i].displayCharacter.charAt(0)] < 23)
         {
-          if(jalview.schemes.ResidueProperties.aaIndex
-             [annotations[i].displayCharacter.charAt(0)]<23)
-          {
-            nonSSLabel = true;
-          }
+          nonSSLabel = true;
         }
+      }
 
-        if (annotations[i].displayCharacter.length() > 0)
-        {
-          hasText = true;
-        }
+      if (annotations[i].displayCharacter.length() > 0)
+      {
+        hasText = true;
       }
+    }
 
-      if(nonSSLabel)
+    if (nonSSLabel)
+    {
+      hasIcons = false;
+      for (int j = 0; j < annotations.length; j++)
       {
-        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].secondaryStructure = ' ';
-          }
-
+          annotations[j].displayCharacter
+              = String.valueOf(annotations[j].secondaryStructure);
+          annotations[j].secondaryStructure = ' ';
         }
 
       }
 
-      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!
-     */
-    public AlignmentAnnotation(String label, String description,
-        Annotation[] annotations, float min, float max, int graphType)
+    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!
+   */
+  public AlignmentAnnotation(String label, String description,
+                             Annotation[] annotations, float min, float max,
+                             int graphType)
+  {
+    // graphs are not editable
+    this.label = label;
+    this.description = description;
+    this.annotations = annotations;
+    graph = graphType;
+
+    boolean drawValues = true;
+
+    if (min == max)
     {
-        // graphs are not editable
-        this.label = label;
-        this.description = description;
-        this.annotations = annotations;
-        graph = graphType;
+      min = 999999999;
+      for (int i = 0; i < annotations.length; i++)
+      {
+        if (annotations[i] == null)
+        {
+          continue;
+        }
 
-        boolean drawValues = true;
+        if (drawValues && annotations[i].displayCharacter.length() > 1)
+        {
+          drawValues = false;
+        }
+
+        if (annotations[i].value > max)
+        {
+          max = annotations[i].value;
+        }
 
-        if (min == max)
+        if (annotations[i].value < min)
         {
-            min = 999999999;
-            for (int i = 0; i < annotations.length; i++)
-            {
-                if (annotations[i] == null)
-                {
-                    continue;
-                }
-
-                if(drawValues && annotations[i].displayCharacter.length() > 1 )
-                {
-                  drawValues = false;
-                }
-
-                if (annotations[i].value > max)
-                {
-                    max = annotations[i].value;
-                }
-
-                if (annotations[i].value < min)
-                {
-                    min = annotations[i].value;
-                }
-            }
+          min = annotations[i].value;
         }
+      }
+    }
 
-        graphMin = min;
-        graphMax = max;
+    graphMin = min;
+    graphMax = max;
 
-        areLabelsSecondaryStructure();
+    areLabelsSecondaryStructure();
 
-        if(!drawValues && graphType!=NO_GRAPH)
+    if (!drawValues && graphType != NO_GRAPH)
+    {
+      for (int i = 0; i < annotations.length; i++)
+      {
+        if (annotations[i] != null)
         {
-          for (int i = 0; i < annotations.length; i++)
-          {
-            if (annotations[i] != null)
-              annotations[i].displayCharacter = "";
-          }
+          annotations[i].displayCharacter = "";
         }
+      }
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String toString()
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public String toString()
+  {
+    StringBuffer buffer = new StringBuffer();
+
+    for (int i = 0; i < annotations.length; i++)
     {
-        StringBuffer buffer = new StringBuffer();
-
-        for (int i = 0; i < annotations.length; i++)
+      if (annotations[i] != null)
+      {
+        if (graph != 0)
         {
-            if (annotations[i] != null)
-            {
-                if (graph!=0)
-                {
-                    buffer.append(annotations[i].value);
-                }
-                else if (hasIcons)
-                {
-                    buffer.append(annotations[i].secondaryStructure);
-                }
-                else
-                {
-                    buffer.append(annotations[i].displayCharacter);
-                }
-            }
-
-            buffer.append(", ");
+          buffer.append(annotations[i].value);
         }
-
-        if (label.equals("Consensus"))
+        else if (hasIcons)
         {
-            buffer.append("\n");
+          buffer.append(annotations[i].secondaryStructure);
+        }
+        else
+        {
+          buffer.append(annotations[i].displayCharacter);
+        }
+      }
+
+      buffer.append(", ");
+    }
 
-            for (int i = 0; i < annotations.length; i++)
-            {
-                if (annotations[i] != null)
-                {
-                    buffer.append(annotations[i].description);
-                }
+    if (label.equals("Consensus"))
+    {
+      buffer.append("\n");
 
-                buffer.append(", ");
-            }
+      for (int i = 0; i < annotations.length; i++)
+      {
+        if (annotations[i] != null)
+        {
+          buffer.append(annotations[i].description);
         }
 
-        return buffer.toString();
+        buffer.append(", ");
       }
+    }
 
-      public void setThreshold(GraphLine line)
-      {
-        threshold = line;
-      }
+    return buffer.toString();
+  }
+
+  public void setThreshold(GraphLine line)
+  {
+    threshold = line;
+  }
+
+  public GraphLine getThreshold()
+  {
+    return threshold;
+  }
+
+  /**
+   * 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)
+  {
+
+    if (seqRef == null)
+    {
+      return;
+    }
 
-      public GraphLine getThreshold()
-      {
-          return threshold;
-      }
+    sequenceMapping = new java.util.Hashtable();
+
+    sequenceRef = seqRef;
+    int seqPos;
 
-      /**
-       * 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)
+    for (int i = 0; i < annotations.length; i++)
+    {
+      if (annotations[i] != null)
       {
+        if (alreadyMapped)
+        {
+          seqPos = seqRef.findPosition(i);
+        }
+        else
+        {
+          seqPos = i + startRes;
+        }
 
-        if(seqRef == null)
-          return;
+        sequenceMapping.put(new Integer(seqPos), annotations[i]);
+      }
+    }
 
+  }
 
-        sequenceMapping = new java.util.Hashtable();
+  public void adjustForAlignment()
+  {
+    int a = 0, aSize = sequenceRef.getLength();
 
-        sequenceRef = seqRef;
-        int seqPos;
+    if (aSize == 0)
+    {
+      //Its been deleted
+      return;
+    }
 
-        for(int i = 0; i < annotations.length; i++)
-        {
-            if (annotations[i] != null)
-            {
-              if(alreadyMapped)
-                seqPos = seqRef.findPosition(i);
-              else
-                seqPos = i+startRes;
+    int position;
+    Annotation[] temp = new Annotation[aSize];
+    Integer index;
 
-              sequenceMapping.put(new Integer(seqPos), annotations[i]);
-            }
-         }
+    for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++)
+    {
+      index = new Integer(a);
+      if (sequenceMapping.containsKey(index))
+      {
+        position = sequenceRef.findIndex(a) - 1;
 
+        temp[position] = (Annotation) sequenceMapping.get(index);
       }
+    }
 
-      public void adjustForAlignment()
-      {
-          int a=0, aSize = sequenceRef.getLength();
-
-          if(aSize == 0)
-          {
-            //Its been deleted
-            return;
-          }
-
-          int position;
-          Annotation[] temp = new Annotation[aSize];
-          Integer index;
-
-          for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++)
-          {
-              index = new Integer(a);
-              if(sequenceMapping.containsKey(index))
-              {
-                position = sequenceRef.findIndex(a)-1;
-
-                temp[position] = (Annotation)sequenceMapping.get(index);
-              }
-          }
-
-          annotations = temp;
-      }
+    annotations = temp;
+  }
 }
-
-
diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index baaebc2..a81a965 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -1,238 +1,231 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 jalview.datamodel;
 
 import java.util.*;
 
-
 /** Data structure to hold and manipulate a multiple sequence alignment
  */
 public interface AlignmentI
 {
-    /**
-     *  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.
-     *
-     * @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.
-     */
-    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.
-     */
-    public void setSequenceAt(int i, SequenceI seq);
-
-    /**
-     * Deletes a sequence from the alignment
-     *
-     * @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.
-     */
-    public void deleteSequence(int i);
-
-
-    /**
-     * Finds sequence in alignment using sequence name as query.
-     *
-     * @param name Id of sequence to search for.
-     *
-     * @return Sequence matching query, if found. If not found returns null.
-     */
-    public SequenceI findName(String name);
-
-    public SequenceI [] findSequenceMatch(String name);
-
-    /**
-     * Finds index of a given sequence in the alignment.
-     *
-     * @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.
-     */
-    public SequenceGroup findGroup(SequenceI s);
-
-    /**
-     * Finds all groups that a given sequence is part of.
-     *
-     * @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.
-     */
-    public void addGroup(SequenceGroup sg);
-
-    /**
-     * Deletes a specific SequenceGroup
-     *
-     * @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.
-     */
-    public void deleteAllGroups();
-
-
-    /**
-     * Adds a new AlignmentAnnotation to this alignment
-     */
-    public void addAnnotation(AlignmentAnnotation aa);
-
-
-    public void setAnnotationIndex(AlignmentAnnotation aa, int index);
-
-    /**
-     * Deletes a specific AlignmentAnnotation from the alignment.
-     *
-     * @param aa DOCUMENT ME!
-     */
-    public void deleteAnnotation(AlignmentAnnotation aa);
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public AlignmentAnnotation[] getAlignmentAnnotation();
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param gc DOCUMENT ME!
-     */
-    public void setGapCharacter(char gc);
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public char getGapCharacter();
-
-
-    /**
-     * Returns true if alignment is nucleotide sequence
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean isNucleotide();
-
-    /**
-     * Set true if the alignment is a nucleotide sequence
-     *
-     * @return
-     */
-    public void setNucleotide(boolean b);
-
-
-    public Alignment getDataset();
-
-    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();
-
-
-    public HiddenSequences getHiddenSequences();
-    /**
-     * Compact representation of alignment
-     * @return CigarArray
-     */
-    public CigarArray getCompactAlignment();
+  /**
+   *  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.
+   *
+   * @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.
+   */
+  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.
+   */
+  public void setSequenceAt(int i, SequenceI seq);
+
+  /**
+   * Deletes a sequence from the alignment
+   *
+   * @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.
+   */
+  public void deleteSequence(int i);
+
+  /**
+   * Finds sequence in alignment using sequence name as query.
+   *
+   * @param name Id of sequence to search for.
+   *
+   * @return Sequence matching query, if found. If not found returns null.
+   */
+  public SequenceI findName(String name);
+
+  public SequenceI[] findSequenceMatch(String name);
+
+  /**
+   * Finds index of a given sequence in the alignment.
+   *
+   * @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.
+   */
+  public SequenceGroup findGroup(SequenceI s);
+
+  /**
+   * Finds all groups that a given sequence is part of.
+   *
+   * @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.
+   */
+  public void addGroup(SequenceGroup sg);
+
+  /**
+   * Deletes a specific SequenceGroup
+   *
+   * @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.
+   */
+  public void deleteAllGroups();
+
+  /**
+   * Adds a new AlignmentAnnotation to this alignment
+   */
+  public void addAnnotation(AlignmentAnnotation aa);
+
+  public void setAnnotationIndex(AlignmentAnnotation aa, int index);
+
+  /**
+   * Deletes a specific AlignmentAnnotation from the alignment.
+   *
+   * @param aa DOCUMENT ME!
+   */
+  public void deleteAnnotation(AlignmentAnnotation aa);
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public AlignmentAnnotation[] getAlignmentAnnotation();
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param gc DOCUMENT ME!
+   */
+  public void setGapCharacter(char gc);
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public char getGapCharacter();
+
+  /**
+   * Returns true if alignment is nucleotide sequence
+   *
+   * @return DOCUMENT ME!
+   */
+  public boolean isNucleotide();
+
+  /**
+   * Set true if the alignment is a nucleotide sequence
+   *
+   * @return
+   */
+  public void setNucleotide(boolean b);
+
+  public Alignment getDataset();
+
+  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();
+
+  public HiddenSequences getHiddenSequences();
+
+  /**
+   * Compact representation of alignment
+   * @return CigarArray
+   */
+  public CigarArray getCompactAlignment();
 }
diff --git a/src/jalview/datamodel/AlignmentOrder.java b/src/jalview/datamodel/AlignmentOrder.java
index 639dd47..b149749 100755
--- a/src/jalview/datamodel/AlignmentOrder.java
+++ b/src/jalview/datamodel/AlignmentOrder.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -20,7 +20,6 @@ package jalview.datamodel;
 
 import java.util.*;
 
-
 /**
  * <p>Title: </p>
  *
@@ -35,241 +34,283 @@ import java.util.*;
  */
 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.
+  // 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;
-       }
-     */
+  /*  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 FILE = 0;
 
-    /** DOCUMENT ME!! */
-    public static final int MSA = 1;
+  /** 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;
+  /** 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()
-    {
-    }
+  /**
+   * Creates a new AlignmentOrder object.
+   */
+  public AlignmentOrder()
+  {
+  }
 
-    /**
-     * AlignmentOrder
-     *
-     * @param anOrder Vector
-     */
-    public AlignmentOrder(Vector anOrder)
+  /**
+   * 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 = anOrder;
+      Order.addElement(orderFrom.getSequenceAt(i));
     }
+  }
 
-    /**
-     * AlignmentOrder
-     *
-     * @param orderFrom AlignmentI
-     */
-    public AlignmentOrder(AlignmentI orderFrom)
-    {
-        Order = new Vector();
+  /**
+   * Creates a new AlignmentOrder object.
+   *
+   * @param orderFrom DOCUMENT ME!
+   */
+  public AlignmentOrder(SequenceI[] orderFrom)
+  {
+    Order = new Vector();
 
-        for (int i = 0, ns = orderFrom.getHeight(); i < ns; i++)
-        {
-            Order.addElement(orderFrom.getSequenceAt(i));
-        }
+    for (int i = 0, ns = orderFrom.length; i < ns; i++)
+    {
+      Order.addElement(orderFrom[i]);
     }
+  }
 
-    /**
-     * Creates a new AlignmentOrder object.
-     *
-     * @param orderFrom DOCUMENT ME!
-     */
-    public AlignmentOrder(SequenceI[] orderFrom)
-    {
-        Order = new Vector();
+  /**
+   * DOCUMENT ME!
+   *
+   * @param Type DOCUMENT ME!
+   */
+  public void setType(int Type)
+  {
+    this.Type = Type;
+  }
 
-        for (int i = 0, ns = orderFrom.length; i < ns; i++)
-        {
-            Order.addElement(orderFrom[i]);
-        }
-    }
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public int getType()
+  {
+    return Type;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param Type DOCUMENT ME!
-     */
-    public void setType(int Type)
-    {
-        this.Type = Type;
-    }
+  /**
+   * DOCUMENT ME!
+   *
+   * @param Name DOCUMENT ME!
+   */
+  public void setName(String Name)
+  {
+    this.Name = Name;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getType()
-    {
-        return Type;
-    }
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public String getName()
+  {
+    return Name;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param Name DOCUMENT ME!
-     */
-    public void setName(String Name)
-    {
-        this.Name = Name;
-    }
+  /**
+   * DOCUMENT ME!
+   *
+   * @param Order DOCUMENT ME!
+   */
+  public void setOrder(Vector Order)
+  {
+    this.Order = Order;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String getName()
-    {
-        return Name;
-    }
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Vector getOrder()
+  {
+    return Order;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param Order DOCUMENT ME!
-     */
-    public void setOrder(Vector 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)
     {
-        this.Order = Order;
+      Order.setElementAt(newref, found);
     }
+    return found > -1;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Vector getOrder()
+  /**
+   * 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)
     {
-        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);
+      if (o == null)
+      {
+        return false;
       }
-      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))
+      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;
+        }
+      }
+      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;
+    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;
+        }
+      }
+      else
+      {
+        return false;
       }
-      return true;
     }
-    /**
-     * AlignmentOrder
-     *
-     * @param orderThis AlignmentI
-     * @param byThat AlignmentI
-     */
+    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
+  /* 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 8b86a82..79e0ba2 100644
--- a/src/jalview/datamodel/AlignmentView.java
+++ b/src/jalview/datamodel/AlignmentView.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,8 +18,6 @@
  */
 package jalview.datamodel;
 
-
-
 /**
  * <p>Title: </p>
  *
@@ -34,30 +32,34 @@ package jalview.datamodel;
  */
 public class AlignmentView
 {
-    /**
-     * Transient object compactly representing a 'view' of an alignment - with discontinuities marked.
-     */
-    private SeqCigar[] sequences = null;
+  /**
+   * 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;
+  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) {
+  public AlignmentView(CigarArray sdata, int firstcol)
+  {
     this(sdata);
-    firstCol=firstcol;
+    firstCol = firstcol;
   }
 
   public void setSequences(SeqCigar[] sequences)
@@ -74,6 +76,7 @@ public class AlignmentView
   {
     return sequences;
   }
+
   /**
    * @see CigarArray.getDeletedRegions
    * @return int[] { vis_start, sym_start, length }
@@ -82,16 +85,22 @@ public class AlignmentView
   {
     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) {
+  public Object[] getAlignmentAndColumnSelection(char gapCharacter)
+  {
     ColumnSelection colsel = new ColumnSelection();
 
-    return new Object[] { SeqCigar.createAlignmentSequences(sequences, gapCharacter, colsel, contigs), colsel};
+    return new Object[]
+        {
+        SeqCigar.createAlignmentSequences(sequences, gapCharacter, colsel,
+                                          contigs), colsel};
   }
+
   /**
    * getSequenceStrings
    *
@@ -100,8 +109,9 @@ public class AlignmentView
    */
   public String[] getSequenceStrings(char c)
   {
-    String[] seqs=new String[sequences.length];
-    for (int n=0; n<sequences.length; n++) {
+    String[] seqs = new String[sequences.length];
+    for (int n = 0; n < sequences.length; n++)
+    {
       String fullseq = sequences[n].getSequenceString(c);
       if (contigs != null)
       {
@@ -113,32 +123,42 @@ public class AlignmentView
           p = contigs[h + 1] + contigs[h + 2];
         }
         seqs[n] += fullseq.substring(p);
-      } else
+      }
+      else
+      {
         seqs[n] = fullseq;
+      }
     }
     return seqs;
   }
+
   /**
    *
    * @return visible number of columns in alignment view
    */
-  public int getWidth() {
+  public int getWidth()
+  {
     return width;
   }
 
-  protected void setWidth(int 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) {
+  public SequenceI[][] getVisibleContigs(char gapCharacter)
+  {
     SequenceI[][] smsa;
     int njobs = 1;
-    if (sequences==null || width<=0)
+    if (sequences == null || width <= 0)
+    {
       return null;
+    }
     if (contigs != null && contigs.length > 0)
     {
       int start = 0;
@@ -198,20 +218,25 @@ public class AlignmentView
     }
     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) {
+  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];
@@ -231,10 +256,15 @@ public class AlignmentView
             if (nvismsa[j] != null)
             {
               SequenceI mseq[] = nvismsa[j];
-              AlignmentOrder order=(orders==null) ? null : orders[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+")");
+              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++)
               {
@@ -250,7 +280,8 @@ public class AlignmentView
                   {
                     alignment[s].setEnd(mseq[s].getEnd());
                   }
-                  if (order!=null) {
+                  if (order != null)
+                  {
                     order.updateSequence(mseq[s], alignment[s]);
                   }
                 }
@@ -264,8 +295,9 @@ public class AlignmentView
                 // recover input data
                 for (int s = 0; s < sequences.length; s++)
                 {
-                  SequenceI oseq = sequences[s].getSeq(gapCharacter).getSubSequence(start,
-                      contigs[contig + 1]);
+                  SequenceI oseq = sequences[s].getSeq(gapCharacter).
+                      getSubSequence(start,
+                                     contigs[contig + 1]);
                   if (swidth < oseq.getLength())
                   {
                     swidth = oseq.getLength();
@@ -295,7 +327,8 @@ public class AlignmentView
           // 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 +
+            SequenceI hseq = sequences[s].getSeq(gapCharacter).getSubSequence(
+                contigs[contig +
                 1], start);
             if (alignment[s] == null)
             {
@@ -322,7 +355,7 @@ public class AlignmentView
           if (nvismsa[j] != null)
           {
             SequenceI mseq[] = nvismsa[j];
-            AlignmentOrder order = (orders!=null) ? orders[j] : null;
+            AlignmentOrder order = (orders != null) ? orders[j] : null;
             swidth = mseq[0].getLength();
             for (int s = 0; s < mseq.length; s++)
             {
@@ -338,7 +371,8 @@ public class AlignmentView
                 {
                   alignment[s].setEnd(mseq[s].getEnd());
                 }
-                if (order!=null) {
+                if (order != null)
+                {
                   order.updateSequence(mseq[s], alignment[s]);
                 }
               }
@@ -354,8 +388,9 @@ public class AlignmentView
                 // recover input data
                 for (int s = 0; s < sequences.length; s++)
                 {
-                  SequenceI oseq = sequences[s].getSeq(gapCharacter).getSubSequence(start,
-                      owidth + 1);
+                  SequenceI oseq = sequences[s].getSeq(gapCharacter).
+                      getSubSequence(start,
+                                     owidth + 1);
                   if (swidth < oseq.getLength())
                   {
                     swidth = oseq.getLength();
@@ -385,22 +420,37 @@ public class AlignmentView
           }
         }
       }
-      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()};
+      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() {
+  public int[] getVisibleContigs()
+  {
     if (contigs != null && contigs.length > 0)
     {
       int start = 0;
@@ -419,33 +469,41 @@ public class AlignmentView
       {
         nvis++;
       }
-      int viscontigs[] = new int[nvis*2];
-      nvis=0;
-      start=0;
-      for (int contig=0; contig<contigs.length; contig+=3) {
+      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;
+          viscontigs[nvis + 1] = contigs[contig + 1] - 1; // end is inclusive
+          nvis += 2;
         }
         start = contigs[contig + 1] + contigs[contig + 2];
       }
-      if (start<fwidth) {
+      if (start < fwidth)
+      {
         viscontigs[nvis] = start;
-        viscontigs[nvis+1]=fwidth; // end is inclusive
-        nvis+=2;
+        viscontigs[nvis + 1] = fwidth; // end is inclusive
+        nvis += 2;
       }
       return viscontigs;
-    } else {
-      return new int[] { 0, width};
+    }
+    else
+    {
+      return new int[]
+          {
+          0, width};
     }
   }
+
   /**
    *
    * @return position of first visible column of AlignmentView within its parent's alignment reference frame
    */
-  public int getAlignmentOrigin() {
+  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 18e4ee7..e0c49c8 100755
--- a/src/jalview/datamodel/Annotation.java
+++ b/src/jalview/datamodel/Annotation.java
@@ -1,26 +1,25 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 jalview.datamodel;
 
 import java.awt.*;
 
-
 /**
  * DOCUMENT ME!
  *
@@ -29,52 +28,52 @@ import java.awt.*;
  */
 public class Annotation
 {
-    /** DOCUMENT ME!! */
-    public String displayCharacter = "";
+  /** DOCUMENT ME!! */
+  public String displayCharacter = "";
 
-    /** DOCUMENT ME!! */
-    public String description = ""; // currently used as mouse over
+  /** DOCUMENT ME!! */
+  public String description = ""; // currently used as mouse over
 
-    /** DOCUMENT ME!! */
-    public char secondaryStructure = ' '; // recognises H and E
+  /** DOCUMENT ME!! */
+  public char secondaryStructure = ' '; // recognises H and E
 
-    /** DOCUMENT ME!! */
-    public float value;
+  /** DOCUMENT ME!! */
+  public float value;
 
-    // add visual cues here
+  // add visual cues here
 
-    /** DOCUMENT ME!! */
-    public Color colour = Color.black;
+  /** DOCUMENT ME!! */
+  public Color colour = Color.black;
 
-    /**
-     * Creates a new Annotation object.
-     *
-     * @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)
-    {
-        displayCharacter = displayChar;
-        description = desc;
-        secondaryStructure = ss;
-        value = val;
-    }
+  /**
+   * Creates a new Annotation object.
+   *
+   * @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)
+  {
+    displayCharacter = displayChar;
+    description = desc;
+    secondaryStructure = ss;
+    value = val;
+  }
 
-    /**
-     * 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!
-     */
-    public Annotation(String displayChar, String desc, char ss, float val,
-        Color colour)
-    {
-        this(displayChar, desc, ss, val);
-        this.colour = colour;
-    }
+  /**
+   * 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!
+   */
+  public Annotation(String displayChar, String desc, char ss, float val,
+                    Color colour)
+  {
+    this(displayChar, desc, ss, val);
+    this.colour = colour;
+  }
 }
diff --git a/src/jalview/datamodel/BinaryNode.java b/src/jalview/datamodel/BinaryNode.java
index 215ea6d..a7e8254 100755
--- a/src/jalview/datamodel/BinaryNode.java
+++ b/src/jalview/datamodel/BinaryNode.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -26,259 +26,259 @@ package jalview.datamodel;
  */
 public class BinaryNode
 {
-    Object element;
-    String name;
-    BinaryNode left;
-    BinaryNode right;
-    BinaryNode parent;
+  Object element;
+  String name;
+  BinaryNode left;
+  BinaryNode right;
+  BinaryNode parent;
 
-    /** DOCUMENT ME!! */
-    public int bootstrap;
+  /** DOCUMENT ME!! */
+  public int bootstrap;
 
-    /**
-     * Creates a new BinaryNode object.
-     */
-    public BinaryNode()
-    {
-        left = right = parent = null;
-        bootstrap = 0;
-    }
+  /**
+   * 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;
+  /**
+   * 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;
-    }
+    left = right = null;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Object element()
-    {
-        return element;
-    }
+  /**
+   * 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!
+   *
+   * @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!
+   *
+   * @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!
+   *
+   * @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!
+   *
+   * @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!
+   *
+   * @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!
+   *
+   * @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!
+   *
+   * @param n DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public BinaryNode setParent(BinaryNode n)
+  {
+    return parent = n;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean isLeaf()
+  /**
+   * 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)
     {
-        return (left == null) && (right == null);
+      this.setLeft(leftchild);
+      leftchild.detach();
+      leftchild.setParent(this);
     }
 
-    /**
-     * 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 (rightchild != null)
     {
-        if (leftchild != null)
-        {
-            this.setLeft(leftchild);
-            leftchild.detach();
-            leftchild.setParent(this);
-        }
-
-        if (rightchild != null)
-        {
-            this.setRight(rightchild);
-            rightchild.detach();
-            rightchild.setParent(this);
-        }
+      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()
+  /**
+   * 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 != null)
+      if (this.parent.left == this)
+      {
+        this.parent.left = null;
+      }
+      else
+      {
+        if (this.parent.right == this)
         {
-            if (this.parent.left == this)
-            {
-                this.parent.left = null;
-            }
-            else
-            {
-                if (this.parent.right == this)
-                {
-                    this.parent.right = null;
-                }
-            }
+          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;
+    this.parent = null;
 
-        do
-        {
-            c = c.parent();
-        }
-        while ((c != null) && (c.left() != null) && !c.left().isLeaf());
+    return this;
+  }
 
-        return c;
-    }
+  /**
+   * Traverses up through the tree until a node with a free leftchild is discovered.
+   * @return BinaryNode
+   */
+  public BinaryNode ascendLeft()
+  {
+    BinaryNode c = this;
 
-    /**
-     * 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()
+    do
     {
-        BinaryNode c = this;
+      c = c.parent();
+    }
+    while ( (c != null) && (c.left() != null) && !c.left().isLeaf());
 
-        do
-        {
-            c = c.parent();
-        }
-        while ((c != null) && (c.right() != null) && !c.right().isLeaf());
+    return c;
+  }
 
-        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;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param name DOCUMENT ME!
-     */
-    public void setName(String name)
+    do
     {
-        this.name = name;
+      c = c.parent();
     }
+    while ( (c != null) && (c.right() != null) && !c.right().isLeaf());
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String getName()
-    {
-        return this.name;
-    }
+    return c;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param boot DOCUMENT ME!
-     */
-    public void setBootstrap(int boot)
-    {
-        this.bootstrap = boot;
-    }
+  /**
+   * DOCUMENT ME!
+   *
+   * @param name DOCUMENT ME!
+   */
+  public void setName(String name)
+  {
+    this.name = name;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getBootstrap()
-    {
-        return bootstrap;
-    }
+  /**
+   * 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 a9e80b8..1cdc934 100755
--- a/src/jalview/datamodel/BinarySequence.java
+++ b/src/jalview/datamodel/BinarySequence.java
@@ -1,164 +1,169 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 jalview.datamodel;
 
 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!
-     */
-    public BinarySequence(String s)
+  int[] binary;
+  double[] dbinary;
+
+  /**
+   * Creates a new BinarySequence object.
+   *
+   * @param s DOCUMENT ME!
+   */
+  public BinarySequence(String s)
+  {
+    super("", s, 0, s.length());
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void encode()
+  {
+    // Set all matrix to 0
+    dbinary = new double[getSequence().length * 21];
+
+    int nores = 21;
+
+    for (int i = 0; i < dbinary.length; i++)
     {
-        super("", s, 0, s.length());
+      dbinary[i] = 0.0;
     }
 
-    /**
-     * DOCUMENT ME!
-     */
-    public void encode()
+    for (int i = 0; i < getSequence().length; i++)
     {
-        // Set all matrix to 0
-        dbinary = new double[getSequence().length * 21];
-
-        int nores = 21;
-
-        for (int i = 0; i < dbinary.length; i++)
-        {
-            dbinary[i] = 0.0;
-        }
-
-        for (int i = 0; i < getSequence().length; i++)
-        {
-            int aanum = 20;
-
-            try
-            {
-                aanum = ResidueProperties.aaIndex[getCharAt(i)];
-            }
-            catch (NullPointerException e)
-            {
-                aanum = 20;
-            }
-
-            if (aanum > 20)
-            {
-                aanum = 20;
-            }
-
-            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());
+      int aanum = 20;
+
+      try
+      {
+        aanum = ResidueProperties.aaIndex[getCharAt(i)];
+      }
+      catch (NullPointerException e)
+      {
+        aanum = 20;
+      }
+
+      if (aanum > 20)
+      {
+        aanum = 20;
+      }
+
+      dbinary[ (i * nores) + aanum] = 1.0;
     }
-    /**
-     * DOCUMENT ME!
-     */
-    public void blosumEncode()
+  }
+
+  /**
+   * ancode using substitution matrix given in matrix
+   * @param matrix
+   */
+  public void matrixEncode(ScoreMatrix matrix)
+  {
+    matrixEncode(matrix.isDNA() ? ResidueProperties.nucleotideIndex :
+                 ResidueProperties.aaIndex, matrix.getMatrix());
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void blosumEncode()
+  {
+    matrixEncode(ResidueProperties.aaIndex, ResidueProperties.getBLOSUM62());
+  }
+
+  private void matrixEncode(int[] aaIndex, int[][] matrix)
+  {
+    // Set all matrix to 0
+    dbinary = new double[getSequence().length * 21];
+
+    int nores = 21;
+
+    //for (int i = 0; i < dbinary.length; i++) {
+    //  dbinary[i] = 0.0;
+    //}
+    for (int i = 0; i < getSequence().length; i++)
     {
-      matrixEncode(ResidueProperties.aaIndex, ResidueProperties.getBLOSUM62());
+      int aanum = 20;
+
+      try
+      {
+        aanum = aaIndex[getCharAt(i)];
+      }
+      catch (NullPointerException e)
+      {
+        aanum = 20;
+      }
+
+      if (aanum > 20)
+      {
+        aanum = 20;
+      }
+
+      // Do the blosum thing
+
+      for (int j = 0; j < 20; j++)
+      {
+        dbinary[ (i * nores) + j] = matrix[aanum][j];
+      }
     }
-    private void matrixEncode(int[] aaIndex, int[][] matrix) {
-      // Set all matrix to 0
-        dbinary = new double[getSequence().length * 21];
-
-        int nores = 21;
-
-        //for (int i = 0; i < dbinary.length; i++) {
-        //  dbinary[i] = 0.0;
-        //}
-        for (int i = 0; i < getSequence().length; i++)
-        {
-            int aanum = 20;
-
-            try
-            {
-                aanum = aaIndex[getCharAt(i)];
-            }
-            catch (NullPointerException e)
-            {
-                aanum = 20;
-            }
-
-            if (aanum > 20)
-            {
-                aanum = 20;
-            }
-
-            // Do the blosum thing
-       
-            for (int j = 0; j < 20; j++)
-            {
-                dbinary[(i * nores) + j] = matrix[aanum][j];
-            }
-        }
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String toBinaryString()
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public String toBinaryString()
+  {
+    String out = "";
+
+    for (int i = 0; i < binary.length; i++)
     {
-        String out = "";
-
-        for (int i = 0; i < binary.length; i++)
-        {
-            out += (new Integer(binary[i])).toString();
+      out += (new Integer(binary[i])).toString();
 
-            if (i < (binary.length - 1))
-            {
-                out += " ";
-            }
-        }
-
-        return out;
+      if (i < (binary.length - 1))
+      {
+        out += " ";
+      }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public double[] getDBinary()
-    {
-        return dbinary;
-    }
+    return out;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public double[] getDBinary()
+  {
+    return dbinary;
+  }
 
 }
diff --git a/src/jalview/datamodel/CigarArray.java b/src/jalview/datamodel/CigarArray.java
index 9b60e56..c17e01e 100644
--- a/src/jalview/datamodel/CigarArray.java
+++ b/src/jalview/datamodel/CigarArray.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,19 +18,21 @@
  */
 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.
-     */
-    /**
-     * array of subject cigars
-     */
-    public CigarSimple refCigars[]=null;
-    private boolean seqcigararray=false;
-  private CigarArray() {
+  /**
+   * 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();
   }
 
@@ -42,12 +44,14 @@ public class CigarArray extends CigarBase
   {
     return seqcigararray;
   }
+
   /**
    * 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) {
+  public CigarArray(CigarSimple[] cigars)
+  {
     super();
     seqcigararray = true;
     if (cigars != null && cigars.length > 0)
@@ -64,27 +68,34 @@ public class CigarArray extends CigarBase
       }
     }
   }
+
   /**
    * @see Cigar.getSequenceAndDeletions
    * @param GapChar char
    * @return Object[][]
    */
-  protected Object[][] getArrayofSequenceAndDeletions(char GapChar) {
-      if (refCigars == null || refCigars.length == 0 || length == 0) {
-        return null;
+  protected Object[][] getArrayofSequenceAndDeletions(char GapChar)
+  {
+    if (refCigars == null || refCigars.length == 0 || length == 0)
+    {
+      return null;
+    }
+    Object[][] sqanddels = new Object[refCigars.length][];
+    for (int c = 0; c < refCigars.length; c++)
+    {
+      String refString = refCigars[c].getSequenceString(GapChar);
+      if (refString != null)
+      {
+        sqanddels[c] = getSequenceAndDeletions(refString, GapChar);
       }
-      Object[][] sqanddels = new Object[refCigars.length][];
-      for (int c=0; c<refCigars.length; c++) {
-        String refString = refCigars[c].getSequenceString(GapChar);
-        if (refString != null)
-        {
-          sqanddels[c] = getSequenceAndDeletions(refString, GapChar);
-        } else {
-          sqanddels[c] = null;
-        }
+      else
+      {
+        sqanddels[c] = null;
       }
-      return sqanddels;
     }
+    return sqanddels;
+  }
+
   /**
    * 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.
@@ -93,12 +104,16 @@ public class CigarArray extends CigarBase
    */
   public String getSequenceString(char GapChar)
   {
-    if (length==0 || refCigars==null)
+    if (length == 0 || refCigars == null)
+    {
       return "";
+    }
     StringBuffer seqStrings = new StringBuffer();
     Object[][] sqanddels = getArrayofSequenceAndDeletions(GapChar);
-    for (int c=0; c<refCigars.length; c++) {
-      if (sqanddels[c]!=null) {
+    for (int c = 0; c < refCigars.length; c++)
+    {
+      if (sqanddels[c] != null)
+      {
         seqStrings.append( (String) sqanddels[c][0]);
         sqanddels[c][0] = null;
       }
@@ -106,32 +121,38 @@ public class CigarArray extends CigarBase
     }
     return seqStrings.toString();
   }
+
   /**
    * return string results of applying cigar string to all reference cigars
    * @param GapChar char
    * @return String[]
    */
-  public String[] getSequenceStrings(char GapChar) {
+  public String[] getSequenceStrings(char GapChar)
+  {
 
-    if (length==0 || refCigars==null || refCigars.length==0)
+    if (length == 0 || refCigars == null || refCigars.length == 0)
+    {
       return null;
+    }
     Object[][] sqanddels = getArrayofSequenceAndDeletions(GapChar);
     String[] seqs = new String[sqanddels.length];
-    for (int c=0; c<refCigars.length; c++) {
+    for (int c = 0; c < refCigars.length; c++)
+    {
       seqs[c] = (String) sqanddels[c][0];
     }
     return seqs;
   }
+
   /**
    * Combines the CigarArray cigar operations with the operations in each
    * reference cigar - creating a new reference cigar
    * @return Cigar[]
 
-  public CigarBase[] getEditedCigars() {
+     public CigarBase[] getEditedCigars() {
 
     return new CigarBase[] {};
-  }
-*/
+     }
+   */
   /**
    * applyDeletions
    * edits underlying refCigars to propagate deleted regions, and removes deletion
@@ -140,28 +161,37 @@ public class CigarArray extends CigarBase
    */
   public int[] applyDeletions()
   {
-    java.util.Vector delpos=null;
-    if (length==0)
+    java.util.Vector delpos = null;
+    if (length == 0)
+    {
       return null;
-    int cursor=0; // range counter for deletions
-    int vcursor=0; // visible column index
-    int offset=0; // shift in visible column index as deletions are made
-    int i=0;
-    while (i<length) {
-      if (operation[i]!=D) {
-        if (operation[i]==M)
-          cursor+=range[i];
-        vcursor+=range[i++];
+    }
+    int cursor = 0; // range counter for deletions
+    int vcursor = 0; // visible column index
+    int offset = 0; // shift in visible column index as deletions are made
+    int i = 0;
+    while (i < length)
+    {
+      if (operation[i] != D)
+      {
+        if (operation[i] == M)
+        {
+          cursor += range[i];
+        }
+        vcursor += range[i++];
       }
       else
       {
-        if (delpos==null)
-          delpos=new java.util.Vector();
-        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
-        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);
+        if (delpos == null)
+        {
+          delpos = new java.util.Vector();
+        }
+        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
+        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++) {
@@ -171,36 +201,44 @@ public class CigarArray extends CigarBase
          }
          offset+=dmax; // shift in visible column coordinates
          */
-        for (int s=0; s<refCigars.length; s++) {
+        for (int s = 0; s < refCigars.length; s++)
+        {
           int d = refCigars[s].deleteRange(delstart, delend);
         }
 
       }
     }
-    if (delpos!=null)
+    if (delpos != null)
     {
-      int[] pos=new int[delpos.size()*2];
-      for (int k = 0, l = delpos.size(); k < l; k++) {
-        int[] dr = ((int[]) delpos.elementAt(k));
-        pos[k*2] = dr[0];
-        pos[k*2+1] = dr[1];
-        delpos.setElementAt(null,k);
+      int[] pos = new int[delpos.size() * 2];
+      for (int k = 0, l = delpos.size(); k < l; k++)
+      {
+        int[] dr = ( (int[]) delpos.elementAt(k));
+        pos[k * 2] = dr[0];
+        pos[k * 2 + 1] = dr[1];
+        delpos.setElementAt(null, k);
       }
-      delpos=null;
+      delpos = null;
       return pos;
     }
     return null;
   }
+
   /**
    *
    * @return SeqCigar[] or null if CigarArray is not a SeqCigarArray (ie it does not resolve to set of seqCigars)
    */
-  public SeqCigar[] getSeqCigarArray() {
+  public SeqCigar[] getSeqCigarArray()
+  {
     if (!isSeqCigarArray())
+    {
       return null;
+    }
     SeqCigar[] sa = new SeqCigar[refCigars.length];
-    for (int i=0; i<refCigars.length; i++)
+    for (int i = 0; i < refCigars.length; i++)
+    {
       sa[i] = (SeqCigar) refCigars[i];
+    }
     return sa;
   }
 }
diff --git a/src/jalview/datamodel/CigarBase.java b/src/jalview/datamodel/CigarBase.java
index a36bf76..d44d599 100644
--- a/src/jalview/datamodel/CigarBase.java
+++ b/src/jalview/datamodel/CigarBase.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,7 +18,7 @@
  */
 package jalview.datamodel;
 
-import java.util.Vector;
+import java.util.*;
 
 public abstract class CigarBase
 {
@@ -58,18 +58,21 @@ public abstract class CigarBase
    */
   public Object[] getSequenceAndDeletions(String reference, char GapChar)
   {
-    int rlength=0;
+    int rlength = 0;
     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)
     {
       return null;
     }
-    if (reference!=null)
-      rlength=reference.length();
+    if (reference != null)
+    {
+      rlength = reference.length();
+    }
     boolean modstart = true;
     for (int i = 0; i < length; i++)
     {
@@ -99,22 +102,26 @@ public abstract class CigarBase
           if (modstart)
           {
             start = cursor;
-            startpos=alcursor;
+            startpos = alcursor;
             modstart = false;
           }
-          if (reference!=null) {
-            int sbend = cursor+range[i];
-            if (sbend>rlength) {
+          if (reference != null)
+          {
+            int sbend = cursor + range[i];
+            if (sbend > rlength)
+            {
               sq.append(reference.substring(cursor, rlength));
               while (sbend-- >= rlength)
               {
                 sq.append(GapChar);
               }
-            } else {
+            }
+            else
+            {
               sq.append(reference.substring(cursor, sbend));
             }
           }
-          alcursor+=range[i];
+          alcursor += range[i];
           cursor += range[i];
           end = cursor - 1;
           endpos = alcursor;
@@ -131,29 +138,40 @@ public abstract class CigarBase
     deletions = null;
     return new Object[]
         {
-        ((reference!=null) ? sq.toString() : null),
-        new int[] {
+        ( (reference != null) ? sq.toString() : null),
+        new int[]
+        {
         start, startpos, end, endpos}, trunc_deletions};
   }
-  protected void compact_operations() {
-    int i=1;
-    if (operation==null)
+
+  protected void compact_operations()
+  {
+    int i = 1;
+    if (operation == null)
+    {
       return;
+    }
     char last = operation[0];
-    while (i<length) {
-      if (last==operation[i]) {
-        range[i-1]+=range[i];
-        int r = length-i;
-        if (r>0) {
+    while (i < length)
+    {
+      if (last == operation[i])
+      {
+        range[i - 1] += range[i];
+        int r = length - i;
+        if (r > 0)
+        {
           System.arraycopy(range, i + 1, range, i, r);
           System.arraycopy(operation, i + 1, operation, i, r);
         }
         length--;
-      } else {
+      }
+      else
+      {
         last = operation[i++];
       }
     }
   }
+
   /**
    * turn a cigar string into a series of operation range pairs
    * @param cigarString String
@@ -235,8 +253,10 @@ public abstract class CigarBase
     {
       throw new Error("Implementation error. Invalid operation string.");
     }
-    if (range<=0)
+    if (range <= 0)
+    {
       throw new Error("Invalid range string (must be non-zero positive number)");
+    }
     int lngth = 0;
     if (operation == null)
     {
@@ -254,10 +274,14 @@ 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.
+    }
     else
-      this.range[length]=0; // reset range
+    {
+      this.range[length] = 0; // reset range
+    }
     this.operation[length] = op;
     this.range[length++] += range;
   }
@@ -284,9 +308,9 @@ public abstract class CigarBase
    * @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.
+     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)
@@ -373,7 +397,7 @@ public abstract class CigarBase
               }
           break;
         default:
-          throw new Error("Implementation Error: Unknown operation in addOperation!");
+   throw new Error("Implementation Error: Unknown operation in addOperation!");
       }
       // finally, add remaining ops.
       while (e_o<e_length) {
@@ -381,95 +405,113 @@ public abstract class CigarBase
         e_o++;
       }
     }
-  }
-**/
+     }
+   **/
   /**
    * 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) {
-    int deleted=0;
-    if (length==0) {
+  public int deleteRange(int start, int end)
+  {
+    int deleted = 0;
+    if (length == 0)
+    {
       // nothing to do here
       return deleted;
     }
-    if (start<0 || start>end)
+    if (start < 0 || start > 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.
-    int rlength=1+end-start; // number of positions to delete
-    int oldlen=length;
+    int rlength = 1 + end - start; // number of positions to delete
+    int oldlen = length;
     int o = 0;
-    boolean editing=false;
+    boolean editing = false;
     char[] oldops = operation;
     int[] oldrange = range;
-    length=0;
+    length = 0;
     operation = null;
     range = null;
     compact_operations();
-    while (o<oldlen && cursor<=end && rlength>0) {
-      if (oldops[o] == D) {
+    while (o < oldlen && cursor <= end && rlength > 0)
+    {
+      if (oldops[o] == D)
+      {
         // absorbed into new deleted region.
         addDeleted(oldrange[o++]);
         continue;
       }
 
       int remain = oldrange[o]; // number of op characters left to edit
-      if (!editing) {
+      if (!editing)
+      {
         if ( (cursor + remain) <= start)
         {
-          addOperation(oldops[o],oldrange[o]);
-          cursor+=oldrange[o++];
+          addOperation(oldops[o], oldrange[o]);
+          cursor += oldrange[o++];
           continue; // next operation
         }
-        editing=true;
+        editing = true;
         // add operations before hidden region
-        if (start-cursor>0) {
-          addOperation(oldops[o], start- cursor);
+        if (start - cursor > 0)
+        {
+          addOperation(oldops[o], start - cursor);
           remain -= start - cursor;
         }
       }
       // start inserting new ops
-      if (o<oldlen && editing && rlength>0 && remain>0) {
-        switch (oldops[o]) {
+      if (o < oldlen && editing && rlength > 0 && remain > 0)
+      {
+        switch (oldops[o])
+        {
           case M:
-            if (rlength>remain) {
+            if (rlength > remain)
+            {
               addDeleted(remain);
-              deleted+=remain;
-            } else {
-              deleted+=rlength;
+              deleted += remain;
+            }
+            else
+            {
+              deleted += rlength;
               addDeleted(rlength);
-              if (remain-rlength>0)
-                this.addOperation(M,remain-rlength); // add remaining back.
-              rlength=0;
-              remain=0;
+              if (remain - rlength > 0)
+              {
+                this.addOperation(M, remain - rlength); // add remaining back.
+              }
+              rlength = 0;
+              remain = 0;
             }
             break;
           case I:
-            if (remain-rlength>0) {
+            if (remain - rlength > 0)
+            {
               // only remove some gaps
-              addInsertion(remain-rlength);
-              rlength=0;
+              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]+"'");
+            throw new Error("Implementation Error! Unknown operation '" +
+                            oldops[o] + "'");
         }
-        rlength-=remain;
+        rlength -= remain;
         remain = oldrange[++o]; // number of op characters left to edit
       }
     }
     // add remaining
-    while (o<oldlen) {
-      addOperation(oldops[o],oldrange[o++]);
+    while (o < oldlen)
+    {
+      addOperation(oldops[o], oldrange[o++]);
     }
     //if (cursor<(start+1)) {
-      // ran out of ops - nothing to do here ?
-     // addInsertion(start-cursor);
+    // ran out of ops - nothing to do here ?
+    // addInsertion(start-cursor);
     //}
     return deleted;
   }
@@ -481,7 +523,7 @@ public abstract class CigarBase
    */
   public boolean hasDeletedRegions()
   {
-    for (int i = 0; i<length ; i++)
+    for (int i = 0; i < length; i++)
     {
       if (operation[i] == D)
       {
@@ -490,38 +532,49 @@ public abstract class CigarBase
     }
     return false;
   }
+
   /**
    * enumerate the ranges on seq that are marked as deleted in this cigar
    * @return int[] { vis_start, sym_start, length }
    */
-  public int[] getDeletedRegions() {
-    if (length==0)
+  public int[] getDeletedRegions()
+  {
+    if (length == 0)
+    {
       return null;
+    }
     Vector dr = new Vector();
-    int cursor=0, vcursor=0;
-    for (int i=0;i<length;i++) {
-      switch (operation[i]) {
+    int cursor = 0, vcursor = 0;
+    for (int i = 0; i < length; i++)
+    {
+      switch (operation[i])
+      {
         case M:
-          cursor+=range[i];
+          cursor += range[i];
         case I:
-          vcursor+=range[i];
+          vcursor += range[i];
           break;
         case D:
-          dr.addElement(new int[] { vcursor, cursor, range[i]});
-          cursor+=range[i];
+          dr.addElement(new int[]
+                        {vcursor, cursor, range[i]});
+          cursor += range[i];
       }
     }
-    if (dr.size()==0)
+    if (dr.size() == 0)
+    {
       return null;
-    int[] delregions = new int[dr.size()*3];
-    for (int i=0,l=dr.size(); i<l; i++) {
+    }
+    int[] delregions = new int[dr.size() * 3];
+    for (int i = 0, l = dr.size(); i < l; i++)
+    {
       int[] reg = (int[]) dr.elementAt(i);
-      delregions[i*3] = reg[0];
-      delregions[i*3+1] = reg[1];
-      delregions[i*3+2] = reg[2];
+      delregions[i * 3] = reg[0];
+      delregions[i * 3 + 1] = reg[1];
+      delregions[i * 3 + 2] = reg[2];
     }
     return delregions;
   }
+
   /**
    * sum of ranges in cigar string
    * @return int number of residues hidden, matched, or gaps inserted into sequence
@@ -558,6 +611,7 @@ public abstract class CigarBase
     }
     return w;
   }
+
   /**
    * mark a range of inserted residues
    * @param range int
@@ -582,8 +636,8 @@ public abstract class CigarBase
    * @param start alignment column
    * @param end alignment column
    * @return boolean true if residues were marked as deleted.
-  public boolean deleteRange(int start, int end)
-  {
+     public boolean deleteRange(int start, int end)
+     {
     boolean deleted = false;
     int op = 0, prevop = -1, firstm = -1,
         lastm = -1, postop = -1;
@@ -633,8 +687,8 @@ public abstract class CigarBase
       addDeleted(end - start + 1);
     }
     return deleted;
-  }
-*/
+     }
+   */
   /**
    * Return an ENSEMBL style cigar string where D may indicates excluded parts of seq
    * @return String of form ([0-9]+[IMD])+
diff --git a/src/jalview/datamodel/CigarCigar.java b/src/jalview/datamodel/CigarCigar.java
index 57848eb..83cce19 100644
--- a/src/jalview/datamodel/CigarCigar.java
+++ b/src/jalview/datamodel/CigarCigar.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -22,14 +22,16 @@ 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;
-    }
+  /**
+   * 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
@@ -38,13 +40,20 @@ public class CigarCigar
    */
   public String getSequenceString(char GapChar)
   {
-    if (length==0)
+    if (length == 0)
+    {
       return "";
+    }
     String refString = refCigar.getSequenceString(GapChar);
-    if (refString!=null) {
-      return (length==0) ? "" : (String) getSequenceAndDeletions(refString, GapChar)[0];
-    } else
+    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 c33da7a..3891687 100644
--- a/src/jalview/datamodel/CigarSimple.java
+++ b/src/jalview/datamodel/CigarSimple.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -33,11 +33,11 @@ package jalview.datamodel;
 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);
+  /**
+   * 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 e51afd0..6ef1799 100644
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,10 +18,10 @@
  */
 package jalview.datamodel;
 
-import jalview.util.ShiftList;
-
 import java.util.*;
 
+import jalview.util.*;
+
 /**
  * NOTE: Columns are zero based.
  */
@@ -77,7 +77,7 @@ public class ColumnSelection
   public void removeElements(int start, int end)
   {
     Integer colInt;
-    for(int i=start; i<end; i++)
+    for (int i = start; i < end; i++)
     {
       colInt = new Integer(i);
       if (selected.contains(colInt))
@@ -86,6 +86,7 @@ public class ColumnSelection
       }
     }
   }
+
   /**
    *
    * @return Vector containing selected columns as Integers
@@ -115,7 +116,7 @@ public class ColumnSelection
    */
   public int columnAt(int i)
   {
-    return ((Integer) selected.elementAt(i)).intValue();
+    return ( (Integer) selected.elementAt(i)).intValue();
   }
 
   /**
@@ -168,7 +169,6 @@ public class ColumnSelection
     return min;
   }
 
-
   /**
    * propagate shift in alignment columns to column selection
    *
@@ -188,14 +188,14 @@ public class ColumnSelection
       }
     }
 
-    if(hiddenColumns!=null)
+    if (hiddenColumns != null)
     {
       deletedHiddenColumns = new Vector();
       int hSize = hiddenColumns.size();
-      for(int i=0; i<hSize; i++)
+      for (int i = 0; i < hSize; i++)
       {
         int[] region = (int[]) hiddenColumns.elementAt(i);
-        if ( region[0]>start && start+change>region[1] )
+        if (region[0] > start && start + change > region[1])
         {
           deletedHiddenColumns.addElement(
               hiddenColumns.elementAt(i));
@@ -206,14 +206,16 @@ public class ColumnSelection
           continue;
         }
 
-        if(region[0]>start)
+        if (region[0] > start)
         {
           region[0] -= change;
           region[1] -= change;
         }
 
-        if(region[0]<0)
+        if (region[0] < 0)
+        {
           region[0] = 0;
+        }
 
       }
 
@@ -222,6 +224,7 @@ public class ColumnSelection
 
     return deletedHiddenColumns;
   }
+
   /**
    * propagate shift in alignment columns to column selection
    * special version of compensateForEdit - allowing for edits within hidden regions
@@ -240,51 +243,63 @@ public class ColumnSelection
       }
     }
 
-    if(hiddenColumns!=null)
+    if (hiddenColumns != null)
     {
-      for(int i=0; i<hiddenColumns.size(); i++)
+      for (int i = 0; i < hiddenColumns.size(); i++)
       {
         int[] region = (int[]) hiddenColumns.elementAt(i);
-        if(region[0] >= start)
+        if (region[0] >= start)
         {
           region[0] -= change;
         }
-        if (region[1]>= start) {
-          region[1] -=change;
+        if (region[1] >= start)
+        {
+          region[1] -= change;
         }
-        if (region[1]<region[0]) {
+        if (region[1] < region[0])
+        {
           hiddenColumns.removeElementAt(i--);
         }
 
-        if(region[0]<0)
+        if (region[0] < 0)
+        {
           region[0] = 0;
-        if(region[1] <0)
+        }
+        if (region[1] < 0)
+        {
           region[1] = 0;
+        }
       }
     }
   }
+
   /**
    * Adjust hidden column boundaries based on a series of column
    * additions or deletions in visible regions.
    * @param shiftrecord
    * @return
    */
-  public ShiftList compensateForEdits(ShiftList shiftrecord) {
-    if (shiftrecord!=null) {
+  public ShiftList compensateForEdits(ShiftList shiftrecord)
+  {
+    if (shiftrecord != null)
+    {
       Vector shifts = shiftrecord.shifts;
-      if (shifts!=null && shifts.size()>0) {
-        int shifted=0;
-        for (int i=0,j=shifts.size(); i<j; i++) {
+      if (shifts != null && shifts.size() > 0)
+      {
+        int shifted = 0;
+        for (int i = 0, j = shifts.size(); i < j; i++)
+        {
           int[] sh = (int[]) shifts.elementAt(i);
           //compensateForEdit(shifted+sh[0], sh[1]);
-          compensateForDelEdits(shifted+sh[0], sh[1]);
-          shifted-=sh[1];
+          compensateForDelEdits(shifted + sh[0], sh[1]);
+          shifted -= sh[1];
         }
       }
       return shiftrecord.getInverse();
     }
     return null;
   }
+
   /**
    * removes intersection of position,length ranges in deletions
    * from the start,end regions marked in intervals.
@@ -292,110 +307,155 @@ public class ColumnSelection
    * @param intervals
    * @return
    */
-  private boolean pruneIntervalVector(Vector deletions, Vector intervals) {
-    boolean pruned=false;
-    int i=0,j=intervals.size()-1, s=0, t=deletions.size()-1;
-    int hr[]=(int[]) intervals.elementAt(i);
-    int sr[]=(int[]) deletions.elementAt(s);
-    while (i<=j && s<=t) {
-      boolean trailinghn=hr[1]>=sr[0];
-      if (!trailinghn) {
-        if (i<j)
-          hr=(int[]) intervals.elementAt(++i);
+  private boolean pruneIntervalVector(Vector deletions, Vector intervals)
+  {
+    boolean pruned = false;
+    int i = 0, j = intervals.size() - 1, s = 0, t = deletions.size() - 1;
+    int hr[] = (int[]) intervals.elementAt(i);
+    int sr[] = (int[]) deletions.elementAt(s);
+    while (i <= j && s <= t)
+    {
+      boolean trailinghn = hr[1] >= sr[0];
+      if (!trailinghn)
+      {
+        if (i < j)
+        {
+          hr = (int[]) intervals.elementAt(++i);
+        }
         else
+        {
           i++;
+        }
         continue;
       }
-      int endshift=sr[0]+sr[1]; // deletion ranges - -ve means an insert
-      if (endshift<hr[0] || endshift<sr[0]) { // leadinghc disjoint or not a deletion
-        if (s<t)
-          sr=(int[]) deletions.elementAt(++s);
+      int endshift = sr[0] + sr[1]; // deletion ranges - -ve means an insert
+      if (endshift < hr[0] || endshift < sr[0])
+      { // leadinghc disjoint or not a deletion
+        if (s < t)
+        {
+          sr = (int[]) deletions.elementAt(++s);
+        }
         else
+        {
           s++;
+        }
         continue;
       }
-      boolean leadinghn=hr[0]>=sr[0];
-      boolean leadinghc=hr[0]<endshift;
-      boolean trailinghc=hr[1]<endshift;
-      if (leadinghn) {
-        if (trailinghc) {// deleted hidden region.
+      boolean leadinghn = hr[0] >= sr[0];
+      boolean leadinghc = hr[0] < endshift;
+      boolean trailinghc = hr[1] < endshift;
+      if (leadinghn)
+      {
+        if (trailinghc)
+        { // deleted hidden region.
           intervals.removeElementAt(i);
-          pruned=true;
+          pruned = true;
           j--;
-          if (i<=j)
-            hr=(int[]) intervals.elementAt(i);
+          if (i <= j)
+          {
+            hr = (int[]) intervals.elementAt(i);
+          }
           continue;
         }
-        if (leadinghc) {
-          hr[0]=endshift; // clip c terminal region
-          leadinghn=!leadinghn;
-          pruned=true;
+        if (leadinghc)
+        {
+          hr[0] = endshift; // clip c terminal region
+          leadinghn = !leadinghn;
+          pruned = true;
         }
       }
-      if (!leadinghn) {
-        if (trailinghc) {
-          if (trailinghn) {
-            hr[1]=sr[0]-1;
-            pruned=true;
+      if (!leadinghn)
+      {
+        if (trailinghc)
+        {
+          if (trailinghn)
+          {
+            hr[1] = sr[0] - 1;
+            pruned = true;
           }
-        } else {
+        }
+        else
+        {
           // sr contained in hr
-          if (s<t)
-            sr=(int[]) deletions.elementAt(++s);
+          if (s < t)
+          {
+            sr = (int[]) deletions.elementAt(++s);
+          }
           else
+          {
             s++;
+          }
           continue;
         }
       }
     }
     return pruned; // true if any interval was removed or modified by operations.
   }
-  private boolean pruneColumnList(Vector deletion, Vector list) {
-    int s=0,t=deletion.size();
-    int[] sr=(int[])list.elementAt(s++);
-    boolean pruned=false;
-    int i=0, j=list.size();
-    while (i<j && s<=t) {
-      int c=((Integer)list.elementAt(i++)).intValue();
-      if (sr[0]<=c) {
-        if (sr[1]+sr[0]>=c) { // sr[1] -ve means inseriton.
+
+  private boolean pruneColumnList(Vector deletion, Vector list)
+  {
+    int s = 0, t = deletion.size();
+    int[] sr = (int[]) list.elementAt(s++);
+    boolean pruned = false;
+    int i = 0, j = list.size();
+    while (i < j && s <= t)
+    {
+      int c = ( (Integer) list.elementAt(i++)).intValue();
+      if (sr[0] <= c)
+      {
+        if (sr[1] + sr[0] >= c)
+        { // sr[1] -ve means inseriton.
           list.removeElementAt(--i);
           j--;
-        } else {
-          if (s<t)
-            sr = (int[])deletion.elementAt(s);
+        }
+        else
+        {
+          if (s < t)
+          {
+            sr = (int[]) deletion.elementAt(s);
+          }
           s++;
         }
       }
     }
     return pruned;
   }
+
   /**
    * remove any hiddenColumns or selected columns and shift remaining
    * based on a series of position, range deletions.
    * @param deletions
    */
-  public void pruneDeletions(ShiftList deletions) {
-    if (deletions!=null) {
-      Vector shifts=deletions.shifts;
-      if (shifts!=null && shifts.size()>0) {
+  public void pruneDeletions(ShiftList deletions)
+  {
+    if (deletions != null)
+    {
+      Vector shifts = deletions.shifts;
+      if (shifts != null && shifts.size() > 0)
+      {
         // delete any intervals intersecting.
-        if (hiddenColumns!=null) {
+        if (hiddenColumns != null)
+        {
           pruneIntervalVector(shifts, hiddenColumns);
-          if (hiddenColumns!=null && hiddenColumns.size()==0) {
-            hiddenColumns=null;
+          if (hiddenColumns != null && hiddenColumns.size() == 0)
+          {
+            hiddenColumns = null;
           }
         }
-        if (selected!=null && selected.size()>0) {
+        if (selected != null && selected.size() > 0)
+        {
           pruneColumnList(shifts, selected);
-          if (selected!=null && selected.size()==0)
-            selected=null;
+          if (selected != null && selected.size() == 0)
+          {
+            selected = null;
+          }
         }
         // and shift the rest.
         this.compensateForEdits(deletions);
       }
     }
   }
+
   /**
    * This Method is used to return all the HiddenColumn regions
    * less than the given index.
@@ -406,6 +466,7 @@ public class ColumnSelection
   {
     return hiddenColumns;
   }
+
   /**
    * Return absolute column index for a visible column index
    * @param column int column index in alignment view
@@ -446,7 +507,7 @@ public class ColumnSelection
         int[] region = (int[]) hiddenColumns.elementAt(index);
         if (hiddenColumn > region[1])
         {
-          result -= region[1]+1-region[0];
+          result -= region[1] + 1 - region[0];
         }
         index++;
       }
@@ -471,16 +532,16 @@ public class ColumnSelection
       do
       {
         int[] region = (int[]) hiddenColumns.elementAt(index);
-        if(hiddenRegion==0)
+        if (hiddenRegion == 0)
         {
           return region[0];
         }
 
-        gaps +=  region[1] +1 - region[0];
-        result = region[1] +1;
+        gaps += region[1] + 1 - region[0];
+        result = region[1] + 1;
         index++;
       }
-      while(index < hiddenRegion+1);
+      while (index < hiddenRegion + 1);
 
       result -= gaps;
     }
@@ -502,17 +563,20 @@ public class ColumnSelection
       do
       {
         int[] region = (int[]) hiddenColumns.elementAt(index);
-        if(alPos < region[0])
+        if (alPos < region[0])
+        {
           return region[0];
+        }
 
         index++;
       }
-      while(index < hiddenColumns.size());
+      while (index < hiddenColumns.size());
     }
 
     return alPos;
 
   }
+
   /**
    * THis method returns the rightmost limit of a
    * region of an alignment with hidden columns.
@@ -523,16 +587,18 @@ public class ColumnSelection
   {
     if (hiddenColumns != null)
     {
-      int index = hiddenColumns.size()-1;
+      int index = hiddenColumns.size() - 1;
       do
       {
         int[] region = (int[]) hiddenColumns.elementAt(index);
-        if(alPos > region[1])
+        if (alPos > region[1])
+        {
           return region[1];
+        }
 
         index--;
       }
-      while(index >-1);
+      while (index > -1);
     }
 
     return alPos;
@@ -551,8 +617,10 @@ public class ColumnSelection
 
   public void hideColumns(int start, int end)
   {
-    if(hiddenColumns==null)
+    if (hiddenColumns == null)
+    {
       hiddenColumns = new Vector();
+    }
 
     boolean added = false;
     boolean overlap = false;
@@ -560,7 +628,7 @@ public class ColumnSelection
     for (int i = 0; i < hiddenColumns.size(); i++)
     {
       int[] region = (int[]) hiddenColumns.elementAt(i);
-      if ( start<=region[1] && end>=region[0])
+      if (start <= region[1] && end >= region[0])
       {
         hiddenColumns.removeElementAt(i);
         overlap = true;
@@ -569,18 +637,21 @@ public class ColumnSelection
       else if (end < region[0] && start < region[0])
       {
         hiddenColumns.insertElementAt(new int[]
-                                              {start, end}, i);
+                                      {start, end}, i);
         added = true;
         break;
       }
     }
 
-    if(overlap)
+    if (overlap)
     {
       hideColumns(start, end);
     }
     else if (!added)
-      hiddenColumns.addElement(new int[] {start, end});
+    {
+      hiddenColumns.addElement(new int[]
+                               {start, end});
+    }
 
   }
 
@@ -592,28 +663,37 @@ public class ColumnSelection
   public void hideColumns(int col)
   {
     // First find out range of columns to hide
-    int min = col, max = col+1;
-    while( contains(min) )
-    {  removeElement(min); min --;  }
+    int min = col, max = col + 1;
+    while (contains(min))
+    {
+      removeElement(min);
+      min--;
+    }
 
-    while( contains(max) )
-    { removeElement(max);  max ++;  }
+    while (contains(max))
+    {
+      removeElement(max);
+      max++;
+    }
 
-    min++; max--;
-    if(min>max)
+    min++;
+    max--;
+    if (min > max)
+    {
       min = max;
+    }
 
     hideColumns(min, max);
   }
 
   public void revealAllHiddenColumns()
   {
-    if(hiddenColumns!=null)
+    if (hiddenColumns != null)
     {
       for (int i = 0; i < hiddenColumns.size(); i++)
       {
         int[] region = (int[]) hiddenColumns.elementAt(i);
-        for (int j = region[0]; j < region[1]+1; j++)
+        for (int j = region[0]; j < region[1] + 1; j++)
         {
           addElement(j);
         }
@@ -625,12 +705,12 @@ public class ColumnSelection
 
   public void revealHiddenColumns(int res)
   {
-    for(int i=0; i<hiddenColumns.size(); i++)
+    for (int i = 0; i < hiddenColumns.size(); i++)
     {
-      int [] region = (int[])hiddenColumns.elementAt(i);
-      if( res == region[0])
+      int[] region = (int[]) hiddenColumns.elementAt(i);
+      if (res == region[0])
       {
-        for (int j = region[0]; j < region[1]+1; j++)
+        for (int j = region[0]; j < region[1] + 1; j++)
         {
           addElement(j);
         }
@@ -639,40 +719,50 @@ public class ColumnSelection
         break;
       }
     }
-    if(hiddenColumns.size()==0)
+    if (hiddenColumns.size() == 0)
+    {
       hiddenColumns = null;
+    }
   }
 
   public boolean isVisible(int column)
   {
-    for(int i=0; i<hiddenColumns.size(); i++)
+    for (int i = 0; i < hiddenColumns.size(); i++)
     {
-      int [] region = (int[])hiddenColumns.elementAt(i);
-      if( column >= region[0] && column <= region[1])
+      int[] region = (int[]) hiddenColumns.elementAt(i);
+      if (column >= region[0] && column <= region[1])
       {
         return false;
       }
     }
     return true;
   }
+
   /**
    * Copy constructor
    * @param copy
    */
-  public ColumnSelection(ColumnSelection copy) {
-    if (copy!=null) {
-      if (copy.selected!=null) {
+  public ColumnSelection(ColumnSelection copy)
+  {
+    if (copy != null)
+    {
+      if (copy.selected != null)
+      {
         selected = new Vector();
-        for (int i=0,j=copy.selected.size(); i<j; i++) {
+        for (int i = 0, j = copy.selected.size(); i < j; i++)
+        {
           selected.addElement(copy.selected.elementAt(i));
         }
       }
-      if (copy.hiddenColumns!=null) {
-        hiddenColumns=new Vector(copy.hiddenColumns.size());
-        for (int i=0,j=copy.hiddenColumns.size(); i<j; i++) {
-          int[] rh,cp;
-          rh = (int[])copy.hiddenColumns.elementAt(i);
-          if (rh!=null) {
+      if (copy.hiddenColumns != null)
+      {
+        hiddenColumns = new Vector(copy.hiddenColumns.size());
+        for (int i = 0, j = copy.hiddenColumns.size(); i < j; i++)
+        {
+          int[] rh, cp;
+          rh = (int[]) copy.hiddenColumns.elementAt(i);
+          if (rh != null)
+          {
             cp = new int[rh.length];
             System.arraycopy(rh, 0, cp, 0, rh.length);
             hiddenColumns.addElement(cp);
@@ -681,6 +771,7 @@ public class ColumnSelection
       }
     }
   }
+
   /**
    * ColumnSelection
    */
@@ -688,17 +779,20 @@ public class ColumnSelection
   {
   }
 
-  public String[] getVisibleSequenceStrings(int start, int end, SequenceI[] seqs) {
-    int i,iSize=seqs.length;
+  public String[] getVisibleSequenceStrings(int start, int end,
+                                            SequenceI[] seqs)
+  {
+    int i, iSize = seqs.length;
     String selection[] = new String[iSize];
-    if (hiddenColumns!=null && hiddenColumns.size()>0)
+    if (hiddenColumns != null && hiddenColumns.size() > 0)
     {
-      for (i=0; i<iSize; i++) {
+      for (i = 0; i < iSize; i++)
+      {
         StringBuffer visibleSeq = new StringBuffer();
         Vector regions = getHiddenColumns();
 
-        int blockStart = start, blockEnd=end;
-        int [] region;
+        int blockStart = start, blockEnd = end;
+        int[] region;
         int hideStart, hideEnd;
 
         for (int j = 0; j < regions.size(); j++)
@@ -707,35 +801,36 @@ public class ColumnSelection
           hideStart = region[0];
           hideEnd = region[1];
 
-          if(hideStart < start)
+          if (hideStart < start)
           {
             continue;
           }
 
-          blockStart = Math.min(blockStart, hideEnd+1);
+          blockStart = Math.min(blockStart, hideEnd + 1);
           blockEnd = Math.min(blockEnd, hideStart);
 
-          if(blockStart>blockEnd)
+          if (blockStart > blockEnd)
           {
             break;
           }
 
-
           visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));
 
-          blockStart = hideEnd+1;
+          blockStart = hideEnd + 1;
           blockEnd = end;
         }
 
-        if(end>blockStart)
+        if (end > blockStart)
+        {
           visibleSeq.append(seqs[i].getSequence(blockStart, end));
+        }
 
         selection[i] = visibleSeq.toString();
       }
     }
     else
     {
-      for(i=0; i<iSize; i++)
+      for (i = 0; i < iSize; i++)
       {
         selection[i] = seqs[i].getSequenceAsString(start, end);
       }
@@ -743,6 +838,7 @@ public class ColumnSelection
 
     return selection;
   }
+
   /**
    * return all visible segments between the given start and end boundaries
    *
@@ -750,47 +846,56 @@ public class ColumnSelection
    * @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) {
-    if (hiddenColumns!=null && hiddenColumns.size()>0)
+  public int[] getVisibleContigs(int start, int end)
+  {
+    if (hiddenColumns != null && hiddenColumns.size() > 0)
     {
-      Vector visiblecontigs=new Vector();
+      Vector visiblecontigs = new Vector();
       Vector regions = getHiddenColumns();
 
       int vstart = start;
-      int [] region;
+      int[] region;
       int hideStart, hideEnd;
 
-      for (int j = 0; vstart<end && j < regions.size(); j++)
+      for (int j = 0; vstart < end && j < regions.size(); j++)
       {
         region = (int[]) regions.elementAt(j);
         hideStart = region[0];
         hideEnd = region[1];
 
-        if(hideEnd < vstart)
+        if (hideEnd < vstart)
         {
           continue;
         }
-        if (hideStart>vstart) {
-          visiblecontigs.addElement(new int[] {vstart, hideStart-1});
+        if (hideStart > vstart)
+        {
+          visiblecontigs.addElement(new int[]
+                                    {vstart, hideStart - 1});
         }
-        vstart=hideEnd+1;
+        vstart = hideEnd + 1;
       }
 
-      if(vstart<end)
-        visiblecontigs.addElement(new int[] { vstart, end-1});
-      int[] vcontigs = new int[visiblecontigs.size()*2];
-      for (int i=0,j=visiblecontigs.size(); i<j; i++) {
-        int [] vc = (int[]) visiblecontigs.elementAt(i);
+      if (vstart < end)
+      {
+        visiblecontigs.addElement(new int[]
+                                  {vstart, end - 1});
+      }
+      int[] vcontigs = new int[visiblecontigs.size() * 2];
+      for (int i = 0, j = visiblecontigs.size(); i < j; i++)
+      {
+        int[] vc = (int[]) visiblecontigs.elementAt(i);
         visiblecontigs.setElementAt(null, i);
-        vcontigs[i*2] = vc[0];
-        vcontigs[i*2+1] = vc[1];
+        vcontigs[i * 2] = vc[0];
+        vcontigs[i * 2 + 1] = vc[1];
       }
       visiblecontigs.removeAllElements();
       return vcontigs;
     }
     else
     {
-      return new int[] { start, end-1 };
+      return new int[]
+          {
+          start, end - 1};
     }
   }
 }
diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java
index 01d422c..c35c8c2 100755
--- a/src/jalview/datamodel/DBRefEntry.java
+++ b/src/jalview/datamodel/DBRefEntry.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -30,12 +30,18 @@ public class DBRefEntry
   }
 
   public String getSource()
-  {    return source; }
+  {
+    return source;
+  }
 
   public String getVersion()
-  { return version; }
+  {
+    return version;
+  }
 
   public String getAccessionId()
-  { return accessionId; }
+  {
+    return accessionId;
+  }
 
 }
diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java
index 4830bc6..aaf0ada 100755
--- a/src/jalview/datamodel/DBRefSource.java
+++ b/src/jalview/datamodel/DBRefSource.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -20,28 +20,28 @@ package jalview.datamodel;
 
 public class DBRefSource
 {
-    /**
-     * UNIPROT Accession Number
-     */
-    public static String UNIPROT="UNIPROT";
-    /**
-     * UNIPROT Entry Name
-     */
-    public static String UP_NAME="UNIPROT_NAME";
-    /**
-     * 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";
-    }
+  /**
+   * UNIPROT Accession Number
+   */
+  public static String UNIPROT = "UNIPROT";
+  /**
+   * UNIPROT Entry Name
+   */
+  public static String UP_NAME = "UNIPROT_NAME";
+  /**
+   * 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";
+}
diff --git a/src/jalview/datamodel/GraphLine.java b/src/jalview/datamodel/GraphLine.java
index df48804..33ad62c 100755
--- a/src/jalview/datamodel/GraphLine.java
+++ b/src/jalview/datamodel/GraphLine.java
@@ -1,37 +1,41 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 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 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)
+  public GraphLine(float value, String label, java.awt.Color col)
+  {
+    this.value = value;
+    if (label != null)
     {
-      this.value = value;
-      if(label != null)
-        this.label = label;
+      this.label = label;
+    }
 
-      if(col != null )
-        this.colour = col;
+    if (col != null)
+    {
+      this.colour = col;
     }
+  }
 }
diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index 9491329..0514fb8 100755
--- a/src/jalview/datamodel/HiddenSequences.java
+++ b/src/jalview/datamodel/HiddenSequences.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -23,7 +23,7 @@ import java.util.*;
 
 public class HiddenSequences
 {
-  public SequenceI []  hiddenSequences;
+  public SequenceI[] hiddenSequences;
   AlignmentI alignment;
 
   public HiddenSequences(AlignmentI al)
@@ -33,14 +33,18 @@ public class HiddenSequences
 
   public int getSize()
   {
-    if(hiddenSequences==null)
+    if (hiddenSequences == null)
     {
       return 0;
     }
     int count = 0;
-    for(int i=0; i<hiddenSequences.length; i++)
-      if(hiddenSequences[i] !=null )
-        count ++;
+    for (int i = 0; i < hiddenSequences.length; i++)
+    {
+      if (hiddenSequences[i] != null)
+      {
+        count++;
+      }
+    }
 
     return count;
   }
@@ -49,8 +53,12 @@ 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();
+      }
+    }
 
     return width;
   }
@@ -61,28 +69,34 @@ public class HiddenSequences
    */
   public void adjustHeightSequenceDeleted(int seqIndex)
   {
-    if(hiddenSequences==null)
+    if (hiddenSequences == null)
     {
       return;
     }
 
     int alHeight = alignment.getHeight();
 
-    SequenceI [] tmp = new SequenceI [alHeight + getSize()];
+    SequenceI[] tmp = new SequenceI[alHeight + getSize()];
     int deletionIndex = adjustForHiddenSeqs(seqIndex);
 
     for (int i = 0; i < hiddenSequences.length; i++)
     {
-      if(hiddenSequences[i]==null)
+      if (hiddenSequences[i] == null)
+      {
         continue;
+      }
 
       if (i > deletionIndex)
-        tmp[i-1] = hiddenSequences[i];
+      {
+        tmp[i - 1] = hiddenSequences[i];
+      }
       else
-       tmp[i] = hiddenSequences[i];
+      {
+        tmp[i] = hiddenSequences[i];
+      }
     }
 
-   hiddenSequences = tmp;
+    hiddenSequences = tmp;
 
   }
 
@@ -92,29 +106,32 @@ public class HiddenSequences
    */
   public void adjustHeightSequenceAdded()
   {
-    if(hiddenSequences==null)
+    if (hiddenSequences == null)
     {
       return;
     }
 
     int alHeight = alignment.getHeight();
 
-    SequenceI [] tmp = new SequenceI [alHeight + getSize()];
-    System.arraycopy(hiddenSequences,0,tmp,0,hiddenSequences.length);
+    SequenceI[] tmp = new SequenceI[alHeight + getSize()];
+    System.arraycopy(hiddenSequences, 0, tmp, 0, hiddenSequences.length);
     hiddenSequences = tmp;
   }
 
-
   public void hideSequence(SequenceI sequence)
   {
-    if(hiddenSequences==null)
+    if (hiddenSequences == null)
+    {
       hiddenSequences = new SequenceI[alignment.getHeight()];
+    }
 
     int alignmentIndex = alignment.findIndex(sequence);
     alignmentIndex = adjustForHiddenSeqs(alignmentIndex);
 
-    if(hiddenSequences[alignmentIndex]!=null)
+    if (hiddenSequences[alignmentIndex] != null)
+    {
       System.out.println("ERROR!!!!!!!!!!!");
+    }
 
     hiddenSequences[alignmentIndex] = sequence;
 
@@ -123,14 +140,16 @@ public class HiddenSequences
 
   public Vector showAll(Hashtable hiddenReps)
   {
-   Vector revealedSeqs = new Vector();
-   for(int i=0; i<hiddenSequences.length; i++)
+    Vector revealedSeqs = new Vector();
+    for (int i = 0; i < hiddenSequences.length; i++)
     {
-      if(hiddenSequences[i]!=null)
+      if (hiddenSequences[i] != null)
       {
         Vector tmp = showSequence(i, hiddenReps);
         for (int t = 0; t < tmp.size(); t++)
+        {
           revealedSeqs.addElement(tmp.elementAt(t));
+        }
       }
     }
     return revealedSeqs;
@@ -140,33 +159,37 @@ 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);
     }
 
-    int start = adjustForHiddenSeqs(alignmentIndex-1);
+    int start = adjustForHiddenSeqs(alignmentIndex - 1);
     int end = adjustForHiddenSeqs(alignmentIndex);
-    if(end>=hiddenSequences.length)
-      end = hiddenSequences.length-1;
+    if (end >= hiddenSequences.length)
+    {
+      end = hiddenSequences.length - 1;
+    }
 
-    for(int index = end; index > start; index--)
+    for (int index = end; index > start; index--)
     {
-      SequenceI seq =  hiddenSequences[index];
+      SequenceI seq = hiddenSequences[index];
       hiddenSequences[index] = null;
 
-      if(seq!=null)
+      if (seq != null)
       {
-        if(seq.getLength()>0)
-         {
-           revealedSeqs.addElement(seq);
-           alignment.getSequences().insertElementAt(seq, alignmentIndex);
-         }
-         else
-           System.out.println(seq.getName()+" has been deleted whilst hidden");
+        if (seq.getLength() > 0)
+        {
+          revealedSeqs.addElement(seq);
+          alignment.getSequences().insertElementAt(seq, alignmentIndex);
+        }
+        else
+        {
+          System.out.println(seq.getName() + " has been deleted whilst hidden");
+        }
       }
 
     }
@@ -183,48 +206,53 @@ public class HiddenSequences
   {
     int index = 0;
     int hiddenSeqs = 0;
-    if(hiddenSequences.length<=alignmentIndex)
-      alignmentIndex = hiddenSequences.length-1;
+    if (hiddenSequences.length <= alignmentIndex)
+    {
+      alignmentIndex = hiddenSequences.length - 1;
+    }
 
-    while(index <= alignmentIndex)
+    while (index <= alignmentIndex)
     {
-     if(hiddenSequences[index]!=null)
-     {
-       hiddenSeqs ++;
-     }
-      index ++;
-    };
+      if (hiddenSequences[index] != null)
+      {
+        hiddenSeqs++;
+      }
+      index++;
+    }
+    ;
 
-    return (alignmentIndex - hiddenSeqs) ;
+    return (alignmentIndex - hiddenSeqs);
   }
 
   public int adjustForHiddenSeqs(int alignmentIndex)
   {
     int index = 0;
     int hSize = hiddenSequences.length;
-    while(index <= alignmentIndex && index<hSize)
+    while (index <= alignmentIndex && index < hSize)
     {
-      if(hiddenSequences[index]!=null)
+      if (hiddenSequences[index] != null)
       {
-        alignmentIndex ++;
+        alignmentIndex++;
       }
-      index ++;
-    };
+      index++;
+    }
+    ;
 
-    return alignmentIndex ;
+    return alignmentIndex;
   }
 
-
   public AlignmentI getFullAlignment()
   {
     int isize = hiddenSequences.length;
-    SequenceI [] seq = new Sequence[isize];
+    SequenceI[] seq = new Sequence[isize];
 
     int index = 0;
-    for(int i=0; i<hiddenSequences.length; i++)
+    for (int i = 0; i < hiddenSequences.length; i++)
     {
-      if(hiddenSequences[i]!=null)
+      if (hiddenSequences[i] != null)
+      {
         seq[i] = hiddenSequences[i];
+      }
       else
       {
         seq[i] = alignment.getSequenceAt(index);
@@ -237,9 +265,13 @@ public class HiddenSequences
 
   public boolean isHidden(SequenceI seq)
   {
-    for(int i=0; i<hiddenSequences.length; i++)
-      if(hiddenSequences[i] !=null && hiddenSequences[i]==seq)
+    for (int i = 0; i < hiddenSequences.length; i++)
+    {
+      if (hiddenSequences[i] != null && hiddenSequences[i] == seq)
+      {
         return true;
+      }
+    }
 
     return false;
   }
diff --git a/src/jalview/datamodel/PDBEntry.java b/src/jalview/datamodel/PDBEntry.java
index 20fd3f0..16f8864 100755
--- a/src/jalview/datamodel/PDBEntry.java
+++ b/src/jalview/datamodel/PDBEntry.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -19,6 +19,7 @@
 package jalview.datamodel;
 
 import java.util.*;
+
 public class PDBEntry
 {
   String file;
@@ -27,25 +28,37 @@ public class PDBEntry
   Hashtable properties;
 
   public PDBEntry()
-  {  }
+  {}
 
   public void setFile(String file)
-  { this.file = file; }
+  {
+    this.file = file;
+  }
 
   public String getFile()
-  {  return file; }
+  {
+    return file;
+  }
 
   public void setType(String type)
-  { this.type = type; }
+  {
+    this.type = type;
+  }
 
   public String getType()
-  { return type; }
+  {
+    return type;
+  }
 
   public void setId(String id)
-  { this.id = id; }
+  {
+    this.id = id;
+  }
 
   public String getId()
-  { return id; }
+  {
+    return id;
+  }
 
   public void setProperty(Hashtable property)
   {
@@ -57,5 +70,4 @@ public class PDBEntry
     return properties;
   }
 
-
 }
diff --git a/src/jalview/datamodel/Provenance.java b/src/jalview/datamodel/Provenance.java
index 4bfeadf..f8afedf 100755
--- a/src/jalview/datamodel/Provenance.java
+++ b/src/jalview/datamodel/Provenance.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -17,6 +17,7 @@
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
 package jalview.datamodel;
+
 import java.util.*;
 
 public class Provenance
@@ -29,16 +30,18 @@ public class Provenance
 
   public ProvenanceEntry[] getEntries()
   {
-    ProvenanceEntry [] ret = new ProvenanceEntry[entries.size()];
-    for(int i=0; i<entries.size(); i++)
-       ret[i] = (ProvenanceEntry)entries.elementAt(i);
+    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)
+  public void addEntry(String user, String action, java.util.Date date,
+                       String id)
   {
-    entries.addElement( new ProvenanceEntry(user,action,date,id));
+    entries.addElement(new ProvenanceEntry(user, action, date, id));
   }
 
 }
-
diff --git a/src/jalview/datamodel/ProvenanceEntry.java b/src/jalview/datamodel/ProvenanceEntry.java
index 240e6ee..b08dd6d 100755
--- a/src/jalview/datamodel/ProvenanceEntry.java
+++ b/src/jalview/datamodel/ProvenanceEntry.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -20,22 +20,33 @@ 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;
-    }
+  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 getUser()
+  {
+    return user;
+  }
 
-    public String getAction()
-    {return action;}
+  public String getAction()
+  {
+    return action;
+  }
 
-    public java.util.Date getDate()
-    {return date;}
+  public java.util.Date getDate()
+  {
+    return date;
+  }
 
-    public String getID()
-    {return id;}
+  public String getID()
+  {
+    return id;
+  }
 }
diff --git a/src/jalview/datamodel/SearchResults.java b/src/jalview/datamodel/SearchResults.java
index c29b0e7..f8e1c5a 100755
--- a/src/jalview/datamodel/SearchResults.java
+++ b/src/jalview/datamodel/SearchResults.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -21,29 +21,31 @@ package jalview.datamodel;
 public class SearchResults
 {
 
-  Match [] matches;
+  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)
+    if (matches == null)
     {
-      matches = new Match[]{new Match(seq, start, end)};
+      matches = new Match[]
+          {
+          new Match(seq, start, end)};
       return;
     }
 
     int mSize = matches.length;
 
-    Match [] tmp = new Match[mSize+1];
+    Match[] tmp = new Match[mSize + 1];
     int m;
-    for(m=0; m<mSize; m++)
+    for (m = 0; m < mSize; m++)
     {
       tmp[m] = matches[m];
     }
@@ -54,45 +56,54 @@ 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
-  */
-  public int [] getResults(SequenceI sequence, int start, int end)
+   * 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)
   {
-    if(matches==null)
+    if (matches == null)
+    {
       return null;
+    }
 
-    int [] result = null;
-    int [] tmp = null;
+    int[] result = null;
+    int[] tmp = null;
     int resultLength;
 
-    for(int m=0; m<matches.length; m++)
+    for (int m = 0; m < matches.length; m++)
     {
-      if( matches[m].sequence == sequence )
+      if (matches[m].sequence == sequence)
       {
-        int matchStart = matches[m].sequence.findIndex( matches[m].start ) - 1;
-        int matchEnd = matches[m].sequence.findIndex( matches[m].end ) - 1;
+        int matchStart = matches[m].sequence.findIndex(matches[m].start) - 1;
+        int matchEnd = matches[m].sequence.findIndex(matches[m].end) - 1;
 
-        if(matchStart<=end && matchEnd>=start)
+        if (matchStart <= end && matchEnd >= start)
         {
-          if(matchStart<start)
+          if (matchStart < start)
+          {
             matchStart = start;
+          }
 
-          if(matchEnd>end)
+          if (matchEnd > end)
+          {
             matchEnd = end;
+          }
 
-
-          if(result==null)
-            result = new int[]{matchStart, matchEnd};
+          if (result == null)
+          {
+            result = new int[]
+                {
+                matchStart, matchEnd};
+          }
           else
           {
             resultLength = result.length;
-            tmp = new int[resultLength+2];
-            System.arraycopy(result,0,tmp,0,resultLength);
+            tmp = new int[resultLength + 2];
+            System.arraycopy(result, 0, tmp, 0, resultLength);
             result = tmp;
             result[resultLength] = matchStart;
-            result[resultLength+1] = matchEnd;
+            result[resultLength + 1] = matchEnd;
           }
         }
       }
@@ -102,17 +113,23 @@ public class SearchResults
 
   public int getSize()
   {
-    return matches==null ? 0 : matches.length;
+    return matches == null ? 0 : matches.length;
   }
 
   public SequenceI getResultSequence(int index)
-  {    return matches[index].sequence;  }
+  {
+    return matches[index].sequence;
+  }
 
   public int getResultStart(int index)
-  {    return matches[index].start;  }
+  {
+    return matches[index].start;
+  }
 
   public int getResultEnd(int index)
-  {    return matches[index].end;  }
+  {
+    return matches[index].end;
+  }
 
   class Match
   {
@@ -122,9 +139,9 @@ public class SearchResults
 
     public Match(SequenceI seq, int start, int end)
     {
-     sequence = seq;
-     this.start = start;
-     this.end = end;
+      sequence = seq;
+      this.start = start;
+      this.end = end;
     }
   }
 }
diff --git a/src/jalview/datamodel/SeqCigar.java b/src/jalview/datamodel/SeqCigar.java
index 7363e9e..c896555 100644
--- a/src/jalview/datamodel/SeqCigar.java
+++ b/src/jalview/datamodel/SeqCigar.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -19,16 +19,15 @@
 package jalview.datamodel;
 
 import jalview.analysis.*;
-import jalview.util.ShiftList;
-import java.util.Vector;
+import jalview.util.*;
 
 public class SeqCigar
     extends CigarSimple
 {
-    /**
-     * start(inclusive) and end(exclusive) of subsequence on refseq
-     */
-    private int start, end;
+  /**
+   * start(inclusive) and end(exclusive) of subsequence on refseq
+   */
+  private int start, end;
   private SequenceI refseq = null;
   /**
    * Reference dataset sequence for the cigar string
@@ -38,20 +37,25 @@ public class SeqCigar
   {
     return refseq;
   }
+
   /**
    *
    * @return int start index of cigar ops on refSeq
    */
-  public int getStart() {
+  public int getStart()
+  {
     return start;
   }
+
   /**
    *
    * @return int end index (exclusive) of cigar ops on refSeq
    */
-  public int getEnd() {
+  public int getEnd()
+  {
     return end;
   }
+
   /**
    * Returns sequence as a string with cigar operations applied to it
    * @return String
@@ -59,7 +63,8 @@ public class SeqCigar
   public String getSequenceString(char GapChar)
   {
     return (length == 0) ? "" :
-        (String) getSequenceAndDeletions(refseq.getSequenceAsString(start, end), GapChar)[0];
+        (String) getSequenceAndDeletions(refseq.getSequenceAsString(start, end),
+                                         GapChar)[0];
   }
 
   /**
@@ -73,7 +78,8 @@ public class SeqCigar
     {
       return null;
     }
-    Object[] edit_result = getSequenceAndDeletions(refseq.getSequenceAsString(start,end),
+    Object[] edit_result = getSequenceAndDeletions(refseq.getSequenceAsString(
+        start, end),
         GapChar);
     if (edit_result == null)
     {
@@ -82,8 +88,9 @@ public class SeqCigar
     }
     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]));
+                       refseq.getStart() + start + bounds[0],
+                       refseq.getStart() + start +
+                       ( (bounds[2] == 0) ? -1 : bounds[2]));
     // seq.checkValidRange(); probably not needed
     seq.setDatasetSequence(refseq);
     seq.setDescription(refseq.getDescription());
@@ -105,30 +112,35 @@ public class SeqCigar
    * @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)
+  private boolean _setSeq(SequenceI seq, boolean initialDeletion, int _s,
+                          int _e)
   {
     boolean hasgaps = false;
     if (seq == null)
     {
       throw new Error("Implementation Error - _setSeq(null,...)");
     }
-    if (_s<0)
-      throw new Error("Implementation Error: _s="+_s);
+    if (_s < 0)
+    {
+      throw new Error("Implementation Error: _s=" + _s);
+    }
     String seq_string = seq.getSequenceAsString();
-    if (_e==0 || _e<_s || _e>seq_string.length())
-      _e=seq_string.length();
+    if (_e == 0 || _e < _s || _e > seq_string.length())
+    {
+      _e = seq_string.length();
+    }
     // resolve start and end positions relative to ungapped reference sequence
-    start = seq.findPosition(_s)-seq.getStart();
-    end = seq.findPosition(_e)-seq.getStart();
-    int l_ungapped = end-start;
+    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
     SequenceI ds = seq.getDatasetSequence();
     if (ds == null)
     {
       // make a new dataset sequence
       String ungapped = AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
-                                               new String(seq_string));
-      l_ungapped=ungapped.length();
+                                             new String(seq_string));
+      l_ungapped = ungapped.length();
       // check that we haven't just duplicated an ungapped sequence.
       if (l_ungapped == seq.getLength())
       {
@@ -138,7 +150,7 @@ public class SeqCigar
       {
         ds = new Sequence(seq.getName(), ungapped,
                           seq.getStart(),
-                          seq.getStart()+ungapped.length()-1);
+                          seq.getStart() + ungapped.length() - 1);
         // JBPNote: this would be consistent but may not be useful
         //        seq.setDatasetSequence(ds);
       }
@@ -146,29 +158,35 @@ public class SeqCigar
     // add in offset between seq and the dataset sequence
     if (ds.getStart() < seq.getStart())
     {
-      int offset=seq.getStart()-ds.getStart();
-      if (initialDeletion) {
-          // absolute cigar string
-          addDeleted(_s+offset);
-          start=0;
-          end+=offset;
-      } else {
-          // normal behaviour - just mark start and end subsequence
-          start+=offset;
-          end+=offset;
+      int offset = seq.getStart() - ds.getStart();
+      if (initialDeletion)
+      {
+        // absolute cigar string
+        addDeleted(_s + offset);
+        start = 0;
+        end += offset;
+      }
+      else
+      {
+        // normal behaviour - just mark start and end subsequence
+        start += offset;
+        end += offset;
 
       }
 
     }
 
     // any gaps to process ?
-    if (l_ungapped!=(_e-_s))
-      hasgaps=true;
+    if (l_ungapped != (_e - _s))
+    {
+      hasgaps = true;
+    }
 
     this.refseq = ds;
 
     // Check  offsets
-    if (end>ds.getLength()) {
+    if (end > ds.getLength())
+    {
       throw new Error("SeqCigar: Possible implementation error: sequence is longer than dataset sequence");
 //      end = ds.getLength();
     }
@@ -223,7 +241,7 @@ public class SeqCigar
       this.operation = null;
       this.range = null;
       this.length = 0;
-      if (_setSeq(seq, false,0, 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.");
       }
@@ -238,6 +256,7 @@ public class SeqCigar
   {
     this.addOperation(M, range);
   }
+
   /**
    * Adds
    * insertion and match operations based on seq to the cigar up to
@@ -250,15 +269,17 @@ public class SeqCigar
    * @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;
     int p = 0, res = seq.getLength();
 
     if (!initialDeletions)
-      p=startpos;
-
+    {
+      p = startpos;
+    }
 
     while (p <= endpos)
     {
@@ -324,7 +345,7 @@ public class SeqCigar
     }
     _setSeq(seq, false, 0, 0);
     // there is still work to do
-    addSequenceOps(this, seq, 0, seq.getLength()-1, false);
+    addSequenceOps(this, seq, 0, seq.getLength() - 1, false);
   }
 
   /**
@@ -340,7 +361,7 @@ public class SeqCigar
     {
       throw new Error("Implementation error for new Cigar(SequenceI)");
     }
-    _setSeq(seq, false, start, end+1);
+    _setSeq(seq, false, start, end + 1);
     // there is still work to do
     addSequenceOps(this, seq, start, end, false);
   }
@@ -371,13 +392,14 @@ public class SeqCigar
   {
     SequenceI[] seqs = new SequenceI[alseqs.length];
     StringBuffer[] g_seqs = new StringBuffer[alseqs.length];
-    String[] alseqs_string=new String[alseqs.length];
+    String[] alseqs_string = new String[alseqs.length];
     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);
-      gs_regions[i] = alseqs[i].getSequenceAndDeletions(alseqs_string[i], gapCharacter); // gapped sequence, {start, start col, end. endcol}, hidden regions {{start, end, col}})
+      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}})
       if (gs_regions[i] == null)
       {
         throw new Error("Implementation error: " + i +
@@ -420,13 +442,16 @@ public class SeqCigar
             else
             {
               g_seqs[s].insert(inspos,
-                               alseqs_string[i].substring(region[0], region[1] + 1));
+                               alseqs_string[i].substring(region[0],
+                  region[1] + 1));
             }
           }
           shifts.addShift(region[2], insert.length); // update shift in alignment frame of reference
-          if (segments==null)
+          if (segments == null)
+          {
             // add a hidden column for this deletion
-            colsel.hideColumns(inspos, inspos+insert.length-1);
+            colsel.hideColumns(inspos, inspos + insert.length - 1);
+          }
         }
       }
     }
@@ -435,16 +460,20 @@ public class SeqCigar
       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]));
+                             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());
     }
-    if (segments!=null) {
-      for (int i=0; i<segments.length; i+=3) {
+    if (segments != null)
+    {
+      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);
+        colsel.hideColumns(segments[i + 1],
+                           segments[i + 1] + segments[i + 2] - 1);
       }
     }
     return seqs;
@@ -474,7 +503,7 @@ public class SeqCigar
   public static boolean testSeqRecovery(SeqCigar gen_sgapped,
                                         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()))
     {
@@ -491,17 +520,20 @@ public class SeqCigar
   {
     String o_seq;
     Sequence s = new Sequence("MySeq",
-                              o_seq = "asdfktryasdtqwrtsaslldddptyipqqwaslchvhttt",
+                              o_seq =
+                              "asdfktryasdtqwrtsaslldddptyipqqwaslchvhttt",
                               39, 80);
     String orig_gapped;
     Sequence s_gapped = new Sequence("MySeq",
-        orig_gapped = "----asdf------ktryas---dtqwrtsasll----dddptyipqqwa----slchvhttt",
+                                     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",
+                                                 sub_gapped_s =
+        "------ktryas---dtqwrtsasll----dddptyipqqwa----slchvh",
                                                  43, 77);
 
     s_subsequence_gapped.setDatasetSequence(s);
@@ -564,7 +596,7 @@ public class SeqCigar
         sub_se_gp.deleteRange(st, e);
         String ssgapedseq = sub_se_gp.getSeq('-').getSequenceAsString();
         System.out.println(st + "," + e + "\t:" + ssgapedseq);
-        st -=3;
+        st -= 3;
       }
     }
     {
diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index a0a858a..2303d5d 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1,27 +1,26 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 jalview.datamodel;
 
-
 import java.util.*;
-import jalview.analysis.AlignSeq;
 
+import jalview.analysis.*;
 
 /**
  * DOCUMENT ME!
@@ -29,11 +28,12 @@ import jalview.analysis.AlignSeq;
  * @author $author$
  * @version $Revision$
  */
-public class Sequence implements SequenceI
+public class Sequence
+    implements SequenceI
 {
   SequenceI datasetSequence;
   String name;
-  private char [] sequence;
+  private char[] sequence;
   String description;
   int start;
   int end;
@@ -48,7 +48,6 @@ public class Sequence implements SequenceI
   /** DOCUMENT ME!! */
   public SequenceFeature[] sequenceFeatures;
 
-
   /**
    * Creates a new Sequence object.
    *
@@ -67,7 +66,7 @@ public class Sequence implements SequenceI
     checkValidRange();
   }
 
-  public Sequence(String name, char [] sequence, int start, int end)
+  public Sequence(String name, char[] sequence, int start, int end)
   {
     this.name = name;
     this.sequence = sequence;
@@ -102,7 +101,7 @@ public class Sequence implements SequenceI
       int endRes = 0;
       for (int j = 0; j < sequence.length; j++)
       {
-        if (!jalview.util.Comparison.isGap( sequence[j] ))
+        if (!jalview.util.Comparison.isGap(sequence[j]))
         {
           endRes++;
         }
@@ -142,7 +141,6 @@ public class Sequence implements SequenceI
     description = seq.getDescription();
   }
 
-
   /**
    * DOCUMENT ME!
    *
@@ -177,10 +175,12 @@ public class Sequence implements SequenceI
 
   public void deleteFeature(SequenceFeature sf)
   {
-    if(sequenceFeatures==null)
+    if (sequenceFeatures == null)
+    {
       return;
+    }
 
-    int index=0;
+    int index = 0;
     for (index = 0; index < sequenceFeatures.length; index++)
     {
       if (sequenceFeatures[index].equals(sf))
@@ -189,25 +189,28 @@ public class Sequence implements SequenceI
       }
     }
 
-
-    if(index==sequenceFeatures.length)
+    if (index == sequenceFeatures.length)
+    {
       return;
+    }
 
     int sfLength = sequenceFeatures.length;
-    if(sfLength<2)
+    if (sfLength < 2)
     {
       sequenceFeatures = null;
     }
     else
     {
-      SequenceFeature[] temp = new SequenceFeature[sfLength-1];
+      SequenceFeature[] temp = new SequenceFeature[sfLength - 1];
       System.arraycopy(sequenceFeatures, 0, temp, 0, index);
 
-      if(index<sfLength)
+      if (index < sfLength)
+      {
         System.arraycopy(sequenceFeatures,
                          index + 1,
                          temp,
-                         index, sequenceFeatures.length - index -1);
+                         index, sequenceFeatures.length - index - 1);
+      }
 
       sequenceFeatures = temp;
     }
@@ -226,7 +229,9 @@ public class Sequence implements SequenceI
   public void addPDBId(PDBEntry entry)
   {
     if (pdbIds == null)
+    {
       pdbIds = new Vector();
+    }
 
     pdbIds.addElement(entry);
   }
@@ -349,7 +354,6 @@ public class Sequence implements SequenceI
     checkValidRange();
   }
 
-
   public String getSequenceAsString()
   {
     return new String(sequence);
@@ -360,8 +364,7 @@ public class Sequence implements SequenceI
     return new String(getSequence(start, end));
   }
 
-
-  public char [] getSequence()
+  public char[] getSequence()
   {
     return sequence;
   }
@@ -374,7 +377,7 @@ public class Sequence implements SequenceI
    *
    * @return DOCUMENT ME!
    */
-  public char [] getSequence(int start, int end)
+  public char[] getSequence(int start, int end)
   {
     // JBPNote - left to user to pad the result here (TODO:Decide on this policy)
     if (start >= sequence.length)
@@ -387,13 +390,12 @@ public class Sequence implements SequenceI
       end = sequence.length;
     }
 
-    char [] reply = new char[end-start];
-    System.arraycopy(sequence, start, reply, 0, end-start);
+    char[] reply = new char[end - start];
+    System.arraycopy(sequence, start, reply, 0, end - start);
 
     return reply;
   }
 
-
   /**
    * make a new Sequence object from start to end (including gaps) over this seqeunce
    * @param start int
@@ -403,19 +405,27 @@ public class Sequence implements SequenceI
   public SequenceI getSubSequence(int start, int end)
   {
     if (start < 0)
+    {
       start = 0;
-    char [] seq = getSequence(start, end);
+    }
+    char[] seq = getSequence(start, end);
     if (seq.length == 0)
+    {
       return null;
+    }
     int nstart = findPosition(start);
     int nend = findPosition(end) - 1;
     // JBPNote - this is an incomplete copy.
     SequenceI nseq = new Sequence(this.getName(), seq, nstart, nend);
     nseq.setDescription(description);
-    if (datasetSequence!=null)
-        nseq.setDatasetSequence(datasetSequence);
+    if (datasetSequence != null)
+    {
+      nseq.setDatasetSequence(datasetSequence);
+    }
     else
-        nseq.setDatasetSequence(this);
+    {
+      nseq.setDatasetSequence(this);
+    }
     return nseq;
   }
 
@@ -505,7 +515,7 @@ public class Sequence implements SequenceI
     int seqlen = sequence.length;
     while ( (j < i) && (j < seqlen))
     {
-      if (!jalview.util.Comparison.isGap( sequence[j] ))
+      if (!jalview.util.Comparison.isGap(sequence[j]))
       {
         pos++;
       }
@@ -555,18 +565,18 @@ public class Sequence implements SequenceI
       return;
     }
 
-    char [] tmp;
+    char[] tmp;
 
     if (j >= sequence.length)
     {
       tmp = new char[i];
-      System.arraycopy(sequence,0,tmp,0,i);
+      System.arraycopy(sequence, 0, tmp, 0, i);
     }
     else
     {
-      tmp = new char[sequence.length-j+i];
-      System.arraycopy(sequence,0,tmp,0,i);
-      System.arraycopy(sequence,j,tmp,i,sequence.length-j);
+      tmp = new char[sequence.length - j + i];
+      System.arraycopy(sequence, 0, tmp, 0, i);
+      System.arraycopy(sequence, j, tmp, i, sequence.length - j);
     }
 
     if (this.datasetSequence != null)
@@ -593,7 +603,6 @@ public class Sequence implements SequenceI
 
   }
 
-
   /**
    * DOCUMENT ME!
    *
@@ -603,7 +612,7 @@ public class Sequence implements SequenceI
    */
   public void insertCharAt(int i, int length, char c)
   {
-    char [] tmp = new char[sequence.length+length];
+    char[] tmp = new char[sequence.length + length];
 
     if (i >= sequence.length)
     {
@@ -611,21 +620,20 @@ public class Sequence implements SequenceI
       i = sequence.length;
     }
     else
-   {
+    {
       System.arraycopy(sequence, 0, tmp, 0, i);
-   }
-
+    }
 
     int index = i;
     while (length > 0)
     {
-      tmp[ index++ ] = c;
+      tmp[index++] = c;
       length--;
     }
 
     if (i < sequence.length)
     {
-      System.arraycopy(sequence, i, tmp, index, sequence.length-i );
+      System.arraycopy(sequence, i, tmp, index, sequence.length - i);
     }
 
     sequence = tmp;
@@ -659,17 +667,21 @@ public class Sequence implements SequenceI
   public void addDBRef(DBRefEntry entry)
   {
     if (dbrefs == null)
+    {
       dbrefs = new DBRefEntry[0];
+    }
 
     int i, iSize = dbrefs.length;
 
-    for(i=0; i<iSize; i++)
-      if(dbrefs[i].getAccessionId().equals(entry.getAccessionId())
-      && dbrefs[i].getSource().equals(entry.getSource())
-      && dbrefs[i].getVersion().equals(entry.getVersion()))
+    for (i = 0; i < iSize; i++)
+    {
+      if (dbrefs[i].getAccessionId().equals(entry.getAccessionId())
+          && dbrefs[i].getSource().equals(entry.getSource())
+          && dbrefs[i].getVersion().equals(entry.getVersion()))
       {
         return;
       }
+    }
 
     DBRefEntry[] temp = new DBRefEntry[iSize + 1];
     System.arraycopy(dbrefs, 0, temp, 0, iSize);
@@ -691,11 +703,15 @@ public class Sequence implements SequenceI
   public AlignmentAnnotation[] getAnnotation()
   {
     if (annotation == null)
+    {
       return null;
+    }
 
     AlignmentAnnotation[] ret = new AlignmentAnnotation[annotation.size()];
     for (int r = 0; r < ret.length; r++)
+    {
       ret[r] = (AlignmentAnnotation) annotation.elementAt(r);
+    }
 
     return ret;
   }
@@ -703,40 +719,53 @@ public class Sequence implements SequenceI
   public void addAlignmentAnnotation(AlignmentAnnotation annotation)
   {
     if (this.annotation == null)
+    {
       this.annotation = new Vector();
+    }
 
     this.annotation.addElement(annotation);
   }
 
-
   /**
    * test if this is a valid candidate for another
    * sequence's dataset sequence.
    *
    */
-  private boolean isValidDatasetSequence() {
-      if (datasetSequence!=null)
-          return false;
-      for (int i=0;i<sequence.length; i++)
-          if (jalview.util.Comparison.isGap(sequence[i]))
-              return false;
-      return true;
+  private boolean isValidDatasetSequence()
+  {
+    if (datasetSequence != null)
+    {
+      return false;
+    }
+    for (int i = 0; i < sequence.length; i++)
+    {
+      if (jalview.util.Comparison.isGap(sequence[i]))
+      {
+        return false;
+      }
+    }
+    return true;
   }
+
   /* (non-Javadoc)
    * @see jalview.datamodel.SequenceI#deriveSequence()
    */
-  public SequenceI deriveSequence() {
-      SequenceI seq = new Sequence(name, sequence, start, end);
-      seq.setDescription(description);
-      if (datasetSequence!=null) {
-          seq.setDatasetSequence(datasetSequence);
-      } else {
-          if (isValidDatasetSequence())
-              seq.setDatasetSequence(this);
+  public SequenceI deriveSequence()
+  {
+    SequenceI seq = new Sequence(name, sequence, start, end);
+    seq.setDescription(description);
+    if (datasetSequence != null)
+    {
+      seq.setDatasetSequence(datasetSequence);
+    }
+    else
+    {
+      if (isValidDatasetSequence())
+      {
+        seq.setDatasetSequence(this);
       }
-      return seq;
+    }
+    return seq;
   }
 
 }
-
-
diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index 14ce0ff..e8c5a36 100755
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,9 +18,7 @@
  */
 package jalview.datamodel;
 
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.Vector;
+import java.util.*;
 
 /**
  * DOCUMENT ME!
@@ -30,241 +28,271 @@ import java.util.Vector;
  */
 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
-    // as a group of features between STARTGROUP and ENDGROUP markers
-    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.
-     * @param cpy
-     */
-    public SequenceFeature(SequenceFeature cpy) {
-        if (cpy!=null) {
-            begin = cpy.begin;
-            end = cpy.end;
-            score = cpy.score;
-            if (cpy.type != null)
-              type = new String(cpy.type);
-            if (cpy.description != null)
-              description = new String(cpy.description);
-            if (cpy.featureGroup != null)
-              featureGroup = new String(cpy.featureGroup);
-            if (cpy.otherDetails!=null) {
-                try {
-                    otherDetails = (Hashtable) cpy.otherDetails.clone();
-                } catch (Exception e) {
-                    // Uncloneable objects in the otherDetails - don't complain
-                }
-            }
-            if (cpy.links!=null && cpy.links.size()>0) {
-                links=new Vector();
-                for (int i=0,iSize=cpy.links.size(); i<iSize; i++) {
-                    links.setElementAt(cpy.links.elementAt(i), i);
-                }
-            }
-        }
-    }
-    public SequenceFeature(String type,
-                           String desc,
-                           String status,
-                           int begin, int end,
-                           String featureGroup)
-    {
-      this.type = type;
-      this.description = desc;
-      setValue("status", status);
-      this.begin = begin;
-      this.end = end;
-      this.featureGroup = featureGroup;
-    }
-
-    public SequenceFeature(String type,
-                           String desc,
-                           int begin, int end,
-                           float score,
-                           String featureGroup)
-    {
-      this.type = type;
-      this.description = desc;
-      this.begin = begin;
-      this.end = end;
-      this.score = score;
-      this.featureGroup = featureGroup;
-    }
-
-    public boolean equals(SequenceFeature sf)
-    {
-      if (begin != sf.begin
-          || end != sf.end
-          || score != sf.score)
-        return false;
-
-      if(!(type+description+featureGroup).equals
-         (sf.type+sf.description+sf.featureGroup))
-        return false;
-
-      return true;
-    }
-
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getBegin()
-    {
-        return begin;
-    }
-
-    public void setBegin(int start)
-    {
-      this.begin = start;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getEnd()
-    {
-        return end;
-    }
-
-    public void setEnd(int end)
-    {
-      this.end = end;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String getType()
-    {
-        return type;
-    }
-
-    public void setType(String type)
-    {
-      this.type = type;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String getDescription()
+  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
+  // as a group of features between STARTGROUP and ENDGROUP markers
+  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.
+   * @param cpy
+   */
+  public SequenceFeature(SequenceFeature cpy)
+  {
+    if (cpy != null)
     {
-        return description;
-    }
-
-    public void setDescription(String desc)
-    {
-      description = desc;
-    }
-
-    public String getFeatureGroup()
-    {
-      return featureGroup;
+      begin = cpy.begin;
+      end = cpy.end;
+      score = cpy.score;
+      if (cpy.type != null)
+      {
+        type = new String(cpy.type);
+      }
+      if (cpy.description != null)
+      {
+        description = new String(cpy.description);
+      }
+      if (cpy.featureGroup != null)
+      {
+        featureGroup = new String(cpy.featureGroup);
+      }
+      if (cpy.otherDetails != null)
+      {
+        try
+        {
+          otherDetails = (Hashtable) cpy.otherDetails.clone();
+        }
+        catch (Exception e)
+        {
+          // Uncloneable objects in the otherDetails - don't complain
+        }
+      }
+      if (cpy.links != null && cpy.links.size() > 0)
+      {
+        links = new Vector();
+        for (int i = 0, iSize = cpy.links.size(); i < iSize; i++)
+        {
+          links.setElementAt(cpy.links.elementAt(i), i);
+        }
+      }
     }
-
-    public void setFeatureGroup(String featureGroup)
+  }
+
+  public SequenceFeature(String type,
+                         String desc,
+                         String status,
+                         int begin, int end,
+                         String featureGroup)
+  {
+    this.type = type;
+    this.description = desc;
+    setValue("status", status);
+    this.begin = begin;
+    this.end = end;
+    this.featureGroup = featureGroup;
+  }
+
+  public SequenceFeature(String type,
+                         String desc,
+                         int begin, int end,
+                         float score,
+                         String featureGroup)
+  {
+    this.type = type;
+    this.description = desc;
+    this.begin = begin;
+    this.end = end;
+    this.score = score;
+    this.featureGroup = featureGroup;
+  }
+
+  public boolean equals(SequenceFeature sf)
+  {
+    if (begin != sf.begin
+        || end != sf.end
+        || score != sf.score)
     {
-      this.featureGroup = featureGroup;
+      return false;
     }
 
-    public void addLink(String labelLink)
+    if (! (type + description + featureGroup).equals
+        (sf.type + sf.description + sf.featureGroup))
     {
-      if(links==null)
-        links = new java.util.Vector();
-
-      links.insertElementAt(labelLink,0);
+      return false;
     }
 
-    public float getScore()
+    return true;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public int getBegin()
+  {
+    return begin;
+  }
+
+  public void setBegin(int start)
+  {
+    this.begin = start;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public int getEnd()
+  {
+    return end;
+  }
+
+  public void setEnd(int end)
+  {
+    this.end = end;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public String getType()
+  {
+    return type;
+  }
+
+  public void setType(String type)
+  {
+    this.type = type;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public String getDescription()
+  {
+    return description;
+  }
+
+  public void setDescription(String desc)
+  {
+    description = desc;
+  }
+
+  public String getFeatureGroup()
+  {
+    return featureGroup;
+  }
+
+  public void setFeatureGroup(String featureGroup)
+  {
+    this.featureGroup = featureGroup;
+  }
+
+  public void addLink(String labelLink)
+  {
+    if (links == null)
     {
-      return score;
+      links = new java.util.Vector();
     }
 
-    public void setScore(float value)
+    links.insertElementAt(labelLink, 0);
+  }
+
+  public float getScore()
+  {
+    return score;
+  }
+
+  public void setScore(float value)
+  {
+    score = value;
+  }
+
+  /**
+   * 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)
+  {
+    if (otherDetails == null)
     {
-      score = value;
+      return null;
     }
-
-    /**
-     * 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)
+    else
     {
-      if(otherDetails==null)
-        return null;
-      else
-        return otherDetails.get(key);
+      return otherDetails.get(key);
     }
-
-    /**
-     * 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)
+  }
+
+  /**
+   * 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)
+  {
+    if (value != null)
     {
-      if(value!=null)
+      if (otherDetails == null)
       {
-        if (otherDetails == null)
-          otherDetails = new Hashtable();
-
-        otherDetails.put(key, value);
+        otherDetails = new Hashtable();
       }
-    }
-
-
-    /*
-     * The following methods are added to maintain
-     * the castor Uniprot mapping file for the moment.
-     */
-    public void setStatus(String status)
-    {
-      setValue("status", status);
-    }
 
-    public String getStatus()
-    {
-      if (otherDetails != null)
-        return otherDetails.get("status").toString();
-      else
-        return null;
+      otherDetails.put(key, value);
     }
-
-    public void setPosition(int pos)
+  }
+
+  /*
+   * The following methods are added to maintain
+   * the castor Uniprot mapping file for the moment.
+   */
+  public void setStatus(String status)
+  {
+    setValue("status", status);
+  }
+
+  public String getStatus()
+  {
+    if (otherDetails != null)
     {
-      begin = pos;
-      end = pos;
+      return otherDetails.get("status").toString();
     }
-
-    public int getPosition()
+    else
     {
-      return begin;
+      return null;
     }
+  }
+
+  public void setPosition(int pos)
+  {
+    begin = pos;
+    end = pos;
+  }
+
+  public int getPosition()
+  {
+    return begin;
+  }
 
 }
diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 31ccf69..e22042c 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,14 +18,12 @@
  */
 package jalview.datamodel;
 
-import jalview.analysis.*;
-
-import jalview.schemes.*;
+import java.util.*;
 
 import java.awt.*;
 
-import java.util.*;
-
+import jalview.analysis.*;
+import jalview.schemes.*;
 
 /**
  * DOCUMENT ME!
@@ -35,67 +33,66 @@ import java.util.*;
  */
 public class SequenceGroup
 {
-    String groupName;
-    String description;
-    Conservation conserve;
-    Vector aaFrequency;
-    boolean displayBoxes = true;
-    boolean displayText = true;
-    boolean colourText = true;
-    private Vector sequences = new Vector();
-    int width = -1;
-
-    /** DOCUMENT ME!! */
-    public ColourSchemeI cs;
-    int startRes = 0;
-    int endRes = 0;
-    Color outlineColour = Color.black;
-    public int thresholdTextColour = 0;
-    public Color textColour = Color.black;
-    public Color textColour2 = Color.white;
-
-
-    /**
-     * Creates a new SequenceGroup object.
-     */
-    public SequenceGroup()
-    {
-        groupName = "JGroup:"+this.hashCode();
-    }
-
-    /**
-     * Creates a new SequenceGroup object.
-     *
-     * @param sequences DOCUMENT ME!
-     * @param groupName DOCUMENT ME!
-     * @param scheme DOCUMENT ME!
-     * @param displayBoxes DOCUMENT ME!
-     * @param displayText DOCUMENT ME!
-     * @param colourText DOCUMENT ME!
-     * @param start DOCUMENT ME!
-     * @param end DOCUMENT ME!
-     */
-    public SequenceGroup(Vector sequences, String groupName,
-        ColourSchemeI scheme, boolean displayBoxes, boolean displayText,
-        boolean colourText, int start, int end)
-    {
-        this.sequences = sequences;
-        this.groupName = groupName;
-        this.displayBoxes = displayBoxes;
-        this.displayText = displayText;
-        this.colourText = colourText;
-        this.cs = scheme;
-        startRes = start;
-        endRes = end;
-        recalcConservation();
-    }
-
-    public SequenceI [] getSelectionAsNewSequences(AlignmentI align)
-    {
-      int iSize = sequences.size();
-      SequenceI [] seqs = new SequenceI[iSize];
-      SequenceI [] inorder = getSequencesInOrder(align);
-
+  String groupName;
+  String description;
+  Conservation conserve;
+  Vector aaFrequency;
+  boolean displayBoxes = true;
+  boolean displayText = true;
+  boolean colourText = true;
+  private Vector sequences = new Vector();
+  int width = -1;
+
+  /** DOCUMENT ME!! */
+  public ColourSchemeI cs;
+  int startRes = 0;
+  int endRes = 0;
+  Color outlineColour = Color.black;
+  public int thresholdTextColour = 0;
+  public Color textColour = Color.black;
+  public Color textColour2 = Color.white;
+
+  /**
+   * Creates a new SequenceGroup object.
+   */
+  public SequenceGroup()
+  {
+    groupName = "JGroup:" + this.hashCode();
+  }
+
+  /**
+   * Creates a new SequenceGroup object.
+   *
+   * @param sequences DOCUMENT ME!
+   * @param groupName DOCUMENT ME!
+   * @param scheme DOCUMENT ME!
+   * @param displayBoxes DOCUMENT ME!
+   * @param displayText DOCUMENT ME!
+   * @param colourText DOCUMENT ME!
+   * @param start DOCUMENT ME!
+   * @param end DOCUMENT ME!
+   */
+  public SequenceGroup(Vector sequences, String groupName,
+                       ColourSchemeI scheme, boolean displayBoxes,
+                       boolean displayText,
+                       boolean colourText, int start, int end)
+  {
+    this.sequences = sequences;
+    this.groupName = groupName;
+    this.displayBoxes = displayBoxes;
+    this.displayText = displayText;
+    this.colourText = colourText;
+    this.cs = scheme;
+    startRes = start;
+    endRes = end;
+    recalcConservation();
+  }
+
+  public SequenceI[] getSelectionAsNewSequences(AlignmentI align)
+  {
+    int iSize = sequences.size();
+    SequenceI[] seqs = new SequenceI[iSize];
+    SequenceI[] inorder = getSequencesInOrder(align);
 
     for (int i = 0; i < iSize; i++)
     {
@@ -110,477 +107,494 @@ public class SequenceGroup
       seqs[i].setDBRef(seq.getDBRef());
       seqs[i].setSequenceFeatures(seq.getSequenceFeatures());
       if (seq.getDatasetSequence() != null)
+      {
         seqs[i].setDatasetSequence(seq.getDatasetSequence());
+      }
 
-      if(seq.getAnnotation()!=null)
+      if (seq.getAnnotation() != null)
       {
-        for(int a=0; a<seq.getAnnotation().length; a++)
+        for (int a = 0; a < seq.getAnnotation().length; a++)
+        {
           seqs[i].addAlignmentAnnotation(seq.getAnnotation()[a]);
+        }
       }
     }
 
     return seqs;
 
-    }
-
-    /**
-     * If sequence ends in gaps, the end residue can
-     * be correctly calculated here
-     * @param seq SequenceI
-     * @return int
-     */
-    public int findEndRes(SequenceI seq)
-    {
-      int eres = 0;
-      char ch;
-
-      for (int j = 0; j < endRes + 1 && j < seq.getLength(); j++)
-      {
-        ch = seq.getCharAt(j);
-        if (!jalview.util.Comparison.isGap( (ch)))
-        {
-          eres++;
-        }
-      }
-
-      if (eres > 0)
-      {
-        eres += seq.getStart() - 1;
-      }
+  }
 
-      return eres;
-    }
+  /**
+   * If sequence ends in gaps, the end residue can
+   * be correctly calculated here
+   * @param seq SequenceI
+   * @return int
+   */
+  public int findEndRes(SequenceI seq)
+  {
+    int eres = 0;
+    char ch;
 
-    public Vector getSequences(Hashtable hiddenReps)
+    for (int j = 0; j < endRes + 1 && j < seq.getLength(); j++)
     {
-      if(hiddenReps == null)
-        return sequences;
-      else
+      ch = seq.getCharAt(j);
+      if (!jalview.util.Comparison.isGap( (ch)))
       {
-        Vector allSequences = new Vector();
-        SequenceI seq, seq2;
-        for (int i = 0; i < sequences.size(); i++)
-        {
-          seq = (SequenceI) sequences.elementAt(i);
-          allSequences.addElement(seq);
-          if (hiddenReps.containsKey(seq) )
-          {
-            SequenceGroup hsg = (SequenceGroup)hiddenReps.get(seq);
-            for (int h = 0; h < hsg.getSize(); h++)
-            {
-              seq2 = hsg.getSequenceAt(h);
-              if (seq2 != seq
-                  && !allSequences.contains(seq2))
-                allSequences.addElement(seq2);
-            }
-          }
-        }
-
-        return allSequences;
+        eres++;
       }
     }
 
-    public SequenceI[] getSequencesAsArray(Hashtable hiddenReps)
+    if (eres > 0)
     {
-      Vector tmp = getSequences(hiddenReps);
-      if(tmp==null)
-        return null;
-      SequenceI [] result = new SequenceI[tmp.size()];
-      for(int i=0; i<result.length; i++)
-        result[i] = (SequenceI)tmp.elementAt(i);
-
-      return result;
+      eres += seq.getStart() - 1;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param col DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean adjustForRemoveLeft(int col)
-    {
-        // return value is true if the group still exists
-        if (startRes >= col)
-        {
-            startRes = startRes - col;
-        }
-
-        if (endRes >= col)
-        {
-            endRes = endRes - col;
+    return eres;
+  }
 
-            if (startRes > endRes)
-            {
-                startRes = 0;
-            }
-        }
-        else
-        {
-            // must delete this group!!
-            return false;
-        }
-
-        return true;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param col DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean adjustForRemoveRight(int col)
+  public Vector getSequences(Hashtable hiddenReps)
+  {
+    if (hiddenReps == null)
     {
-        if (startRes > col)
-        {
-            // delete this group
-            return false;
-        }
-
-        if (endRes >= col)
-        {
-            endRes = col;
-        }
-
-        return true;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String getName()
-    {
-        return groupName;
-    }
-
-    public String getDescription()
-    {
-      return description;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param name DOCUMENT ME!
-     */
-    public void setName(String name)
-    {
-        groupName = name;
-    }
-
-    public void setDescription(String desc)
-    {
-      description = desc;
+      return sequences;
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Conservation getConservation()
-    {
-        return conserve;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param c DOCUMENT ME!
-     */
-    public void setConservation(Conservation c)
+    else
     {
-        conserve = c;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param s DOCUMENT ME!
-     * @param recalc DOCUMENT ME!
-     */
-    public void addSequence(SequenceI s, boolean recalc)
-    {
-        if (s!=null && !sequences.contains(s))
-        {
-            sequences.addElement(s);
-        }
-
-        if (recalc)
-        {
-            recalcConservation();
-        }
-    }
-
-    /**
-     * DOCUMENT ME!
-     */
-    public void recalcConservation()
-    {
-        if(cs == null)
-          return;
-
-        try
+      Vector allSequences = new Vector();
+      SequenceI seq, seq2;
+      for (int i = 0; i < sequences.size(); i++)
+      {
+        seq = (SequenceI) sequences.elementAt(i);
+        allSequences.addElement(seq);
+        if (hiddenReps.containsKey(seq))
         {
-          cs.setConsensus(AAFrequency.calculate(sequences, startRes, endRes+1));
-
-          if (cs instanceof ClustalxColourScheme)
+          SequenceGroup hsg = (SequenceGroup) hiddenReps.get(seq);
+          for (int h = 0; h < hsg.getSize(); h++)
           {
-            ( (ClustalxColourScheme) cs).resetClustalX(sequences, getWidth());
-          }
-
-          if (cs.conservationApplied())
-          {
-            Conservation c = new Conservation(groupName,
-                                              ResidueProperties.propHash, 3, sequences,
-                                              startRes, endRes+1);
-            c.calculate();
-            c.verdict(false, 25);
-
-            cs.setConservation(c);
-
-            if (cs instanceof ClustalxColourScheme)
+            seq2 = hsg.getSequenceAt(h);
+            if (seq2 != seq
+                && !allSequences.contains(seq2))
             {
-              ( (ClustalxColourScheme) cs).resetClustalX(sequences,
-                                                         getWidth());
+              allSequences.addElement(seq2);
             }
           }
         }
-        catch (java.lang.OutOfMemoryError err)
-        {
-          System.out.println("Out of memory loading groups: " + err);
-        }
-
-    }
+      }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param s DOCUMENT ME!
-     * @param recalc DOCUMENT ME!
-     */
-    public void addOrRemove(SequenceI s, boolean recalc)
-    {
-        if (sequences.contains(s))
-        {
-            deleteSequence(s, recalc);
-        }
-        else
-        {
-            addSequence(s, recalc);
-        }
+      return allSequences;
     }
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param s DOCUMENT ME!
-     * @param recalc DOCUMENT ME!
-     */
-    public void deleteSequence(SequenceI s, boolean recalc)
+  public SequenceI[] getSequencesAsArray(Hashtable hiddenReps)
+  {
+    Vector tmp = getSequences(hiddenReps);
+    if (tmp == null)
     {
-        sequences.removeElement(s);
-
-        if (recalc)
-        {
-            recalcConservation();
-        }
+      return null;
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getStartRes()
+    SequenceI[] result = new SequenceI[tmp.size()];
+    for (int i = 0; i < result.length; i++)
     {
-        return startRes;
+      result[i] = (SequenceI) tmp.elementAt(i);
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getEndRes()
-    {
-        return endRes;
-    }
+    return result;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     */
-    public void setStartRes(int i)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param col DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public boolean adjustForRemoveLeft(int col)
+  {
+    // return value is true if the group still exists
+    if (startRes >= col)
     {
-        startRes = i;
+      startRes = startRes - col;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     */
-    public void setEndRes(int i)
+    if (endRes >= col)
     {
-        endRes = i;
-    }
+      endRes = endRes - col;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getSize()
-    {
-        return sequences.size();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public SequenceI getSequenceAt(int i)
-    {
-        return (SequenceI) sequences.elementAt(i);
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param state DOCUMENT ME!
-     */
-    public void setColourText(boolean state)
-    {
-        colourText = state;
+      if (startRes > endRes)
+      {
+        startRes = 0;
+      }
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getColourText()
+    else
+    {
+      // must delete this group!!
+      return false;
+    }
+
+    return true;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param col DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public boolean adjustForRemoveRight(int col)
+  {
+    if (startRes > col)
     {
-        return colourText;
+      // delete this group
+      return false;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param state DOCUMENT ME!
-     */
-    public void setDisplayText(boolean state)
+    if (endRes >= col)
     {
-        displayText = state;
+      endRes = col;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getDisplayText()
-    {
-        return displayText;
-    }
+    return true;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param state DOCUMENT ME!
-     */
-    public void setDisplayBoxes(boolean state)
-    {
-        displayBoxes = state;
-    }
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public String getName()
+  {
+    return groupName;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getDisplayBoxes()
-    {
-        return displayBoxes;
-    }
+  public String getDescription()
+  {
+    return description;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getWidth()
-    {
-        // MC This needs to get reset when characters are inserted and deleted
-        if (sequences.size() > 0)
-        {
-            width = ((SequenceI) sequences.elementAt(0)).getLength();
-        }
+  /**
+   * DOCUMENT ME!
+   *
+   * @param name DOCUMENT ME!
+   */
+  public void setName(String name)
+  {
+    groupName = name;
+  }
 
-        for (int i = 1; i < sequences.size(); i++)
-        {
-            SequenceI seq = (SequenceI) sequences.elementAt(i);
+  public void setDescription(String desc)
+  {
+    description = desc;
+  }
 
-            if (seq.getLength() > width)
-            {
-                width = seq.getLength();
-            }
-        }
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Conservation getConservation()
+  {
+    return conserve;
+  }
 
-        return width;
-    }
+  /**
+   * DOCUMENT ME!
+   *
+   * @param c DOCUMENT ME!
+   */
+  public void setConservation(Conservation c)
+  {
+    conserve = c;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param c DOCUMENT ME!
-     */
-    public void setOutlineColour(Color c)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param s DOCUMENT ME!
+   * @param recalc DOCUMENT ME!
+   */
+  public void addSequence(SequenceI s, boolean recalc)
+  {
+    if (s != null && !sequences.contains(s))
     {
-        outlineColour = c;
+      sequences.addElement(s);
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Color getOutlineColour()
+    if (recalc)
     {
-        return outlineColour;
+      recalcConservation();
     }
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void recalcConservation()
+  {
+    if (cs == null)
+    {
+      return;
+    }
+
+    try
+    {
+      cs.setConsensus(AAFrequency.calculate(sequences, startRes, endRes + 1));
+
+      if (cs instanceof ClustalxColourScheme)
+      {
+        ( (ClustalxColourScheme) cs).resetClustalX(sequences, getWidth());
+      }
 
-    /**
-     *
-     * returns the sequences in the group ordered by the ordering given by al
-     *
-     * @param al Alignment
-     * @return SequenceI[]
-     */
-    public SequenceI[] getSequencesInOrder(AlignmentI al)
-    {
-        int sSize = sequences.size();
-        int alHeight = al.getHeight();
+      if (cs.conservationApplied())
+      {
+        Conservation c = new Conservation(groupName,
+                                          ResidueProperties.propHash, 3,
+                                          sequences,
+                                          startRes, endRes + 1);
+        c.calculate();
+        c.verdict(false, 25);
 
-        SequenceI[] seqs = new SequenceI[sSize];
+        cs.setConservation(c);
 
-        int index = 0;
-        for (int i = 0; i < alHeight && index<sSize; i++)
+        if (cs instanceof ClustalxColourScheme)
         {
-          if(sequences.contains( al.getSequenceAt(i) ) )
-            seqs[index++] = al.getSequenceAt(i);
+          ( (ClustalxColourScheme) cs).resetClustalX(sequences,
+              getWidth());
         }
+      }
+    }
+    catch (java.lang.OutOfMemoryError err)
+    {
+      System.out.println("Out of memory loading groups: " + err);
+    }
+
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param s DOCUMENT ME!
+   * @param recalc DOCUMENT ME!
+   */
+  public void addOrRemove(SequenceI s, boolean recalc)
+  {
+    if (sequences.contains(s))
+    {
+      deleteSequence(s, recalc);
+    }
+    else
+    {
+      addSequence(s, recalc);
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param s DOCUMENT ME!
+   * @param recalc DOCUMENT ME!
+   */
+  public void deleteSequence(SequenceI s, boolean recalc)
+  {
+    sequences.removeElement(s);
+
+    if (recalc)
+    {
+      recalcConservation();
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public int getStartRes()
+  {
+    return startRes;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public int getEndRes()
+  {
+    return endRes;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param i DOCUMENT ME!
+   */
+  public void setStartRes(int i)
+  {
+    startRes = i;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param i DOCUMENT ME!
+   */
+  public void setEndRes(int i)
+  {
+    endRes = i;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public int getSize()
+  {
+    return sequences.size();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param i DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public SequenceI getSequenceAt(int i)
+  {
+    return (SequenceI) sequences.elementAt(i);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param state DOCUMENT ME!
+   */
+  public void setColourText(boolean state)
+  {
+    colourText = state;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public boolean getColourText()
+  {
+    return colourText;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param state DOCUMENT ME!
+   */
+  public void setDisplayText(boolean state)
+  {
+    displayText = state;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public boolean getDisplayText()
+  {
+    return displayText;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param state DOCUMENT ME!
+   */
+  public void setDisplayBoxes(boolean state)
+  {
+    displayBoxes = state;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public boolean getDisplayBoxes()
+  {
+    return displayBoxes;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public int getWidth()
+  {
+    // MC This needs to get reset when characters are inserted and deleted
+    if (sequences.size() > 0)
+    {
+      width = ( (SequenceI) sequences.elementAt(0)).getLength();
+    }
+
+    for (int i = 1; i < sequences.size(); i++)
+    {
+      SequenceI seq = (SequenceI) sequences.elementAt(i);
+
+      if (seq.getLength() > width)
+      {
+        width = seq.getLength();
+      }
+    }
 
-        return seqs;
+    return width;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param c DOCUMENT ME!
+   */
+  public void setOutlineColour(Color c)
+  {
+    outlineColour = c;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Color getOutlineColour()
+  {
+    return outlineColour;
+  }
+
+  /**
+   *
+   * returns the sequences in the group ordered by the ordering given by al
+   *
+   * @param al Alignment
+   * @return SequenceI[]
+   */
+  public SequenceI[] getSequencesInOrder(AlignmentI al)
+  {
+    int sSize = sequences.size();
+    int alHeight = al.getHeight();
+
+    SequenceI[] seqs = new SequenceI[sSize];
+
+    int index = 0;
+    for (int i = 0; i < alHeight && index < sSize; i++)
+    {
+      if (sequences.contains(al.getSequenceAt(i)))
+      {
+        seqs[index++] = al.getSequenceAt(i);
+      }
     }
+
+    return seqs;
+  }
 }
diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 96c6cbf..6694aff 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -20,7 +20,6 @@ package jalview.datamodel;
 
 import java.util.*;
 
-
 /**
  * DOCUMENT ME!
  *
@@ -29,241 +28,239 @@ import java.util.*;
  */
 public interface SequenceI
 {
-    /**
-     * DOCUMENT ME!
-     *
-     * @param name DOCUMENT ME!
-     */
-    public void setName(String name);
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String getName();
-
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param start DOCUMENT ME!
-     */
-    public void setStart(int start);
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getStart();
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String getDisplayId(boolean jvsuffix);
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param end DOCUMENT ME!
-     */
-    public void setEnd(int end);
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getEnd();
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getLength();
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param sequence DOCUMENT ME!
-     */
-    public void setSequence(String sequence);
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String getSequenceAsString();
-
-    /**
-     * 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();
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param start DOCUMENT ME!
-     * @param end DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    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
-     * @return SequenceI
-     */
-    public SequenceI getSubSequence(int start, int end);
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public char getCharAt(int i);
-
-    /**
-     * 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!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int findIndex(int pos);
-
-    /**
-     * Returns the sequence position for an alignment position
-     *
-     * @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
-     */
-    public int[] gapMap();
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     * @param j DOCUMENT ME!
-     */
-    public void deleteChars(int i, int j);
-
-
-    /**
-     * 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!
-     */
-    public void insertCharAt(int i, int length, char c);
-
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public SequenceFeature[] getSequenceFeatures();
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param v DOCUMENT ME!
-     */
-    public void setSequenceFeatures(SequenceFeature [] features);
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param id DOCUMENT ME!
-     */
-    public void setPDBId(Vector ids);
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Vector getPDBId();
-
-    public void addPDBId(PDBEntry entry);
-
-    public String getVamsasId();
-
-    public void setVamsasId(String id);
-
-    public void setDBRef(DBRefEntry[] dbs);
-
-    public DBRefEntry [] getDBRef();
-
-    public void addDBRef(DBRefEntry entry);
-
-    public void addSequenceFeature(SequenceFeature sf);
-
-    public void deleteFeature(SequenceFeature sf);
-
-    public void setDatasetSequence(SequenceI seq);
-
-    public SequenceI getDatasetSequence();
-
-    public AlignmentAnnotation [] getAnnotation();
-
-    public void addAlignmentAnnotation(AlignmentAnnotation annotation);
-
-
-    /**
-     * Derive a sequence (using this one's dataset or as the dataset)
-     * @return duplicate sequence with valid dataset sequence
-     */
-    public SequenceI deriveSequence();
+  /**
+   * DOCUMENT ME!
+   *
+   * @param name DOCUMENT ME!
+   */
+  public void setName(String name);
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public String getName();
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param start DOCUMENT ME!
+   */
+  public void setStart(int start);
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public int getStart();
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public String getDisplayId(boolean jvsuffix);
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param end DOCUMENT ME!
+   */
+  public void setEnd(int end);
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public int getEnd();
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public int getLength();
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param sequence DOCUMENT ME!
+   */
+  public void setSequence(String sequence);
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public String getSequenceAsString();
+
+  /**
+   * 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();
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param start DOCUMENT ME!
+   * @param end DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  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
+   * @return SequenceI
+   */
+  public SequenceI getSubSequence(int start, int end);
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param i DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public char getCharAt(int i);
+
+  /**
+   * 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!
+   *
+   * @return DOCUMENT ME!
+   */
+  public int findIndex(int pos);
+
+  /**
+   * Returns the sequence position for an alignment position
+   *
+   * @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
+   */
+  public int[] gapMap();
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param i DOCUMENT ME!
+   * @param j DOCUMENT ME!
+   */
+  public void deleteChars(int i, int j);
+
+  /**
+   * 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!
+   */
+  public void insertCharAt(int i, int length, char c);
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public SequenceFeature[] getSequenceFeatures();
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param v DOCUMENT ME!
+   */
+  public void setSequenceFeatures(SequenceFeature[] features);
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param id DOCUMENT ME!
+   */
+  public void setPDBId(Vector ids);
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Vector getPDBId();
+
+  public void addPDBId(PDBEntry entry);
+
+  public String getVamsasId();
+
+  public void setVamsasId(String id);
+
+  public void setDBRef(DBRefEntry[] dbs);
+
+  public DBRefEntry[] getDBRef();
+
+  public void addDBRef(DBRefEntry entry);
+
+  public void addSequenceFeature(SequenceFeature sf);
+
+  public void deleteFeature(SequenceFeature sf);
+
+  public void setDatasetSequence(SequenceI seq);
+
+  public SequenceI getDatasetSequence();
+
+  public AlignmentAnnotation[] getAnnotation();
+
+  public void addAlignmentAnnotation(AlignmentAnnotation annotation);
+
+  /**
+   * Derive a sequence (using this one's dataset or as the dataset)
+   * @return duplicate sequence with valid dataset sequence
+   */
+  public SequenceI deriveSequence();
 
 }
diff --git a/src/jalview/datamodel/SequenceNode.java b/src/jalview/datamodel/SequenceNode.java
index c40f746..943751e 100755
--- a/src/jalview/datamodel/SequenceNode.java
+++ b/src/jalview/datamodel/SequenceNode.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -20,130 +20,130 @@ package jalview.datamodel;
 
 import java.awt.*;
 
-
 /**
  * DOCUMENT ME!
  *
  * @author $author$
  * @version $Revision$
  */
-public class SequenceNode extends BinaryNode
+public class SequenceNode
+    extends BinaryNode
 {
-    /** DOCUMENT ME!! */
-    public float dist;
-
-    /** DOCUMENT ME!! */
-    public int count;
-
-    /** DOCUMENT ME!! */
-    public float height;
-
-    /** DOCUMENT ME!! */
-    public float ycount;
-
-    /** DOCUMENT ME!! */
-    public Color color = Color.black;
-
-    /** DOCUMENT ME!! */
-    public boolean dummy = false;
-    private boolean placeholder = false;
-
-    /**
-     * Creates a new SequenceNode object.
-     */
-    public SequenceNode()
-    {
-        super();
-    }
-
-    /**
-     * Creates a new SequenceNode object.
-     *
-     * @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)
-    {
-        super(val, parent, name);
-        this.dist = dist;
-    }
-
-    /**
-     * 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!
-     */
-    public SequenceNode(Object val, SequenceNode parent, String name,
-        float dist, int bootstrap, boolean dummy)
-    {
-        super(val, parent, name);
-        this.dist = dist;
-        this.bootstrap = bootstrap;
-        this.dummy = dummy;
-    }
-
-    /**
-     * @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
-     */
-    public boolean isPlaceholder()
+  /** DOCUMENT ME!! */
+  public float dist;
+
+  /** DOCUMENT ME!! */
+  public int count;
+
+  /** DOCUMENT ME!! */
+  public float height;
+
+  /** DOCUMENT ME!! */
+  public float ycount;
+
+  /** DOCUMENT ME!! */
+  public Color color = Color.black;
+
+  /** DOCUMENT ME!! */
+  public boolean dummy = false;
+  private boolean placeholder = false;
+
+  /**
+   * Creates a new SequenceNode object.
+   */
+  public SequenceNode()
+  {
+    super();
+  }
+
+  /**
+   * Creates a new SequenceNode object.
+   *
+   * @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)
+  {
+    super(val, parent, name);
+    this.dist = dist;
+  }
+
+  /**
+   * 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!
+   */
+  public SequenceNode(Object val, SequenceNode parent, String name,
+                      float dist, int bootstrap, boolean dummy)
+  {
+    super(val, parent, name);
+    this.dist = dist;
+    this.bootstrap = bootstrap;
+    this.dummy = dummy;
+  }
+
+  /**
+   * @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
+   */
+  public boolean isPlaceholder()
+  {
+    return placeholder;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param newstate DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public boolean setDummy(boolean newstate)
+  {
+    boolean oldstate = dummy;
+    dummy = newstate;
+
+    return oldstate;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param Placeholder DOCUMENT ME!
+   */
+  public void setPlaceholder(boolean Placeholder)
+  {
+    this.placeholder = Placeholder;
+  }
+
+  /**
+   * 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.
+   */
+  public SequenceNode AscendTree()
+  {
+    SequenceNode c = this;
+
+    do
     {
-        return placeholder;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param newstate DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean setDummy(boolean newstate)
-    {
-        boolean oldstate = dummy;
-        dummy = newstate;
-
-        return oldstate;
+      c = (SequenceNode) c.parent();
     }
+    while ( (c != null) && c.dummy);
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param Placeholder DOCUMENT ME!
-     */
-    public void setPlaceholder(boolean Placeholder)
-    {
-        this.placeholder = Placeholder;
-    }
-
-    /**
-     * 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.
-     */
-    public SequenceNode AscendTree()
-    {
-        SequenceNode c = this;
-
-        do
-        {
-            c = (SequenceNode) c.parent();
-        }
-        while ((c != null) && c.dummy);
-
-        return c;
-    }
+    return c;
+  }
 }
diff --git a/src/jalview/datamodel/SequencePoint.java b/src/jalview/datamodel/SequencePoint.java
index 5c3a71a..9c28672 100755
--- a/src/jalview/datamodel/SequencePoint.java
+++ b/src/jalview/datamodel/SequencePoint.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -26,18 +26,18 @@ package jalview.datamodel;
  */
 public class SequencePoint
 {
-    // SMJS PUBLIC
+  // SMJS PUBLIC
 
-    /** DOCUMENT ME!! */
-    public SequenceI sequence;
+  /** DOCUMENT ME!! */
+  public SequenceI sequence;
 
-    /** DOCUMENT ME!! */
-    public float[] coord;
+  /** DOCUMENT ME!! */
+  public float[] coord;
 
-    // SMJS ENDPUBLIC
-    public SequencePoint(SequenceI sequence, float[] coord)
-    {
-        this.sequence = sequence;
-        this.coord = coord;
-    }
+  // SMJS ENDPUBLIC
+  public SequencePoint(SequenceI sequence, float[] coord)
+  {
+    this.sequence = sequence;
+    this.coord = coord;
+  }
 }
diff --git a/src/jalview/datamodel/UniprotEntry.java b/src/jalview/datamodel/UniprotEntry.java
index 7754148..b963022 100755
--- a/src/jalview/datamodel/UniprotEntry.java
+++ b/src/jalview/datamodel/UniprotEntry.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -37,34 +37,34 @@ public class UniprotEntry
 
   public void setFeature(Vector items)
   {
-       feature = items;
-   }
-
-   public Vector getFeature() {
-       return feature;
-   }
-
+    feature = items;
+  }
 
-   public Vector getAccession()
-   {
-     return accession;
-   }
+  public Vector getFeature()
+  {
+    return feature;
+  }
 
-   public void setProtein(UniprotProteinName names)
-   {
-     protName = names;
-   }
+  public Vector getAccession()
+  {
+    return accession;
+  }
 
+  public void setProtein(UniprotProteinName names)
+  {
+    protName = names;
+  }
 
-   public UniprotProteinName getProtein()
-   {
-     return protName;
-   }
+  public UniprotProteinName getProtein()
+  {
+    return protName;
+  }
 
   public void setName(Vector na)
   {
     name = na;
   }
+
   public Vector getName()
   {
     return name;
@@ -87,7 +87,7 @@ public class UniprotEntry
 
   public void setDbReference(Vector dbref)
   {
-   this.dbrefs = dbref;
+    this.dbrefs = dbref;
   }
 
 }
diff --git a/src/jalview/datamodel/UniprotFile.java b/src/jalview/datamodel/UniprotFile.java
index b83b28b..b088ec2 100755
--- a/src/jalview/datamodel/UniprotFile.java
+++ b/src/jalview/datamodel/UniprotFile.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -17,17 +17,20 @@
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
 package jalview.datamodel;
-import java.util.Vector;
+
+import java.util.*;
 
 public class UniprotFile
 {
   Vector _items;
 
-  public void setUniprotEntries(Vector items) {
-       _items = items;
-   }
+  public void setUniprotEntries(Vector items)
+  {
+    _items = items;
+  }
 
-   public Vector getUniprotEntries() {
-       return _items;
-   }
+  public Vector getUniprotEntries()
+  {
+    return _items;
+  }
 }
diff --git a/src/jalview/datamodel/UniprotProteinName.java b/src/jalview/datamodel/UniprotProteinName.java
index 6203a1f..bb9a628 100755
--- a/src/jalview/datamodel/UniprotProteinName.java
+++ b/src/jalview/datamodel/UniprotProteinName.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -20,7 +20,7 @@ package jalview.datamodel;
 
 public class UniprotProteinName
 {
-    /**
+  /**
    * internal content storage
    */
   private java.util.Vector names;
diff --git a/src/jalview/datamodel/UniprotSequence.java b/src/jalview/datamodel/UniprotSequence.java
index c33914c..d5262e3 100755
--- a/src/jalview/datamodel/UniprotSequence.java
+++ b/src/jalview/datamodel/UniprotSequence.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -20,7 +20,7 @@ package jalview.datamodel;
 
 public class UniprotSequence
 {
-    /**
+  /**
    * internal content storage
    */
   private java.lang.String _content = "";
@@ -28,15 +28,19 @@ public class UniprotSequence
   public void setContent(String seq)
   {
     StringBuffer sb = new StringBuffer();
-    for(int i=0; i<seq.length(); i++)
-      if(seq.charAt(i)!=' ')
+    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; }
+  {
+    return _content;
+  }
 
 }
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 08c1aa9..b281767 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -24,18 +24,18 @@ import java.util.*;
 
 import java.awt.*;
 import java.awt.datatransfer.*;
+import java.awt.dnd.*;
 import java.awt.event.*;
 import java.awt.print.*;
 import javax.swing.*;
 
 import jalview.analysis.*;
+import jalview.commands.*;
 import jalview.datamodel.*;
 import jalview.io.*;
 import jalview.jbgui.*;
 import jalview.schemes.*;
-import jalview.commands.*;
 import jalview.ws.*;
-import java.awt.dnd.*;
 
 /**
  * DOCUMENT ME!
@@ -43,7 +43,8 @@ import java.awt.dnd.*;
  * @author $author$
  * @version $Revision$
  */
-public class AlignFrame extends GAlignFrame implements DropTargetListener
+public class AlignFrame
+    extends GAlignFrame implements DropTargetListener
 {
   /** DOCUMENT ME!! */
   public static final int DEFAULT_WIDTH = 700;
@@ -56,13 +57,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
   Vector alignPanels = new Vector();
 
-
   /** DOCUMENT ME!! */
   String currentFileFormat = null;
 
   String fileName = null;
 
-
   /**
    * Creates a new AlignFrame object.
    *
@@ -73,7 +72,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     this(al, null, width, height);
   }
 
-
   /**
    * new alignment window with hidden columns
    * @param al AlignmentI
@@ -87,7 +85,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
     alignPanel = new AlignmentPanel(this, viewport);
 
-    if(al.getDataset()==null)
+    if (al.getDataset() == null)
     {
       al.setDataset(null);
     }
@@ -118,240 +116,264 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
       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");
 
     if (sortby.equals("Id"))
+    {
       sortIDMenuItem_actionPerformed(null);
+    }
     else if (sortby.equals("Pairwise Identity"))
+    {
       sortPairwiseMenuItem_actionPerformed(null);
+    }
 
     if (Desktop.desktop != null)
-   {
-     addServiceListeners();
-     setGUINucleotide(viewport.alignment.isNucleotide());
-   }
+    {
+      addServiceListeners();
+      setGUINucleotide(viewport.alignment.isNucleotide());
+    }
 
-   setMenusFromViewport(viewport);
+    setMenusFromViewport(viewport);
 
-   if (viewport.wrapAlignment)
-   {
-     wrapMenuItem_actionPerformed(null);
-   }
+    if (viewport.wrapAlignment)
+    {
+      wrapMenuItem_actionPerformed(null);
+    }
 
-   addKeyListener();
+    addKeyListener();
 
   }
 
   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)
         {
-          if (viewport.cursorMode
-              && evt.getKeyCode() >= KeyEvent.VK_0
-              && evt.getKeyCode() <= KeyEvent.VK_9)
-          {
-            alignPanel.seqPanel.numberPressed(evt.getKeyChar());
-          }
+          alignPanel.seqPanel.numberPressed(evt.getKeyChar());
+        }
 
-          switch (evt.getKeyCode())
-          {
+        switch (evt.getKeyCode())
+        {
 
-            case 27: // escape key
-              deselectAllSequenceMenuItem_actionPerformed(null);
+          case 27: // escape key
+            deselectAllSequenceMenuItem_actionPerformed(null);
 
-              break;
+            break;
 
-            case KeyEvent.VK_DOWN:
-              if (viewport.cursorMode)
-              {
-                alignPanel.seqPanel.moveCursor(0, 1);
-              }
-              else
-                moveSelectedSequences(false);
-              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 (viewport.cursorMode)
-              {
-                alignPanel.seqPanel.moveCursor( -1, 0);
-              }
-              break;
+          case KeyEvent.VK_LEFT:
+            if (viewport.cursorMode)
+            {
+              alignPanel.seqPanel.moveCursor( -1, 0);
+            }
+            break;
 
-            case KeyEvent.VK_RIGHT:
-              if (viewport.cursorMode)
-              {
-                alignPanel.seqPanel.moveCursor(1, 0);
-              }
-              break;
+          case KeyEvent.VK_RIGHT:
+            if (viewport.cursorMode)
+            {
+              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)
-              {
-                cut_actionPerformed(null);
-              }
-              else
-                alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
-                                           || evt.isShiftDown()
-                                           || evt.isAltDown());
+          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());
+            }
 
-              break;
+            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_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_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;
-              }
-              alignPanel.seqPanel.seqCanvas.repaint();
-              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_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_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:
+              javax.help.HelpBroker hb = hs.createHelpBroker();
+              hb.setCurrentID("home");
+              hb.setDisplayed(true);
+            }
+            catch (Exception ex)
             {
-              boolean toggleSeqs = !evt.isControlDown();
-              boolean toggleCols = !evt.isShiftDown();
+              ex.printStackTrace();
+            }
+            break
+                ;
+          case KeyEvent.VK_H:
+          {
+            boolean toggleSeqs = !evt.isControlDown();
+            boolean toggleCols = !evt.isShiftDown();
 
-              boolean hide = false;
+            boolean hide = false;
 
-              SequenceGroup sg = viewport.getSelectionGroup();
-              if (toggleSeqs)
+            SequenceGroup sg = viewport.getSelectionGroup();
+            if (toggleSeqs)
+            {
+              if (sg != null && sg.getSize() != viewport.alignment.getHeight())
               {
-                if (sg != null && sg.getSize() != viewport.alignment.getHeight())
-                {
-                  hideSelSequences_actionPerformed(null);
-                  hide = true;
-                }
-                else if (! (toggleCols && viewport.colSel.getSelected().size() > 0))
-                  showAllSeqs_actionPerformed(null);
+                hideSelSequences_actionPerformed(null);
+                hide = true;
               }
+              else if (! (toggleCols &&
+                          viewport.colSel.getSelected().size() > 0))
+              {
+                showAllSeqs_actionPerformed(null);
+              }
+            }
 
-              if (toggleCols)
+            if (toggleCols)
+            {
+              if (viewport.colSel.getSelected().size() > 0)
               {
-                if (viewport.colSel.getSelected().size() > 0)
+                hideSelColumns_actionPerformed(null);
+                if (!toggleSeqs)
                 {
-                  hideSelColumns_actionPerformed(null);
-                  if (!toggleSeqs)
-                    viewport.selectionGroup = sg;
+                  viewport.selectionGroup = sg;
                 }
-                else if (!hide)
-                  showAllColumns_actionPerformed(null);
               }
-              break;
+              else if (!hide)
+              {
+                showAllColumns_actionPerformed(null);
+              }
             }
-            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;
+            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 addAlignmentPanel(final AlignmentPanel ap,
                                 boolean newPanel)
   {
@@ -363,9 +385,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
     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);
     }
@@ -383,10 +405,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
       ap.setVisible(false);
     }
 
-    if(newPanel)
+    if (newPanel)
     {
       if (ap.av.padGaps)
+      {
         ap.av.alignment.padGaps();
+      }
       ap.av.updateConservation(ap);
       ap.av.updateConsensus(ap);
     }
@@ -398,11 +422,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     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;
@@ -444,14 +467,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
   public void setGUINucleotide(boolean nucleotide)
   {
-    showTranslation.setVisible( nucleotide );
-    conservationMenuItem.setEnabled( !nucleotide );
-    modifyConservation.setEnabled(   !nucleotide );
+    showTranslation.setVisible(nucleotide);
+    conservationMenuItem.setEnabled(!nucleotide);
+    modifyConservation.setEnabled(!nucleotide);
 
     //Remember AlignFrame always starts as protein
-    if(!nucleotide)
+    if (!nucleotide)
     {
-      calculateMenu.remove(calculateMenu.getItemCount()-2);
+      calculateMenu.remove(calculateMenu.getItemCount() - 2);
     }
   }
 
@@ -487,26 +510,29 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     updateEditMenuBar();
   }
 
-
   Hashtable progressBars;
   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)
-         statusBar.setText(message);
-
-       layout.setRows(layout.getRows() - 1);
-     }
+    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);
+      }
+
+      layout.setRows(layout.getRows() - 1);
+    }
     else
     {
       progressPanel = new JPanel(new BorderLayout(10, 5));
@@ -526,15 +552,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     validate();
   }
 
-
-
-
   /*
    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()
@@ -542,7 +565,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
   }
 
-
   public void fetchSequence_actionPerformed(ActionEvent e)
   {
     new SequenceFetcher(this);
@@ -555,21 +577,24 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
   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))
           {
-            try{
+            try
+            {
               frames[i].setSelected(true);
               Desktop.instance.closeAssociatedWindows();
-            }catch(java.beans.PropertyVetoException ex){}
+            }
+            catch (java.beans.PropertyVetoException ex)
+            {}
           }
 
         }
@@ -592,7 +617,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     }
   }
 
-
   public void addFromText_actionPerformed(ActionEvent e)
   {
     Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
@@ -603,16 +627,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
   }
 
-
   public void save_actionPerformed(ActionEvent e)
   {
-    if(fileName==null
-       || currentFileFormat==null
-       || fileName.startsWith("http")
+    if (fileName == null
+        || currentFileFormat == null
+        || fileName.startsWith("http")
         )
+    {
       saveAs_actionPerformed(null);
+    }
     else
+    {
       saveAlignment(fileName, currentFileFormat);
+    }
   }
 
   /**
@@ -623,15 +650,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
   public void saveAs_actionPerformed(ActionEvent e)
   {
     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
-        getProperty( "LAST_DIRECTORY"),
+        getProperty("LAST_DIRECTORY"),
         new String[]
-        { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc","jar" },
+        {"fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "jar"},
         new String[]
-        { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },
+        {"Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"},
         currentFileFormat,
         false);
 
-
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle("Save Alignment to file");
     chooser.setToolTipText("Save");
@@ -640,18 +666,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
     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);
@@ -679,8 +705,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
       success = new Jalview2XML().SaveAlignment(this, file, shortName);
 
       statusBar.setText("Successfully saved to file: "
-                          +fileName+" in "
-                          +format +" format.");
+                        + fileName + " in "
+                        + format + " format.");
 
     }
     else
@@ -697,7 +723,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
             JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
 
         if (reply == JOptionPane.YES_OPTION)
+        {
           omitHidden = viewport.getViewAsString(false);
+        }
       }
 
       String output = new FormatAdapter().formatSequences(
@@ -732,10 +760,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     }
 
     if (!success)
+    {
       JOptionPane.showInternalMessageDialog(
           this, "Couldn't save file: " + fileName,
           "Error Saving File",
           JOptionPane.WARNING_MESSAGE);
+    }
 
     return success;
   }
@@ -747,17 +777,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
    */
   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);
+          + "\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);
       }
@@ -769,7 +799,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
                              "Alignment output - " + e.getActionCommand(), 600,
                              500);
 
-
     cap.setText(new FormatAdapter().formatSequences(
         e.getActionCommand(),
         viewport.alignment.getSequencesArray(),
@@ -785,7 +814,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
   {
     new HTMLOutput(viewport,
                    alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
-        alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
+                   alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
   }
 
   public void createImageMap(File file, String image)
@@ -813,7 +842,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     alignPanel.makeEPS(f);
   }
 
-
   public void pageSetup_actionPerformed(ActionEvent e)
   {
     PrinterJob printJob = PrinterJob.getPrinterJob();
@@ -837,7 +865,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     new AnnotationExporter().exportFeatures(alignPanel);
   }
 
-
   public void exportAnnotations_actionPerformed(ActionEvent e)
   {
     new AnnotationExporter().exportAnnotations(
@@ -847,7 +874,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
         );
   }
 
-
   public void associatedData_actionPerformed(ActionEvent e)
   {
     // Pick the tree file
@@ -869,7 +895,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
   }
 
-
   /**
    * DOCUMENT ME!
    *
@@ -877,14 +902,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
    */
   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);
@@ -892,6 +920,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
             PaintRefresher.RemoveComponent(ap.idPanel.idCanvas);
             PaintRefresher.RemoveComponent(ap);
           }
+        }
         else
         {
           int index = tabbedPane.getSelectedIndex();
@@ -906,15 +935,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
           tabbedPane.removeTabAt(index);
           tabbedPane.validate();
 
-          if(index==tabbedPane.getTabCount())
-            index --;
+          if (index == tabbedPane.getTabCount())
+          {
+            index--;
+          }
 
           this.tabSelectionChanged(index);
         }
       }
 
       if (closeAllTabs)
+      {
         this.setClosed(true);
+      }
     }
     catch (Exception ex)
     {
@@ -922,7 +955,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     }
   }
 
-
   /**
    * DOCUMENT ME!
    */
@@ -955,10 +987,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     }
   }
 
-
   public void addHistoryItem(CommandI command)
   {
-    if(command.getSize()>0)
+    if (command.getSize() > 0)
     {
       viewport.historyList.push(command);
       viewport.redoList.clear();
@@ -967,8 +998,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     }
   }
 
-
-
   /**
    * DOCUMENT ME!
    *
@@ -976,14 +1005,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
    */
   protected void undoMenuItem_actionPerformed(ActionEvent e)
   {
-    CommandI command = (CommandI)viewport.historyList.pop();
+    CommandI command = (CommandI) viewport.historyList.pop();
     viewport.redoList.push(command);
     command.undoCommand();
 
     AlignViewport originalSource = getOriginatingSource(command);
     updateEditMenuBar();
 
-    if(originalSource!=null)
+    if (originalSource != null)
     {
       originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
       originalSource.firePropertyChange("alignment",
@@ -999,8 +1028,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
    */
   protected void redoMenuItem_actionPerformed(ActionEvent e)
   {
-    if(viewport.redoList.size()<1)
+    if (viewport.redoList.size() < 1)
+    {
       return;
+    }
 
     CommandI command = (CommandI) viewport.redoList.pop();
     viewport.historyList.push(command);
@@ -1009,7 +1040,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     AlignViewport originalSource = getOriginatingSource(command);
     updateEditMenuBar();
 
-    if(originalSource!=null)
+    if (originalSource != null)
     {
       originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
       originalSource.firePropertyChange("alignment",
@@ -1022,9 +1053,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
   {
     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;
+    //the property change event FROM the viewport where the
+    //original alignment was altered
+    AlignmentI al = null;
     if (command instanceof EditCommand)
     {
       EditCommand editCommand = (EditCommand) command;
@@ -1050,7 +1081,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
       //The original view is closed, we must validate
       //the current view against the closed view first
       if (al != null)
+      {
         PaintRefresher.validateSequences(al, viewport.alignment);
+      }
 
       originalSource = viewport;
     }
@@ -1120,8 +1153,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     alignPanel.repaint();
   }
 
-
-
   /**
    * DOCUMENT ME!
    *
@@ -1135,7 +1166,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
       return;
     }
 
-    SequenceI [] seqs = viewport.getSelectionAsNewSequence();
+    SequenceI[] seqs = viewport.getSelectionAsNewSequence();
     String[] omitHidden = null;
 
     if (viewport.hasHiddenColumns)
@@ -1165,42 +1196,44 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     {
       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);
-            }
-          });
+      {
+        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);
+        }
+      });
 
       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);
 
-        hiddenColumns.addElement(new int[]{region[0]-hiddenOffset,
-                          region[1]-hiddenOffset});
+        hiddenColumns.addElement(new int[]
+                                 {region[0] - hiddenOffset,
+                                 region[1] - hiddenOffset});
       }
     }
 
-
-
-    Desktop.jalviewClipboard = new Object[]{ seqs,
+    Desktop.jalviewClipboard = new Object[]
+        {
+        seqs,
         viewport.alignment.getDataset(),
         hiddenColumns};
-    statusBar.setText("Copied "+seqs.length+" sequences to clipboard.");
+    statusBar.setText("Copied " + seqs.length + " sequences to clipboard.");
   }
 
   /**
@@ -1245,7 +1278,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
       {
         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
         if (str.length() < 1)
+        {
           return;
+        }
 
         format = new IdentifyFile().Identify(str, "Paste");
 
@@ -1271,40 +1306,45 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
       SequenceI[] sequences;
 
+      if (Desktop.jalviewClipboard != null)
+      {
+        // The clipboard was filled from within Jalview, we must use the sequences
+        // And dataset from the copied alignment
+        sequences = (SequenceI[]) Desktop.jalviewClipboard[0];
+      }
+      else
+      {
+        sequences = new FormatAdapter().readFile(str, "Paste", format).
+            getSequencesArray();
+      }
 
-     if(Desktop.jalviewClipboard!=null)
-     {
-       // The clipboard was filled from within Jalview, we must use the sequences
-       // And dataset from the copied alignment
-       sequences = (SequenceI[])Desktop.jalviewClipboard[0];
-     }
-     else
-     {
-       sequences = new FormatAdapter().readFile(str, "Paste", format).getSequencesArray();
-     }
-
-     AlignmentI alignment = null;
+      AlignmentI alignment = null;
 
       if (newAlignment)
       {
-          alignment = new Alignment(sequences);
+        alignment = new Alignment(sequences);
 
-          if (Desktop.jalviewClipboard != null)
-            alignment.setDataset( (Alignment) Desktop.jalviewClipboard[1]);
-          else
-            alignment.setDataset(null);
+        if (Desktop.jalviewClipboard != null)
+        {
+          alignment.setDataset( (Alignment) Desktop.jalviewClipboard[1]);
+        }
+        else
+        {
+          alignment.setDataset(null);
+        }
       }
       else
       {
         alignment = viewport.getAlignment();
 
         //!newAlignment
-        SequenceI [] newseqs = new SequenceI[sequences.length];
+        SequenceI[] newseqs = new SequenceI[sequences.length];
         for (int i = 0; i < sequences.length; i++)
         {
           newseqs[i] = new Sequence(sequences[i].getName(),
-              sequences[i].getSequence(), sequences[i].getStart(),
-              sequences[i].getEnd());
+                                    sequences[i].getSequence(),
+                                    sequences[i].getStart(),
+                                    sequences[i].getEnd());
 
           alignment.addSequence(newseqs[i]);
         }
@@ -1321,88 +1361,81 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
             alignment)
             );
 
-
         viewport.setEndSeq(alignment.getHeight());
         alignment.getWidth();
         viewport.firePropertyChange("alignment", null, alignment.getSequences());
       }
 
-
-
       // 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++)
-         {
-           AlignmentAnnotation newAnnot =
-               new AlignmentAnnotation(
-                   sequences[i].getAnnotation()[a].label,
-                   sequences[i].getAnnotation()[a].description,
-                   sequences[i].getAnnotation()[a].annotations,
-                   sequences[i].getAnnotation()[a].graphMin,
-                   sequences[i].getAnnotation()[a].graphMax,
-                   sequences[i].getAnnotation()[a].graph);
-
-           sequences[i].getAnnotation()[a] = newAnnot;
-           newAnnot.sequenceMapping = sequences[i].getAnnotation()[a].
-               sequenceMapping;
-           newAnnot.sequenceRef = sequences[i];
-           newAnnot.adjustForAlignment();
-           alignment.addAnnotation(newAnnot);
-           alignment.setAnnotationIndex(newAnnot, a);
-         }
-
-         alignPanel.annotationPanel.adjustPanelHeight();
-       }
-     }
-
-     if(newAlignment)
-     {
-       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]);
-           }
-         }
+      {
+        if (sequences[i].getAnnotation() != null)
+        {
+          for (int a = 0; a < sequences[i].getAnnotation().length; a++)
+          {
+            AlignmentAnnotation newAnnot =
+                new AlignmentAnnotation(
+                    sequences[i].getAnnotation()[a].label,
+                    sequences[i].getAnnotation()[a].description,
+                    sequences[i].getAnnotation()[a].annotations,
+                    sequences[i].getAnnotation()[a].graphMin,
+                    sequences[i].getAnnotation()[a].graphMax,
+                    sequences[i].getAnnotation()[a].graph);
+
+            sequences[i].getAnnotation()[a] = newAnnot;
+            newAnnot.sequenceMapping = sequences[i].getAnnotation()[a].
+                sequenceMapping;
+            newAnnot.sequenceRef = sequences[i];
+            newAnnot.adjustForAlignment();
+            alignment.addAnnotation(newAnnot);
+            alignment.setAnnotationIndex(newAnnot, a);
+          }
 
+          alignPanel.annotationPanel.adjustPanelHeight();
+        }
+      }
 
-       //>>>This is a fix for the moment, until a better solution is found!!<<<
-       af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(
-           alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
+      if (newAlignment)
+      {
+        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]);
+          }
+        }
 
-       if (title.startsWith("Copied sequences"))
-       {
-         newtitle = title;
-       }
-       else
-       {
-         newtitle = newtitle.concat("- from " + title);
-       }
+        //>>>This is a fix for the moment, until a better solution is found!!<<<
+        af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(
+            alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
 
-       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
-                                DEFAULT_HEIGHT);
+        if (title.startsWith("Copied sequences"))
+        {
+          newtitle = title;
+        }
+        else
+        {
+          newtitle = newtitle.concat("- from " + title);
+        }
 
-     }
+        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
     }
 
-
   }
 
   /**
@@ -1438,36 +1471,34 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
       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);
+    }
 
-   // 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++)
-      cut[i] = (SequenceI)seqs.elementAt(i);
-
+    SequenceI[] cut = new SequenceI[seqs.size()];
+    for (int i = 0; i < seqs.size(); i++)
+    {
+      cut[i] = (SequenceI) seqs.elementAt(i);
+    }
 
     /*
-    //ADD HISTORY ITEM
-    */
+         //ADD HISTORY ITEM
+     */
     addHistoryItem(new EditCommand("Cut Sequences",
-                                      EditCommand.CUT,
-                                      cut,
-                                      sg.getStartRes(),
-                                      sg.getEndRes()-sg.getStartRes()+1,
-                                      viewport.alignment));
-
+                                   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.getAlignment().getSequences());
 
     if (viewport.getAlignment().getHeight() < 1)
     {
@@ -1523,7 +1554,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
    */
   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
-    if(viewport.cursorMode)
+    if (viewport.cursorMode)
     {
       alignPanel.seqPanel.keyboardNo1 = null;
       alignPanel.seqPanel.keyboardNo2 = null;
@@ -1570,7 +1601,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     alignPanel.repaint();
   }
 
-
   /**
    * DOCUMENT ME!
    *
@@ -1588,7 +1618,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
    */
   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
   {
-      trimAlignment(false);
+    trimAlignment(false);
   }
 
   void trimAlignment(boolean trimLeft)
@@ -1598,43 +1628,50 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
     if (colSel.size() > 0)
     {
-      if(trimLeft)
+      if (trimLeft)
+      {
         column = colSel.getMin();
+      }
       else
+      {
         column = colSel.getMax();
+      }
 
-      SequenceI [] seqs;
-      if(viewport.getSelectionGroup()!=null)
-        seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences);
+      SequenceI[] seqs;
+      if (viewport.getSelectionGroup() != null)
+      {
+        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);
+                                           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);
-     }
-
-     statusBar.setText("Removed "+trimRegion.getSize()+" columns.");
+      else
+      {
+        trimRegion = new TrimRegionCommand("Remove Right",
+                                           TrimRegionCommand.TRIM_RIGHT,
+                                           seqs,
+                                           column,
+                                           viewport.alignment,
+                                           viewport.colSel,
+                                           viewport.selectionGroup);
+      }
 
+      statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
 
       addHistoryItem(trimRegion);
 
@@ -1663,18 +1700,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
    */
   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();
     }
     else
+    {
       seqs = viewport.alignment.getSequencesArray();
-
+    }
 
     RemoveGapColCommand removeGapCols =
         new RemoveGapColCommand("Remove Gapped Columns",
@@ -1684,19 +1723,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
     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
     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());
 
   }
 
@@ -1707,17 +1747,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
    */
   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();
     }
     else
+    {
       seqs = viewport.alignment.getSequencesArray();
+    }
 
     //This is to maintain viewport position on first residue
     //of first sequence
@@ -1729,9 +1772,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
                                          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());
 
   }
 
@@ -1765,36 +1809,41 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
         new Jalview2XML().copyAlignPanel(alignPanel, true);
 
     if (viewport.viewName == null)
+    {
       viewport.viewName = "Original";
+    }
 
     newap.av.historyList = viewport.historyList;
     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;
     }
@@ -1803,7 +1852,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
   public void expandViews_actionPerformed(ActionEvent e)
   {
-        Desktop.instance.explodeViews(this);
+    Desktop.instance.explodeViews(this);
   }
 
   public void gatherViews_actionPerformed(ActionEvent e)
@@ -1811,8 +1860,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     Desktop.instance.gatherViews(this);
   }
 
-
-
   /**
    * DOCUMENT ME!
    *
@@ -1823,7 +1870,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     new FontChooser(alignPanel);
   }
 
-
   /**
    * DOCUMENT ME!
    *
@@ -1843,8 +1889,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     alignPanel.repaint();
   }
 
-
-
   /**
    * DOCUMENT ME!
    *
@@ -1965,11 +2009,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     alignPanel.repaint();
   }
 
-
   public FeatureSettings featureSettings;
   public void featureSettings_actionPerformed(ActionEvent e)
   {
-    if(featureSettings !=null )
+    if (featureSettings != null)
     {
       featureSettings.close();
       featureSettings = null;
@@ -2146,7 +2189,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     new AnnotationColourChooser(viewport, alignPanel);
   }
 
-
   /**
    * DOCUMENT ME!
    *
@@ -2166,12 +2208,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
   {
     int threshold = 0;
 
-    if(cs!=null)
+    if (cs != null)
     {
       if (viewport.getAbovePIDThreshold())
       {
         threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
-                                                   "Background");
+            "Background");
 
         cs.setThreshold(threshold,
                         viewport.getIgnoreGapsConsensus());
@@ -2248,30 +2290,34 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
             || 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.getSequences(viewport.
+              hiddenRepSequences),
                                             sg.getStartRes(),
-                                            sg.getEndRes()+1);
+                                            sg.getEndRes() + 1);
           c.calculate();
           c.verdict(false, viewport.ConsPercGaps);
           sg.cs.setConservation(c);
         }
         else
+        {
           sg.cs.setConservation(null);
+        }
       }
     }
 
@@ -2290,7 +2336,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
    */
   protected void modifyPID_actionPerformed(ActionEvent e)
   {
-    if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
+    if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme != null)
     {
       SliderPanel.setPIDSliderSource(alignPanel,
                                      viewport.getGlobalColourScheme(),
@@ -2306,7 +2352,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
    */
   protected void modifyConservation_actionPerformed(ActionEvent e)
   {
-    if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
+    if (viewport.getConservationSelected() && viewport.globalColourScheme != null)
     {
       SliderPanel.setConservationSlider(alignPanel,
                                         viewport.globalColourScheme,
@@ -2390,37 +2436,42 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
       while (userColours.hasMoreElements())
       {
-        final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
+        final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
+            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)
+              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)
               {
-                if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
+                jalview.gui.UserDefinedColours.removeColourFromDefaults(
+                    radioItem.getText());
+                colourMenu.remove(radioItem);
+              }
+              else
+              {
+                radioItem.addActionListener(new ActionListener()
                 {
-                  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)
+                  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)
@@ -2462,10 +2513,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
    */
   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
   {
-    SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
+    SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
     AlignmentSorter.sortByPID(viewport.getAlignment(),
                               viewport.getAlignment().getSequenceAt(0));
-    addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, viewport.alignment));
+    addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
+                                    viewport.alignment));
     alignPanel.repaint();
   }
 
@@ -2476,7 +2528,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
    */
   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.repaint();
@@ -2489,7 +2541,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
    */
   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));
 
@@ -2506,7 +2558,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     new RedundancyPanel(alignPanel, this);
   }
 
-
   /**
    * DOCUMENT ME!
    *
@@ -2551,14 +2602,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
       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,
@@ -2566,7 +2616,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     }
   }
 
-
   /**
    * DOCUMENT ME!
    *
@@ -2618,8 +2667,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
   {
     TreePanel tp;
 
-    if (viewport.getSelectionGroup() != null) {
-      if (viewport.getSelectionGroup().getSize() < 3) {
+    if (viewport.getSelectionGroup() != null)
+    {
+      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",
@@ -2665,16 +2716,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
         return;
       }
 
-      if(viewport.alignment.getHeight()<2)
+      if (viewport.alignment.getHeight() < 2)
+      {
         return;
+      }
 
       tp = new TreePanel(alignPanel, type, pwType);
     }
 
     title += " from ";
 
-    if(viewport.viewName!=null)
-      title+= viewport.viewName+" of ";
+    if (viewport.viewName != null)
+    {
+      title += viewport.viewName + " of ";
+    }
 
     title += this.title;
 
@@ -2695,12 +2750,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     {
       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
         AlignmentSorter.sortBy(viewport.getAlignment(), order);
 
-        addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport.alignment));
+        addHistoryItem(new OrderCommand(order.getName(), oldOrder,
+                                        viewport.alignment));
 
         alignPanel.repaint();
       }
@@ -2720,12 +2776,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
   {
     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));
       }
@@ -2733,7 +2790,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
     iSize = treePanels.size();
 
-    if(iSize<1)
+    if (iSize < 1)
     {
       sortByTreeMenu.setVisible(false);
       return;
@@ -2741,11 +2798,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
     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)
@@ -2780,28 +2837,27 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     {
       // 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)];
+             int sz;
+             msa = new SequenceI[sz = seqs.getSize(false)];
 
-      for (int i = 0; i < sz; i++)
-      {
+             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)
-      {
+             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;
@@ -2815,7 +2871,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
    */
   AlignmentView gatherSeqOrMsaForSecStrPrediction()
   {
-   AlignmentView seqs = null;
+    AlignmentView seqs = null;
 
     if ( (viewport.getSelectionGroup() != null) &&
         (viewport.getSelectionGroup().getSize() > 0))
@@ -2830,10 +2886,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     // 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.setSequences(new SeqCigar[]
+                        {seqs.getSequences()[0]});
     }
     return seqs;
   }
+
   /**
    * DOCUMENT ME!
    *
@@ -2873,18 +2931,23 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     }
   }
 
-
   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)
+
+  public TreePanel ShowNewickTree(NewickFile nf, String title,
+                                  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
    *
@@ -2897,7 +2960,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
    * @param y position
    * @return TreePanel handle
    */
-  public TreePanel ShowNewickTree(NewickFile nf, String title, AlignmentView input, int w,int h,int x, int y) {
+  public TreePanel ShowNewickTree(NewickFile nf, String title,
+                                  AlignmentView input, int w, int h, int x,
+                                  int y)
+  {
     TreePanel tp = null;
 
     try
@@ -2911,11 +2977,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
                            title,
                            nf, input);
 
-        tp.setSize(w,h);
-
-        if(x>0 && y>0)
-          tp.setLocation(x,y);
+        tp.setSize(w, h);
 
+        if (x > 0 && y > 0)
+        {
+          tp.setLocation(x, y);
+        }
 
         Desktop.addInternalFrame(tp, title, w, h);
       }
@@ -2928,7 +2995,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     return tp;
   }
 
-
   /**
    * Generates menu items and listener event actions for web service clients
    *
@@ -2957,7 +3023,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
             {
               AlignmentView msa = gatherSequencesForAlignment();
               new jalview.ws.MsaWSClient(sh, title, msa,
-                  false, true, viewport.getAlignment().getDataset(), af);
+                                         false, true,
+                                         viewport.getAlignment().getDataset(),
+                                         af);
 
             }
 
@@ -2967,14 +3035,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
           if (sh.getName().indexOf("lustal") > -1)
           {
             // We know that ClustalWS can accept partial alignments for refinement.
-            final JMenuItem methodR = new JMenuItem(sh.getName()+" Realign");
+            final JMenuItem methodR = new JMenuItem(sh.getName() + " Realign");
             methodR.addActionListener(new ActionListener()
             {
               public void actionPerformed(ActionEvent e)
               {
                 AlignmentView msa = gatherSequencesForAlignment();
                 new jalview.ws.MsaWSClient(sh, title, msa,
-                    true, true, viewport.getAlignment().getDataset(), af);
+                                           true, true,
+                                           viewport.getAlignment().getDataset(),
+                                           af);
 
               }
 
@@ -3010,7 +3080,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
                 {
                   // Sequence profile based prediction
                   new jalview.ws.JPredClient(sh,
-                      title, true, msa, af, true);
+                                             title, true, msa, af, true);
                 }
               }
             }
@@ -3035,139 +3105,144 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     // TODO: group services by location as well as function.
   }
 
- /* 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);
+  /* public void vamsasStore_actionPerformed(ActionEvent e)
+   {
+     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+         getProperty("LAST_DIRECTORY"));
 
-    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);
-    }
-  }*/
+     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 showTranslation_actionPerformed(ActionEvent e)
-{
-  SequenceI [] selection = viewport.getSelectionAsNewSequence();
-  String [] seqstring = viewport.getViewAsString(true);
-
-  int s, sSize = selection.length;
-  SequenceI [] newSeq = new SequenceI[sSize];
-
-  int res, resSize;
-  StringBuffer protein;
-  String seq;
-  for(s=0; s<sSize; s++)
-  {
-    protein = new StringBuffer();
-    seq = AlignSeq.extractGaps("-. ", seqstring[s]);
-    resSize = seq.length();
-    resSize -= resSize%3;
-
-    for(res = 0; res < resSize; res+=3)
-    {
-      String codon = seq.substring(res, res+3);
-      codon = codon.replace('U', 'T');
-      String aa = ResidueProperties.codonTranslate(codon);
-      if(aa==null)
-        protein.append(viewport.getGapCharacter());
-      else if(aa.equals("STOP"))
-        protein.append("X");
-      else
-        protein.append( aa );
-    }
-    newSeq[s] = new Sequence(selection[s].getName(),
-                             protein.toString());
-  }
 
 
-  AlignmentI al = new Alignment(newSeq);
-  al.setDataset(null);
+  public void showTranslation_actionPerformed(ActionEvent e)
+  {
+    SequenceI[] selection = viewport.getSelectionAsNewSequence();
+    String[] seqstring = viewport.getViewAsString(true);
 
+    int s, sSize = selection.length;
+    SequenceI[] newSeq = new SequenceI[sSize];
 
-  ////////////////////////////////
-  // Copy annotations across
-  jalview.datamodel.AlignmentAnnotation[] annotations
-      = viewport.alignment.getAlignmentAnnotation();
-  int a, aSize;
-  if(annotations!=null)
-  {
-    for (int i = 0; i < annotations.length; i++)
+    int res, resSize;
+    StringBuffer protein;
+    String seq;
+    for (s = 0; s < sSize; s++)
     {
-      if (annotations[i]==viewport.quality ||
-          annotations[i]==viewport.conservation ||
-          annotations[i]==viewport.consensus)
+      protein = new StringBuffer();
+      seq = AlignSeq.extractGaps("-. ", seqstring[s]);
+      resSize = seq.length();
+      resSize -= resSize % 3;
+
+      for (res = 0; res < resSize; res += 3)
       {
-        System.out.println("COPT HERE");
-        continue;
+        String codon = seq.substring(res, res + 3);
+        codon = codon.replace('U', 'T');
+        String aa = ResidueProperties.codonTranslate(codon);
+        if (aa == null)
+        {
+          protein.append(viewport.getGapCharacter());
+        }
+        else if (aa.equals("STOP"))
+        {
+          protein.append("X");
+        }
+        else
+        {
+          protein.append(aa);
+        }
       }
+      newSeq[s] = new Sequence(selection[s].getName(),
+                               protein.toString());
+    }
 
-      aSize = viewport.alignment.getWidth() / 3;
-      jalview.datamodel.Annotation[] anots =
-          new jalview.datamodel.Annotation[aSize];
+    AlignmentI al = new Alignment(newSeq);
+    al.setDataset(null);
 
-      for (a = 0; a < viewport.alignment.getWidth(); a++)
+    ////////////////////////////////
+    // Copy annotations across
+    jalview.datamodel.AlignmentAnnotation[] annotations
+        = viewport.alignment.getAlignmentAnnotation();
+    int a, aSize;
+    if (annotations != null)
+    {
+      for (int i = 0; i < annotations.length; i++)
       {
-        if (annotations[i].annotations[a] == null
-            || annotations[i].annotations[a] == null)
+        if (annotations[i] == viewport.quality ||
+            annotations[i] == viewport.conservation ||
+            annotations[i] == viewport.consensus)
+        {
+          System.out.println("COPT HERE");
           continue;
+        }
 
-        anots[a / 3] = new Annotation(
-            annotations[i].annotations[a].displayCharacter,
-            annotations[i].annotations[a].description,
-            annotations[i].annotations[a].secondaryStructure,
-            annotations[i].annotations[a].value,
-            annotations[i].annotations[a].colour);
-      }
+        aSize = viewport.alignment.getWidth() / 3;
+        jalview.datamodel.Annotation[] anots =
+            new jalview.datamodel.Annotation[aSize];
+
+        for (a = 0; a < viewport.alignment.getWidth(); a++)
+        {
+          if (annotations[i].annotations[a] == null
+              || annotations[i].annotations[a] == null)
+          {
+            continue;
+          }
+
+          anots[a / 3] = new Annotation(
+              annotations[i].annotations[a].displayCharacter,
+              annotations[i].annotations[a].description,
+              annotations[i].annotations[a].secondaryStructure,
+              annotations[i].annotations[a].value,
+              annotations[i].annotations[a].colour);
+        }
 
-      jalview.datamodel.AlignmentAnnotation aa
-          = new jalview.datamodel.AlignmentAnnotation(annotations[i].label,
-          annotations[i].description, anots);
-      al.addAnnotation(aa);
+        jalview.datamodel.AlignmentAnnotation aa
+            = new jalview.datamodel.AlignmentAnnotation(annotations[i].label,
+            annotations[i].description, anots);
+        al.addAnnotation(aa);
+      }
     }
-  }
 
     AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
-    Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),
+    Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
                              DEFAULT_WIDTH,
                              DEFAULT_HEIGHT);
 
+  }
 
-
-
-}
-
-/**
- * DOCUMENT ME!
- *
- * @param String DOCUMENT ME!
- */
-public boolean parseFeaturesFile(String file, String type)
-{
+  /**
+   * DOCUMENT ME!
+   *
+   * @param String DOCUMENT ME!
+   */
+  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);
+    try
+    {
+      featuresFile = new FeaturesFile(file,
+          type).parse(viewport.alignment.getDataset(),
+                      alignPanel.seqPanel.seqCanvas.
+                      getFeatureRenderer().featureColours,
+                      false);
     }
-    catch(Exception ex)
+    catch (Exception ex)
     {
       ex.printStackTrace();
     }
 
-    if(featuresFile)
+    if (featuresFile)
     {
       viewport.showSequenceFeatures = true;
       showSeqFeatures.setSelected(true);
@@ -3175,33 +3250,35 @@ 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");
+      DataFlavor uriListFlavor = new DataFlavor(
+          "text/uri-list;class=java.lang.String");
       if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
       {
         //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))
       {
@@ -3246,15 +3323,16 @@ public void drop(DropTargetDropEvent evt)
         ex.printStackTrace();
       }
     }
-}
+  }
 
   // This method will attempt to load a "dropped" file first by testing
   // whether its and Annotation file, then features file. If both are
   // false then the user may have dropped an alignment file onto this
   // AlignFrame
-   public void loadJalviewDataFile(String file)
+  public void loadJalviewDataFile(String file)
   {
-    try{
+    try
+    {
       String protocol = "File";
 
       if (file.indexOf("http:") > -1 || file.indexOf("file:") > -1)
@@ -3267,12 +3345,12 @@ public void drop(DropTargetDropEvent evt)
 
       if (!isAnnotation)
       {
-        boolean isGroupsFile = parseFeaturesFile(file,protocol);
+        boolean isGroupsFile = parseFeaturesFile(file, protocol);
         if (!isGroupsFile)
         {
           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);
@@ -3283,7 +3361,9 @@ public void drop(DropTargetDropEvent evt)
             alignPanel.repaint();
           }
           else
+          {
             new FileLoader().LoadFile(viewport, file, protocol, format);
+          }
         }
       }
       else
@@ -3292,7 +3372,8 @@ public void drop(DropTargetDropEvent evt)
         alignPanel.adjustAnnotationHeight();
       }
 
-    }catch(Exception ex)
+    }
+    catch (Exception ex)
     {
       ex.printStackTrace();
     }
@@ -3310,7 +3391,7 @@ 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",
@@ -3320,34 +3401,39 @@ public void drop(DropTargetDropEvent evt)
       if (reply != null)
       {
         viewport.viewName = reply;
-        tabbedPane.setTitleAt( tabbedPane.getSelectedIndex() ,reply);
+        tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
       }
     }
   }
 
-
   public AlignViewport getCurrentView()
   {
     return viewport;
   }
 }
 
-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();
 
     if (pf != null)
+    {
       printJob.setPrintable(ap, pf);
+    }
     else
+    {
       printJob.setPrintable(ap);
+    }
 
     if (printJob.printDialog())
     {
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 6c8e0e4..cfffbb9 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -1,6 +1,6 @@
- /*
+/*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,19 +18,15 @@
  */
 package jalview.gui;
 
-import jalview.analysis.*;
+import java.util.*;
 
-import jalview.bin.*;
+import java.awt.*;
 
+import jalview.analysis.*;
+import jalview.bin.*;
 import jalview.datamodel.*;
-
 import jalview.schemes.*;
 
-import java.awt.*;
-
-import java.util.*;
-
-
 /**
  * DOCUMENT ME!
  *
@@ -39,443 +35,258 @@ import java.util.*;
  */
 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
-     */
-    public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns) {
-      setAlignment(al);
-      if (hiddenColumns!=null) {
-        this.colSel = hiddenColumns;
-        if (hiddenColumns.getHiddenColumns() != null)
-          hasHiddenColumns = true;
+  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);
+    if (hiddenColumns != null)
+    {
+      this.colSel = hiddenColumns;
+      if (hiddenColumns.getHiddenColumns() != null)
+      {
+        hasHiddenColumns = true;
       }
-      init();
     }
+    init();
+  }
 
-    void init()
-    {
-        this.startRes = 0;
-        this.endRes = alignment.getWidth() - 1;
-        this.startSeq = 0;
-        this.endSeq = alignment.getHeight() - 1;
-
-      antiAlias = Cache.getDefault("ANTI_ALIAS", false);
-
-      showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);
-      showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
-
-      rightAlignIds = Cache.getDefault("RIGHT_ALIGN_IDS", false);
-
-      autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
-
-      padGaps = Cache.getDefault("PAD_GAPS", true);
+  void init()
+  {
+    this.startRes = 0;
+    this.endRes = alignment.getWidth() - 1;
+    this.startSeq = 0;
+    this.endSeq = alignment.getHeight() - 1;
 
-       String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
-       String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "") ;
-       String fontSize = Cache.getDefault("FONT_SIZE", "10");
+    antiAlias = Cache.getDefault("ANTI_ALIAS", false);
 
-       seqNameItalics = Cache.getDefault("ID_ITALICS", true);
+    showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);
+    showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
 
-       int style = 0;
+    rightAlignIds = Cache.getDefault("RIGHT_ALIGN_IDS", false);
 
-       if (fontStyle.equals("bold"))
-       {
-         style = 1;
-       }
-       else if (fontStyle.equals("italic"))
-       {
-         style = 2;
-       }
+    autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
 
-       setFont(new Font(fontName, style, Integer.parseInt(fontSize)));
+    padGaps = Cache.getDefault("PAD_GAPS", true);
 
-       alignment.setGapCharacter( Cache.getDefault("GAP_SYMBOL", "-").charAt(0) );
+    String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
+    String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "");
+    String fontSize = Cache.getDefault("FONT_SIZE", "10");
 
+    seqNameItalics = Cache.getDefault("ID_ITALICS", true);
 
-        // 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;
+    int style = 0;
 
-
-            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;
-
-              alignment.addAnnotation(quality);
-            }
-          }
-
-          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 (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);
-            }
-        }
-
-        wrapAlignment = jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false);
-    }
-
-
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param b DOCUMENT ME!
-     */
-    public void setShowSequenceFeatures(boolean b)
+    if (fontStyle.equals("bold"))
     {
-        showSequenceFeatures = b;
+      style = 1;
     }
-
-    public boolean getShowSequenceFeatures()
+    else if (fontStyle.equals("italic"))
     {
-      return showSequenceFeatures;
+      style = 2;
     }
 
+    setFont(new Font(fontName, style, Integer.parseInt(fontSize)));
 
+    alignment.setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
 
-    class ConservationThread extends Thread
+    // We must set conservation and consensus before setting colour,
+    // as Blosum and Clustal require this to be done
+    if (hconsensus == null && !isDataset)
     {
-      AlignmentPanel ap;
-      public ConservationThread(AlignmentPanel ap)
+      if (!alignment.isNucleotide())
       {
-        this.ap = ap;
-      }
-
-      public void run()
-      {
-        try
-        {
-          updatingConservation = true;
-
-          while (UPDATING_CONSERVATION)
-          {
-            try
-            {
-              if (ap != null)
-              {
-                ap.repaint();
-              }
-              Thread.sleep(200);
-            }
-            catch (Exception ex)
-            {
-              ex.printStackTrace();
-            }
-          }
-
-          UPDATING_CONSERVATION = true;
-
-
-          int alWidth = alignment.getWidth();
-          if(alWidth<0)
-            return;
-
-          Conservation cons = new jalview.analysis.Conservation("All",
-              jalview.schemes.ResidueProperties.propHash, 3,
-              alignment.getSequences(), 0, alWidth -1);
-
-          cons.calculate();
-          cons.verdict(false, ConsPercGaps);
-
-          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();
-          }
+        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;
 
-          for (int i = 0; i < alWidth; i++)
-          {
-            float value = 0;
-
-            c = sequence[i];
-
-            if (Character.isDigit(c))
-              value = (int) (c - '0');
-            else if (c == '*')
-              value = 11;
-            else if (c == '+')
-              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)));
-            }
-          }
-        }
-        catch (OutOfMemoryError error)
+        if (Cache.getDefault("SHOW_CONSERVATION", true))
         {
-          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;
-
-          System.out.println("Conservation calculation: " + error);
-          System.gc();
-
+          alignment.addAnnotation(conservation);
         }
 
-        UPDATING_CONSERVATION = false;
-        updatingConservation = false;
-
-        if(ap!=null)
+        if (Cache.getDefault("SHOW_QUALITY", true))
         {
-          ap.repaint();
+          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);
         }
-
       }
-    }
 
+      consensus = new AlignmentAnnotation("Consensus", "PID",
+                                          new Annotation[1], 0f, 100f,
+                                          AlignmentAnnotation.BAR_GRAPH);
+      consensus.hasText = true;
+      consensus.autoCalculated = true;
 
-    ConservationThread conservationThread;
-
-    ConsensusThread consensusThread;
-
-    boolean consUpdateNeeded = false;
+      if (Cache.getDefault("SHOW_IDENTITY", true))
+      {
+        alignment.addAnnotation(consensus);
+      }
+    }
 
-    static boolean UPDATING_CONSENSUS = false;
+    if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
+    {
+      globalColourScheme = ColourSchemeProperty.getColour(alignment,
+          jalview.bin.Cache.getProperty("DEFAULT_COLOUR"));
 
-    static boolean UPDATING_CONSERVATION = false;
+      if (globalColourScheme instanceof UserColourScheme)
+      {
+        globalColourScheme = UserDefinedColours.loadDefaultColours();
+        ( (UserColourScheme) globalColourScheme).setThreshold(0,
+            getIgnoreGapsConsensus());
+      }
 
-    boolean updatingConsensus = false;
+      if (globalColourScheme != null)
+      {
+        globalColourScheme.setConsensus(hconsensus);
+      }
+    }
 
-    boolean updatingConservation = false;
+    wrapAlignment = jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false);
+  }
 
-    /**
-     * DOCUMENT ME!
-     */
-    public void updateConservation(final AlignmentPanel ap)
-    {
-      if (alignment.isNucleotide() || conservation==null)
-        return;
+  /**
+   * DOCUMENT ME!
+   *
+   * @param b DOCUMENT ME!
+   */
+  public void setShowSequenceFeatures(boolean b)
+  {
+    showSequenceFeatures = b;
+  }
 
-      conservationThread = new ConservationThread(ap);
-      conservationThread.start();
-    }
+  public boolean getShowSequenceFeatures()
+  {
+    return showSequenceFeatures;
+  }
 
-    /**
-     * DOCUMENT ME!
-     */
-    public void updateConsensus(final AlignmentPanel ap)
+  class ConservationThread
+      extends Thread
+  {
+    AlignmentPanel ap;
+    public ConservationThread(AlignmentPanel ap)
     {
-      consensusThread = new ConsensusThread(ap);
-      consensusThread.start();
+      this.ap = ap;
     }
 
-
-    class ConsensusThread extends Thread
+    public void run()
     {
-      AlignmentPanel ap;
-      public ConsensusThread(AlignmentPanel ap)
+      try
       {
-        this.ap = ap;
-      }
-      public void run()
-      {
-        updatingConsensus = true;
-        while (UPDATING_CONSENSUS)
+        updatingConservation = true;
+
+        while (UPDATING_CONSERVATION)
         {
           try
           {
@@ -483,7 +294,6 @@ public class AlignViewport
             {
               ap.repaint();
             }
-
             Thread.sleep(200);
           }
           catch (Exception ex)
@@ -492,1182 +302,1458 @@ public class AlignViewport
           }
         }
 
+        UPDATING_CONSERVATION = true;
 
-        UPDATING_CONSENSUS = true;
-
-        try
+        int alWidth = alignment.getWidth();
+        if (alWidth < 0)
         {
-          int aWidth = alignment.getWidth();
-          if(aWidth<0)
-            return;
+          return;
+        }
 
-          consensus.annotations = null;
-          consensus.annotations = new Annotation[aWidth];
+        Conservation cons = new jalview.analysis.Conservation("All",
+            jalview.schemes.ResidueProperties.propHash, 3,
+            alignment.getSequences(), 0, alWidth - 1);
 
+        cons.calculate();
+        cons.verdict(false, ConsPercGaps);
 
-          hconsensus = new Hashtable[aWidth];
-          AAFrequency.calculate(alignment.getSequencesArray(),
-                                0,
-                                alignment.getWidth(),
-                                hconsensus);
+        if (quality != null)
+        {
+          cons.findQuality();
+        }
 
-          for (int i = 0; i < aWidth; i++)
-          {
-            float value = 0;
-            if (ignoreGapsInConsensusCalculation)
-              value = ( (Float) hconsensus[i].get(AAFrequency.PID_NOGAPS)).
-                  floatValue();
-            else
-              value = ( (Float) hconsensus[i].get(AAFrequency.PID_GAPS)).
-                  floatValue();
-
-            String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE).toString();
-            String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE) + " ";
-
-            if (maxRes.length() > 1)
-            {
-              mouseOver = "[" + maxRes + "] ";
-              maxRes = "+";
-            }
+        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();
+        }
 
-            mouseOver += ( (int) value + "%");
-            consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);
-          }
+        for (int i = 0; i < alWidth; i++)
+        {
+          float value = 0;
 
+          c = sequence[i];
 
-          if (globalColourScheme != null)
-            globalColourScheme.setConsensus(hconsensus);
+          if (Character.isDigit(c))
+          {
+            value = (int) (c - '0');
+          }
+          else if (c == '*')
+          {
+            value = 11;
+          }
+          else if (c == '+')
+          {
+            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)));
+          }
         }
-        catch (OutOfMemoryError error)
+      }
+      catch (OutOfMemoryError error)
+      {
+        javax.swing.SwingUtilities.invokeLater(new Runnable()
         {
-          alignment.deleteAnnotation(consensus);
 
-          consensus = null;
-          hconsensus = null;
-          javax.swing.SwingUtilities.invokeLater(new Runnable()
+          public void run()
           {
-            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);
-            }
-          });
+            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);
+          }
+        });
 
-          System.out.println("Consensus calculation: " + error);
-          System.gc();
-        }
-        UPDATING_CONSENSUS = false;
-        updatingConsensus = false;
+        conservation = null;
+        quality = null;
+
+        System.out.println("Conservation calculation: " + error);
+        System.gc();
 
-        if (ap != null)
-        {
-          ap.repaint();
-        }
-      }
-    }
-    /**
-     * 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)
-        updateConsensus(null);
-      if (consensus==null)
-        return null;
-      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) == '[')
-            seqs.append(consensus.annotations[i].description.charAt(1));
-          else
-            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;
-    }
+      UPDATING_CONSERVATION = false;
+      updatingConservation = false;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param sg DOCUMENT ME!
-     */
-    public void setSelectionGroup(SequenceGroup sg)
-    {
-        selectionGroup = sg;
-    }
+      if (ap != null)
+      {
+        ap.repaint();
+      }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getConservationSelected()
-    {
-        return conservationColourSelected;
     }
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param b DOCUMENT ME!
-     */
-    public void setConservationSelected(boolean b)
-    {
-        conservationColourSelected = b;
-    }
+  ConservationThread conservationThread;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getAbovePIDThreshold()
-    {
-        return abovePIDThreshold;
-    }
+  ConsensusThread consensusThread;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param b DOCUMENT ME!
-     */
-    public void setAbovePIDThreshold(boolean b)
-    {
-        abovePIDThreshold = b;
-    }
+  boolean consUpdateNeeded = false;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getStartRes()
-    {
-        return startRes;
-    }
+  static boolean UPDATING_CONSENSUS = false;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getEndRes()
-    {
-        return endRes;
-    }
+  static boolean UPDATING_CONSERVATION = false;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getStartSeq()
-    {
-        return startSeq;
-    }
+  boolean updatingConsensus = false;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param cs DOCUMENT ME!
-     */
-    public void setGlobalColourScheme(ColourSchemeI cs)
-    {
-        globalColourScheme = cs;
-    }
+  boolean updatingConservation = false;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public ColourSchemeI getGlobalColourScheme()
+  /**
+   * DOCUMENT ME!
+   */
+  public void updateConservation(final AlignmentPanel ap)
+  {
+    if (alignment.isNucleotide() || conservation == null)
     {
-        return globalColourScheme;
+      return;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param res DOCUMENT ME!
-     */
-    public void setStartRes(int res)
-    {
-        this.startRes = res;
-    }
+    conservationThread = new ConservationThread(ap);
+    conservationThread.start();
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void updateConsensus(final AlignmentPanel ap)
+  {
+    consensusThread = new ConsensusThread(ap);
+    consensusThread.start();
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param seq DOCUMENT ME!
-     */
-    public void setStartSeq(int seq)
+  class ConsensusThread
+      extends Thread
+  {
+    AlignmentPanel ap;
+    public ConsensusThread(AlignmentPanel ap)
     {
-        this.startSeq = seq;
+      this.ap = ap;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param res DOCUMENT ME!
-     */
-    public void setEndRes(int res)
+    public void run()
     {
-        if (res > (alignment.getWidth() - 1))
+      updatingConsensus = true;
+      while (UPDATING_CONSENSUS)
+      {
+        try
         {
-            // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));
-            res = alignment.getWidth() - 1;
-        }
+          if (ap != null)
+          {
+            ap.repaint();
+          }
 
-        if (res < 0)
-        {
-            res = 0;
+          Thread.sleep(200);
         }
-
-        this.endRes = res;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param seq DOCUMENT ME!
-     */
-    public void setEndSeq(int seq)
-    {
-        if (seq > alignment.getHeight())
+        catch (Exception ex)
         {
-            seq = alignment.getHeight();
+          ex.printStackTrace();
         }
+      }
+
+      UPDATING_CONSENSUS = true;
 
-        if (seq < 0)
+      try
+      {
+        int aWidth = alignment.getWidth();
+        if (aWidth < 0)
         {
-            seq = 0;
+          return;
         }
 
-        this.endSeq = seq;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getEndSeq()
-    {
-        return endSeq;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param f DOCUMENT ME!
-     */
-    public void setFont(Font f)
-    {
-        font = f;
-
-        Container c = new Container();
-
-        java.awt.FontMetrics fm = c.getFontMetrics(font);
-        setCharHeight(fm.getHeight());
-        setCharWidth(fm.charWidth('M'));
-        validCharWidth = true;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Font getFont()
-    {
-        return font;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param w DOCUMENT ME!
-     */
-    public void setCharWidth(int w)
-    {
-        this.charWidth = w;
-    }
+        consensus.annotations = null;
+        consensus.annotations = new Annotation[aWidth];
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getCharWidth()
-    {
-        return charWidth;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param h DOCUMENT ME!
-     */
-    public void setCharHeight(int h)
-    {
-        this.charHeight = h;
-    }
+        hconsensus = new Hashtable[aWidth];
+        AAFrequency.calculate(alignment.getSequencesArray(),
+                              0,
+                              alignment.getWidth(),
+                              hconsensus);
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getCharHeight()
-    {
-        return charHeight;
-    }
+        for (int i = 0; i < aWidth; i++)
+        {
+          float value = 0;
+          if (ignoreGapsInConsensusCalculation)
+          {
+            value = ( (Float) hconsensus[i].get(AAFrequency.PID_NOGAPS)).
+                floatValue();
+          }
+          else
+          {
+            value = ( (Float) hconsensus[i].get(AAFrequency.PID_GAPS)).
+                floatValue();
+          }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param w DOCUMENT ME!
-     */
-    public void setWrappedWidth(int w)
-    {
-        this.wrappedWidth = w;
-    }
+          String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE).toString();
+          String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE) + " ";
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getWrappedWidth()
-    {
-        return wrappedWidth;
-    }
+          if (maxRes.length() > 1)
+          {
+            mouseOver = "[" + maxRes + "] ";
+            maxRes = "+";
+          }
 
+          mouseOver += ( (int) value + "%");
+          consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ',
+              value);
+        }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public AlignmentI getAlignment()
-    {
-        return alignment;
-    }
+        if (globalColourScheme != null)
+        {
+          globalColourScheme.setConsensus(hconsensus);
+        }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param align DOCUMENT ME!
-     */
-    public void setAlignment(AlignmentI align)
-    {
-        this.alignment = align;
-    }
+      }
+      catch (OutOfMemoryError error)
+      {
+        alignment.deleteAnnotation(consensus);
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param state DOCUMENT ME!
-     */
-    public void setWrapAlignment(boolean state)
-    {
-        wrapAlignment = state;
-    }
+        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);
+          }
+        });
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param state DOCUMENT ME!
-     */
-    public void setShowText(boolean state)
-    {
-        showText = state;
-    }
+        System.out.println("Consensus calculation: " + error);
+        System.gc();
+      }
+      UPDATING_CONSENSUS = false;
+      updatingConsensus = false;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param state DOCUMENT ME!
-     */
-    public void setRenderGaps(boolean state)
-    {
-        renderGaps = state;
+      if (ap != null)
+      {
+        ap.repaint();
+      }
     }
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getColourText()
+  /**
+   * 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)
     {
-        return showColourText;
+      updateConsensus(null);
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param state DOCUMENT ME!
-     */
-    public void setColourText(boolean state)
+    if (consensus == null)
     {
-        showColourText = state;
+      return null;
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param state DOCUMENT ME!
-     */
-    public void setShowBoxes(boolean state)
+    StringBuffer seqs = new StringBuffer();
+    for (int i = 0; i < consensus.annotations.length; i++)
     {
-        showBoxes = state;
+      if (consensus.annotations[i] != null)
+      {
+        if (consensus.annotations[i].description.charAt(0) == '[')
+        {
+          seqs.append(consensus.annotations[i].description.charAt(1));
+        }
+        else
+        {
+          seqs.append(consensus.annotations[i].displayCharacter);
+        }
+      }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getWrapAlignment()
-    {
-        return wrapAlignment;
-    }
+    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;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public boolean getConservationSelected()
+  {
+    return conservationColourSelected;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param b DOCUMENT ME!
+   */
+  public void setConservationSelected(boolean b)
+  {
+    conservationColourSelected = b;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public boolean getAbovePIDThreshold()
+  {
+    return abovePIDThreshold;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param b DOCUMENT ME!
+   */
+  public void setAbovePIDThreshold(boolean b)
+  {
+    abovePIDThreshold = b;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public int getStartRes()
+  {
+    return startRes;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public int getEndRes()
+  {
+    return endRes;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public int getStartSeq()
+  {
+    return startSeq;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param cs DOCUMENT ME!
+   */
+  public void setGlobalColourScheme(ColourSchemeI cs)
+  {
+    globalColourScheme = cs;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public ColourSchemeI getGlobalColourScheme()
+  {
+    return globalColourScheme;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param res DOCUMENT ME!
+   */
+  public void setStartRes(int res)
+  {
+    this.startRes = res;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param seq DOCUMENT ME!
+   */
+  public void setStartSeq(int seq)
+  {
+    this.startSeq = seq;
+  }
+
+  /**
+   * 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;
+    }
+
+    if (res < 0)
+    {
+      res = 0;
+    }
+
+    this.endRes = res;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param seq DOCUMENT ME!
+   */
+  public void setEndSeq(int seq)
+  {
+    if (seq > alignment.getHeight())
+    {
+      seq = alignment.getHeight();
+    }
+
+    if (seq < 0)
+    {
+      seq = 0;
+    }
+
+    this.endSeq = seq;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public int getEndSeq()
+  {
+    return endSeq;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param f DOCUMENT ME!
+   */
+  public void setFont(Font f)
+  {
+    font = f;
+
+    Container c = new Container();
+
+    java.awt.FontMetrics fm = c.getFontMetrics(font);
+    setCharHeight(fm.getHeight());
+    setCharWidth(fm.charWidth('M'));
+    validCharWidth = true;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Font getFont()
+  {
+    return font;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param w DOCUMENT ME!
+   */
+  public void setCharWidth(int w)
+  {
+    this.charWidth = w;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public int getCharWidth()
+  {
+    return charWidth;
+  }
+
+  /**
+   * 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!
+   *
+   * @param w DOCUMENT ME!
+   */
+  public void setWrappedWidth(int w)
+  {
+    this.wrappedWidth = w;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public int getWrappedWidth()
+  {
+    return wrappedWidth;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public AlignmentI getAlignment()
+  {
+    return alignment;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param align DOCUMENT ME!
+   */
+  public void setAlignment(AlignmentI align)
+  {
+    this.alignment = align;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param state DOCUMENT ME!
+   */
+  public void setWrapAlignment(boolean state)
+  {
+    wrapAlignment = state;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param state DOCUMENT ME!
+   */
+  public void setShowText(boolean state)
+  {
+    showText = state;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param state DOCUMENT ME!
+   */
+  public void setRenderGaps(boolean state)
+  {
+    renderGaps = state;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public boolean getColourText()
+  {
+    return showColourText;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param state DOCUMENT ME!
+   */
+  public void setColourText(boolean state)
+  {
+    showColourText = state;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param state DOCUMENT ME!
+   */
+  public void setShowBoxes(boolean state)
+  {
+    showBoxes = state;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public boolean getWrapAlignment()
+  {
+    return wrapAlignment;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public boolean getShowText()
+  {
+    return showText;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public boolean getShowBoxes()
+  {
+    return showBoxes;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public char getGapCharacter()
+  {
+    return getAlignment().getGapCharacter();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param gap DOCUMENT ME!
+   */
+  public void setGapCharacter(char gap)
+  {
+    if (getAlignment() != null)
+    {
+      getAlignment().setGapCharacter(gap);
+    }
+  }
+
+  /**
+   * 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!
+   *
+   * @param inc DOCUMENT ME!
+   */
+  public void setIncrement(int inc)
+  {
+    increment = inc;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public int getIncrement()
+  {
+    return increment;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public ColumnSelection getColumnSelection()
+  {
+    return colSel;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param tree DOCUMENT ME!
+   */
+  public void setCurrentTree(NJTree tree)
+  {
+    currentTree = tree;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public NJTree getCurrentTree()
+  {
+    return currentTree;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param b DOCUMENT ME!
+   */
+  public void setColourAppliesToAllGroups(boolean b)
+  {
+    colourAppliesToAllGroups = b;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public boolean getColourAppliesToAllGroups()
+  {
+    return colourAppliesToAllGroups;
+  }
+
+  /**
+   * 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!
+   *
+   * @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 getScaleLeftWrapped()
+  {
+    return scaleLeftWrapped;
+  }
+
+  /**
+   * 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 setScaleLeftWrapped(boolean b)
+  {
+    scaleLeftWrapped = 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);
+  }
+
+  /**
+   * 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);
+  }
+
+  public void setIgnoreGapsConsensus(boolean b, AlignmentPanel ap)
+  {
+    ignoreGapsInConsensusCalculation = b;
+    updateConsensus(ap);
+    if (globalColourScheme != null)
+    {
+      globalColourScheme.setThreshold(globalColourScheme.getThreshold(),
+                                      ignoreGapsInConsensusCalculation);
+    }
+  }
+
+  public boolean getIgnoreGapsConsensus()
+  {
+    return ignoreGapsInConsensusCalculation;
+  }
+
+  public void setDataset(boolean b)
+  {
+    isDataset = b;
+  }
+
+  public boolean isDataset()
+  {
+    return isDataset;
+  }
+
+  public void hideSelectedColumns()
+  {
+    if (colSel.size() < 1)
+    {
+      return;
+    }
+
+    colSel.hideSelectedColumns();
+    setSelectionGroup(null);
+
+    hasHiddenColumns = true;
+  }
+
+  public void hideColumns(int start, int end)
+  {
+    if (start == end)
+    {
+      colSel.hideColumns(start);
+    }
+    else
+    {
+      colSel.hideColumns(start, end);
+    }
+
+    hasHiddenColumns = true;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getShowText()
+  public void hideRepSequences(SequenceI repSequence, SequenceGroup sg)
+  {
+    int sSize = sg.getSize();
+    if (sSize < 2)
     {
-        return showText;
+      return;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getShowBoxes()
+    if (hiddenRepSequences == null)
     {
-        return showBoxes;
+      hiddenRepSequences = new Hashtable();
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public char getGapCharacter()
-    {
-        return getAlignment().getGapCharacter();
-    }
+    hiddenRepSequences.put(repSequence, sg);
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param gap DOCUMENT ME!
-     */
-    public void setGapCharacter(char gap)
+    //Hide all sequences except the repSequence
+    SequenceI[] seqs = new SequenceI[sSize - 1];
+    int index = 0;
+    for (int i = 0; i < sSize; i++)
     {
-        if (getAlignment() != null)
+      if (sg.getSequenceAt(i) != repSequence)
+      {
+        if (index == sSize - 1)
         {
-            getAlignment().setGapCharacter(gap);
+          return;
         }
-    }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param thresh DOCUMENT ME!
-     */
-    public void setThreshold(int thresh)
-    {
-        threshold = thresh;
+        seqs[index++] = sg.getSequenceAt(i);
+      }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getThreshold()
-    {
-        return threshold;
-    }
+    hideSequence(seqs);
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param inc DOCUMENT ME!
-     */
-    public void setIncrement(int inc)
-    {
-        increment = inc;
-    }
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getIncrement()
+  public void hideAllSelectedSeqs()
+  {
+    if (selectionGroup == null)
     {
-        return increment;
+      return;
     }
 
+    SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public ColumnSelection getColumnSelection()
-    {
-        return colSel;
-    }
+    hideSequence(seqs);
 
+    setSelectionGroup(null);
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param tree DOCUMENT ME!
-     */
-    public void setCurrentTree(NJTree tree)
-    {
-        currentTree = tree;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public NJTree getCurrentTree()
+  public void hideSequence(SequenceI[] seq)
+  {
+    if (seq != null)
     {
-        return currentTree;
+      for (int i = 0; i < seq.length; i++)
+      {
+        alignment.getHiddenSequences().hideSequence(seq[i]);
+      }
+      hasHiddenRows = true;
+      firePropertyChange("alignment", null, alignment.getSequences());
     }
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param b DOCUMENT ME!
-     */
-    public void setColourAppliesToAllGroups(boolean b)
+  public void showSequence(int index)
+  {
+    Vector tmp = alignment.getHiddenSequences().showSequence(index
+        , hiddenRepSequences);
+    if (tmp.size() > 0)
     {
-        colourAppliesToAllGroups = b;
-    }
+      if (selectionGroup == null)
+      {
+        selectionGroup = new SequenceGroup();
+        selectionGroup.setEndRes(alignment.getWidth() - 1);
+      }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getColourAppliesToAllGroups()
-    {
-        return colourAppliesToAllGroups;
+      for (int t = 0; t < tmp.size(); t++)
+      {
+        selectionGroup.addSequence(
+            (SequenceI) tmp.elementAt(t), false
+            );
+      }
+      firePropertyChange("alignment", null, alignment.getSequences());
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getShowJVSuffix()
+    if (alignment.getHiddenSequences().getSize() < 1)
     {
-        return showJVSuffix;
+      hasHiddenRows = false;
     }
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param b DOCUMENT ME!
-     */
-    public void setShowJVSuffix(boolean b)
+  public void showColumn(int col)
+  {
+    colSel.revealHiddenColumns(col);
+    if (colSel.getHiddenColumns() == null)
     {
-        showJVSuffix = b;
+      hasHiddenColumns = false;
     }
+  }
 
+  public void showAllHiddenColumns()
+  {
+    colSel.revealAllHiddenColumns();
+    hasHiddenColumns = false;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getShowAnnotation()
-    {
-        return showAnnotation;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param b DOCUMENT ME!
-     */
-    public void setShowAnnotation(boolean b)
+  public void showAllHiddenSeqs()
+  {
+    if (alignment.getHiddenSequences().getSize() > 0)
     {
-        showAnnotation = b;
+      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;
     }
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getScaleAboveWrapped()
+  public void invertColumnSelection()
+  {
+    for (int i = 0; i < alignment.getWidth(); i++)
     {
-        return scaleAboveWrapped;
+      if (colSel.contains(i))
+      {
+        colSel.removeElement(i);
+      }
+      else
+      {
+        if (!hasHiddenColumns || colSel.isVisible(i))
+        {
+          colSel.addElement(i);
+        }
+      }
     }
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getScaleLeftWrapped()
-    {
-        return scaleLeftWrapped;
-    }
+  public int adjustForHiddenSeqs(int alignmentIndex)
+  {
+    return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex);
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getScaleRightWrapped()
-    {
-        return scaleRightWrapped;
-    }
+  /**
+   * This method returns the a new SequenceI [] with
+   * the selection sequence and start and end points adjusted
+   * @return String[]
+   */
+  public SequenceI[] getSelectionAsNewSequence()
+  {
+    SequenceI[] sequences;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param b DOCUMENT ME!
-     */
-    public void setScaleAboveWrapped(boolean b)
+    if (selectionGroup == null)
     {
-        scaleAboveWrapped = b;
+      sequences = alignment.getSequencesArray();
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param b DOCUMENT ME!
-     */
-    public void setScaleLeftWrapped(boolean b)
+    else
     {
-        scaleLeftWrapped = b;
+      sequences = selectionGroup.getSelectionAsNewSequences(alignment);
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param b DOCUMENT ME!
-     */
-    public void setScaleRightWrapped(boolean b)
-    {
-        scaleRightWrapped = b;
-    }
+    return sequences;
+  }
 
-    /**
-     * Property change listener for changes in alignment
-     *
-     * @param listener DOCUMENT ME!
-     */
-    public void addPropertyChangeListener(
-        java.beans.PropertyChangeListener listener)
+  /**
+   * 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)
     {
-        changeSupport.addPropertyChangeListener(listener);
+      iSize = selectionGroup.getSize();
+      seqs = selectionGroup.getSequencesInOrder(alignment);
+      start = selectionGroup.getStartRes();
+      end = selectionGroup.getEndRes(); // inclusive for start and end in SeqCigar constructor
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param listener DOCUMENT ME!
-     */
-    public void removePropertyChangeListener(
-        java.beans.PropertyChangeListener listener)
+    else
     {
-        changeSupport.removePropertyChangeListener(listener);
+      iSize = alignment.getHeight();
+      seqs = alignment.getSequencesArray();
+      end = alignment.getWidth() - 1;
     }
-
-    /**
-     * 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)
+    SeqCigar[] selseqs = new SeqCigar[iSize];
+    for (i = 0; i < iSize; i++)
     {
-        changeSupport.firePropertyChange(prop, oldvalue, newvalue);
+      selseqs[i] = new SeqCigar(seqs[i], start, end);
     }
-
-    public void setIgnoreGapsConsensus(boolean b, AlignmentPanel ap)
+    selection = new CigarArray(selseqs);
+    // now construct the CigarArray operations
+    if (hasHiddenColumns)
     {
-      ignoreGapsInConsensusCalculation = b;
-      updateConsensus(ap);
-      if(globalColourScheme!=null)
+      Vector regions = colSel.getHiddenColumns();
+      int[] region;
+      int hideStart, hideEnd;
+      int last = start;
+      for (int j = 0; last < end & j < regions.size(); j++)
       {
-        globalColourScheme.setThreshold(globalColourScheme.getThreshold(), ignoreGapsInConsensusCalculation);
-      }
-    }
-
-    public boolean getIgnoreGapsConsensus()
-    {
-     return ignoreGapsInConsensusCalculation;
-    }
-
-    public void setDataset(boolean b)
-    {
-      isDataset = b;
-    }
-
-    public boolean isDataset()
-    {
-      return isDataset;
-    }
-
-
-    public void hideSelectedColumns()
-    {
-      if (colSel.size() < 1)
-        return;
-
-      colSel.hideSelectedColumns();
-      setSelectionGroup(null);
-
-      hasHiddenColumns = true;
-    }
-
-
-    public void hideColumns(int start, int end)
-    {
-      if(start==end)
-        colSel.hideColumns(start);
-      else
-        colSel.hideColumns(start, end);
-
-      hasHiddenColumns = true;
-    }
-
-    public void hideRepSequences(SequenceI repSequence, SequenceGroup sg)
-    {
-      int sSize = sg.getSize();
-      if(sSize < 2)
-        return;
-
-      if(hiddenRepSequences==null)
-        hiddenRepSequences = new Hashtable();
-
-       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++)
-        if(sg.getSequenceAt(i)!=repSequence)
+        region = (int[]) regions.elementAt(j);
+        hideStart = region[0];
+        hideEnd = region[1];
+        // edit hidden regions to selection range
+        if (hideStart < last)
         {
-          if(index==sSize-1)
-            return;
-
-          seqs[index++] = sg.getSequenceAt(i);
+          if (hideEnd > last)
+          {
+            hideStart = last;
+          }
+          else
+          {
+            continue;
+          }
         }
 
-      hideSequence(seqs);
-
-    }
-
-    public void hideAllSelectedSeqs()
-    {
-      if (selectionGroup == null)
-        return;
-
-      SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
-
-      hideSequence(seqs);
-
-      setSelectionGroup(null);
-    }
-
-    public void hideSequence(SequenceI [] seq)
-    {
-      if(seq!=null)
-      {
-        for (int i = 0; i < seq.length; i++)
+        if (hideStart > end)
         {
-          alignment.getHiddenSequences().hideSequence(seq[i]);
+          break;
         }
-        hasHiddenRows = true;
-        firePropertyChange("alignment", null, alignment.getSequences());
-      }
-    }
 
-    public void showSequence(int index)
-    {
-      Vector tmp = alignment.getHiddenSequences().showSequence(index
-          , hiddenRepSequences);
-      if(tmp.size()>0)
-      {
-        if(selectionGroup==null)
+        if (hideEnd > end)
         {
-          selectionGroup = new SequenceGroup();
-          selectionGroup.setEndRes(alignment.getWidth()-1);
+          hideEnd = end;
         }
 
-        for (int t = 0; t < tmp.size(); t++)
+        if (hideStart > hideEnd)
+        {
+          break;
+        }
+        /**
+         * form operations...
+         */
+        if (last < hideStart)
         {
-          selectionGroup.addSequence(
-              (SequenceI) tmp.elementAt(t), false
-              );
+          selection.addOperation(CigarArray.M, hideStart - last);
         }
-        firePropertyChange("alignment", null, alignment.getSequences());
+        selection.addOperation(CigarArray.D, 1 + hideEnd - hideStart);
+        last = hideEnd + 1;
+      }
+      // Final match if necessary.
+      if (last < end)
+      {
+        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
+   */
+  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);
+    if (aligview != null)
+    {
+      return new AlignmentView(aligview,
+                               (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.
+   * @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();
+    }
+
+    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);
       }
 
-      if(alignment.getHiddenSequences().getSize()<1)
-        hasHiddenRows = false;
     }
+    return selection;
+  }
+
+  public boolean getShowHiddenMarkers()
+  {
+    return showHiddenMarkers;
+  }
 
-    public void showColumn(int col)
+  public void setShowHiddenMarkers(boolean show)
+  {
+    showHiddenMarkers = show;
+  }
+
+  public String getSequenceSetId()
+  {
+    if (sequenceSetID == null)
     {
-      colSel.revealHiddenColumns(col);
-      if(colSel.getHiddenColumns()==null)
-        hasHiddenColumns = false;
+      sequenceSetID = alignment.hashCode() + "";
     }
 
-    public void showAllHiddenColumns()
+    return sequenceSetID;
+  }
+
+  public void alignmentChanged(AlignmentPanel ap)
+  {
+    if (padGaps)
     {
-      colSel.revealAllHiddenColumns();
-      hasHiddenColumns = false;
+      alignment.padGaps();
     }
 
-    public void showAllHiddenSeqs()
+    if (hconsensus != null && autoCalculateConsensus)
     {
-      if(alignment.getHiddenSequences().getSize()>0)
-      {
-        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;
-      }
+      updateConsensus(ap);
+      updateConservation(ap);
     }
 
-
-
-    public void invertColumnSelection()
+    //Reset endRes of groups if beyond alignment width
+    int alWidth = alignment.getWidth();
+    Vector groups = alignment.getGroups();
+    if (groups != null)
     {
-      for(int i=0; i<alignment.getWidth(); i++)
+      for (int i = 0; i < groups.size(); i++)
       {
-        if(colSel.contains(i))
-          colSel.removeElement(i);
-        else
+        SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
+        if (sg.getEndRes() > alWidth)
         {
-          if (!hasHiddenColumns || colSel.isVisible(i))
-          {
-            colSel.addElement(i);
-          }
+          sg.setEndRes(alWidth - 1);
         }
       }
     }
 
-    public int adjustForHiddenSeqs(int alignmentIndex)
+    if (selectionGroup != null && selectionGroup.getEndRes() > alWidth)
     {
-      return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex);
+      selectionGroup.setEndRes(alWidth - 1);
     }
 
-    /**
-     * This method returns the a new SequenceI [] with
-     * the selection sequence and start and end points adjusted
-     * @return String[]
-     */
-    public SequenceI[] getSelectionAsNewSequence()
-    {
-      SequenceI[] sequences;
+    resetAllColourSchemes();
 
-      if (selectionGroup == null)
-        sequences = alignment.getSequencesArray();
-      else
-        sequences = selectionGroup.getSelectionAsNewSequences(alignment);
+    // alignment.adjustSequenceAnnotations();
+  }
 
-      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)
+  void resetAllColourSchemes()
+  {
+    ColourSchemeI cs = globalColourScheme;
+    if (cs != null)
     {
-      CigarArray selection=null;
-      SequenceI [] seqs= null;
-      int i, iSize;
-      int start = 0, end = 0;
-      if(selectedRegionOnly && selectionGroup!=null)
+      if (cs instanceof ClustalxColourScheme)
       {
-        iSize = selectionGroup.getSize();
-        seqs = selectionGroup.getSequencesInOrder(alignment);
-        start = selectionGroup.getStartRes();
-        end = selectionGroup.getEndRes(); // inclusive for start and end in SeqCigar constructor
+        ( (ClustalxColourScheme) cs).
+            resetClustalX(alignment.getSequences(),
+                          alignment.getWidth());
       }
-      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
-      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
-          if(hideStart<last) {
-            if (hideEnd > last)
-            {
-              hideStart = last;
-            } else
-              continue;
-          }
 
-          if (hideStart>end)
-            break;
-
-          if (hideEnd>end)
-            hideEnd=end;
-
-          if (hideStart>hideEnd)
-            break;
-          /**
-           * form operations...
-           */
-          if (last<hideStart)
-            selection.addOperation(CigarArray.M, hideStart-last);
-          selection.addOperation(CigarArray.D, 1+hideEnd-hideStart);
-          last = hideEnd+1;
-        }
-        // Final match if necessary.
-        if (last<end)
-          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
-     */
-    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);
-      if (aligview!=null) {
-        return new AlignmentView(aligview,
-            (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.
-     * @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
+      cs.setConsensus(hconsensus);
+      if (cs.conservationApplied())
       {
-        iSize = alignment.getHeight();
-        seqs = alignment.getSequencesArray();
-        end = alignment.getWidth();
+        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);
       }
-
-      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;
     }
 
-    public boolean getShowHiddenMarkers()
+    int s, sSize = alignment.getGroups().size();
+    for (s = 0; s < sSize; s++)
     {
-      return showHiddenMarkers;
+      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();
     }
+  }
 
-    public void setShowHiddenMarkers(boolean show)
+  public Color getSequenceColour(SequenceI seq)
+  {
+    if (sequenceColours == null || !sequenceColours.containsKey(seq))
     {
-      showHiddenMarkers = show;
+      return Color.white;
     }
-
-    public String getSequenceSetId()
+    else
     {
-      if(sequenceSetID==null)
-        sequenceSetID =  alignment.hashCode()+"";
-
-      return sequenceSetID;
-    }
-
-    public void alignmentChanged(AlignmentPanel ap)
-    {
-        if (padGaps)
-          alignment.padGaps();
-
-        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)
-              sg.setEndRes(alWidth-1);
-          }
-        }
-
-        if(selectionGroup!=null && selectionGroup.getEndRes()>alWidth)
-          selectionGroup.setEndRes(alWidth-1);
-
-        resetAllColourSchemes();
-
-       // alignment.adjustSequenceAnnotations();
+      return (Color) sequenceColours.get(seq);
     }
+  }
 
-
-    void resetAllColourSchemes()
+  public void setSequenceColour(SequenceI seq, Color col)
+  {
+    if (sequenceColours == null)
     {
-      ColourSchemeI cs = globalColourScheme;
-      if(cs!=null)
-      {
-        if (cs instanceof ClustalxColourScheme)
-        {
-          ( (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);
-        }
-      }
-
-      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)
-        {
-          ((ClustalxColourScheme)sg.cs).resetClustalX(
-              sg.getSequences(hiddenRepSequences), sg.getWidth());
-        }
-        sg.recalcConservation();
-      }
+      sequenceColours = new Hashtable();
     }
 
-
-    public Color getSequenceColour(SequenceI seq)
+    if (col == null)
     {
-      if(sequenceColours==null || !sequenceColours.containsKey(seq))
-        return Color.white;
-      else
-        return (Color)sequenceColours.get(seq);
+      sequenceColours.remove(seq);
     }
-
-    public void setSequenceColour(SequenceI seq, Color col)
+    else
     {
-      if(sequenceColours==null)
-        sequenceColours = new Hashtable();
-
-      if(col == null)
-        sequenceColours.remove(seq);
-      else
-        sequenceColours.put(seq, col);
+      sequenceColours.put(seq, col);
     }
-
+  }
 
 }
diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index d912b29..62ee200 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,20 +18,17 @@
  */
 package jalview.gui;
 
-import jalview.datamodel.*;
-
-import jalview.jbgui.*;
-
-import jalview.schemes.*;
+import java.beans.*;
+import java.io.*;
 
 import java.awt.*;
 import java.awt.event.*;
 import java.awt.print.*;
-import java.io.*;
 import javax.swing.*;
-import java.beans.*;
-
 
+import jalview.datamodel.*;
+import jalview.jbgui.*;
+import jalview.schemes.*;
 
 /**
  * DOCUMENT ME!
@@ -39,8 +36,8 @@ import java.beans.*;
  * @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;
@@ -87,7 +84,7 @@ public class AlignmentPanel extends GAlignmentPanel
     fontChanged();
 
     scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
-   seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
+    seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
 
     setScrollValues(0, 0);
 
@@ -110,7 +107,7 @@ public class AlignmentPanel extends GAlignmentPanel
           alignmentChanged();
         }
       }
-      });
+    });
 
     adjustAnnotationHeight();
 
@@ -121,15 +118,15 @@ public class AlignmentPanel extends GAlignmentPanel
     av.alignmentChanged(this);
 
     if (overviewPanel != null)
+    {
       overviewPanel.updateOverviewImage();
+    }
 
     alignFrame.updateEditMenuBar();
 
     repaint();
   }
 
-
-
   /**
    * DOCUMENT ME!
    */
@@ -154,7 +151,9 @@ public class AlignmentPanel extends GAlignmentPanel
     hscrollFillerPanel.setPreferredSize(d);
 
     if (overviewPanel != null)
+    {
       overviewPanel.setBoxPosition();
+    }
 
     repaint();
   }
@@ -169,7 +168,7 @@ public class AlignmentPanel extends GAlignmentPanel
     Container c = new Container();
 
     FontMetrics fm = c.getFontMetrics(
-      new Font(av.font.getName(), Font.ITALIC, av.font.getSize()));
+        new Font(av.font.getName(), Font.ITALIC, av.font.getSize()));
 
     AlignmentI al = av.getAlignment();
 
@@ -231,10 +230,10 @@ public class AlignmentPanel extends GAlignmentPanel
       int start = seq.findIndex(results.getResultStart(0)) - 1;
       int end = seq.findIndex(results.getResultEnd(0)) - 1;
 
-      if(!av.wrapAlignment)
+      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);
         }
@@ -248,8 +247,9 @@ public class AlignmentPanel extends GAlignmentPanel
 
   void scrollToWrappedVisible(int res)
   {
-    int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
-    if( res<=av.getStartRes() || res>=(av.getStartRes()+cwidth) )
+    int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.
+        getWidth());
+    if (res <= av.getStartRes() || res >= (av.getStartRes() + cwidth))
     {
       vscroll.setValue(res / cwidth);
       av.startRes = vscroll.getValue() * cwidth;
@@ -420,10 +420,12 @@ public class AlignmentPanel extends GAlignmentPanel
     int width = av.alignment.getWidth();
     int height = av.alignment.getHeight();
 
-    if(av.hasHiddenColumns)
-     width = av.getColumnSelection().findColumnPosition(width);
+    if (av.hasHiddenColumns)
+    {
+      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;
@@ -487,7 +489,7 @@ public class AlignmentPanel extends GAlignmentPanel
 
       if (av.getWrapAlignment())
       {
-        if(offy>-1)
+        if (offy > -1)
         {
           int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.
               seqCanvas.getWidth());
@@ -500,12 +502,12 @@ public class AlignmentPanel extends GAlignmentPanel
           //was wrapped when saved and user has wrap alignment true
           //as preference setting
           SwingUtilities.invokeLater(new Runnable()
-              {
-                public void run()
-                {
-                  setScrollValues(av.getStartRes(), av.getStartSeq());
-                }
-              });
+          {
+            public void run()
+            {
+              setScrollValues(av.getStartRes(), av.getStartSeq());
+            }
+          });
         }
       }
       else
@@ -532,12 +534,16 @@ public class AlignmentPanel extends GAlignmentPanel
     {
       // Make sure we're not trying to draw a panel
       // larger than the visible window
-      if(scrollX>av.endRes-av.startRes)
-        scrollX = av.endRes-av.startRes;
-      else if(scrollX<av.startRes-av.endRes)
+      if (scrollX > av.endRes - av.startRes)
+      {
+        scrollX = av.endRes - av.startRes;
+      }
+      else if (scrollX < av.startRes - av.endRes)
+      {
         scrollX = av.startRes - av.endRes;
+      }
 
-      if(scrollX!=0 || scrollY!=0)
+      if (scrollX != 0 || scrollY != 0)
       {
         idPanel.idCanvas.fastPaint(scrollY);
         seqPanel.seqCanvas.fastPaint(scrollX,
@@ -571,10 +577,13 @@ public class AlignmentPanel extends GAlignmentPanel
       int maxwidth = av.alignment.getWidth();
 
       if (av.hasHiddenColumns)
+      {
         maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+      }
 
-      int canvasWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
-            if(canvasWidth>0)
+      int canvasWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.
+          seqCanvas.getWidth());
+      if (canvasWidth > 0)
       {
         int max = maxwidth /
             seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.
@@ -590,9 +599,11 @@ public class AlignmentPanel extends GAlignmentPanel
       setScrollValues(av.getStartRes(), av.getStartSeq());
     }
 
-    if( this.getVisibleRect().getBounds() == g.getClipBounds()
+    if (this.getVisibleRect().getBounds() == g.getClipBounds()
         && overviewPanel != null)
-        overviewPanel.updateOverviewImage();
+    {
+      overviewPanel.updateOverviewImage();
+    }
   }
 
   /**
@@ -744,7 +755,7 @@ public class AlignmentPanel extends GAlignmentPanel
             ) - 4;
       }
 
-      pg.drawString(seq.getDisplayId( av.getShowJVSuffix()),
+      pg.drawString(seq.getDisplayId(av.getShowJVSuffix()),
                     xPos,
                     ( ( (i - startSeq) * av.charHeight) + av.getCharHeight()) -
                     (av.getCharHeight() / 5));
@@ -758,9 +769,9 @@ public class AlignmentPanel extends GAlignmentPanel
 
     if (av.showAnnotation && (endSeq == av.alignment.getHeight()))
     {
-      pg.translate( -idWidth-3, (endSeq - startSeq) * av.charHeight + 3);
+      pg.translate( -idWidth - 3, (endSeq - startSeq) * av.charHeight + 3);
       alabels.drawComponent( (Graphics2D) pg, idWidth);
-      pg.translate(idWidth+3, 0);
+      pg.translate(idWidth + 3, 0);
       annotationPanel.drawComponent( (Graphics2D) pg, startRes, endRes +
                                     1);
     }
@@ -795,7 +806,9 @@ public class AlignmentPanel extends GAlignmentPanel
 
     int hgap = av.charHeight;
     if (av.scaleAboveWrapped)
+    {
       hgap += av.charHeight;
+    }
 
     int cHeight = av.getAlignment().getHeight() * av.charHeight
         + hgap
@@ -805,8 +818,9 @@ public class AlignmentPanel extends GAlignmentPanel
 
     int maxwidth = av.alignment.getWidth();
     if (av.hasHiddenColumns)
+    {
       maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
-
+    }
 
     int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth -
         idWidth);
@@ -827,20 +841,18 @@ public class AlignmentPanel extends GAlignmentPanel
 
     int ypos = hgap;
 
-
-
     do
     {
       for (int i = 0; i < av.alignment.getHeight(); i++)
       {
         pg.setFont(idPanel.idCanvas.idfont);
         SequenceI s = av.alignment.getSequenceAt(i);
-        String string = s.getDisplayId( av.getShowJVSuffix());
+        String string = s.getDisplayId(av.getShowJVSuffix());
         int xPos = 0;
         if (av.rightAlignIds)
         {
           FontMetrics fm = pg.getFontMetrics();
-          xPos = idWidth - fm.stringWidth( string ) - 4;
+          xPos = idWidth - fm.stringWidth(string) - 4;
         }
         pg.drawString(string, xPos,
                       ( (i * av.charHeight) + ypos + av.charHeight) -
@@ -848,13 +860,13 @@ public class AlignmentPanel extends GAlignmentPanel
       }
       if (labels != null)
       {
-        pg.translate(-3,
+        pg.translate( -3,
                      ypos +
                      (av.getAlignment().getHeight() * av.charHeight));
 
         pg.setFont(av.getFont());
         labels.drawComponent(pg, idWidth);
-        pg.translate(+3,
+        pg.translate( +3,
                      -ypos -
                      (av.getAlignment().getHeight() * av.charHeight));
       }
@@ -889,7 +901,9 @@ public class AlignmentPanel extends GAlignmentPanel
   {
     int maxwidth = av.alignment.getWidth();
     if (av.hasHiddenColumns)
+    {
       maxwidth = av.getColumnSelection().findColumnPosition(maxwidth);
+    }
 
     int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;
     int width = getVisibleIdWidth() + (maxwidth * av.charWidth);
@@ -906,7 +920,9 @@ public class AlignmentPanel extends GAlignmentPanel
             - alignFrame.getInsets().right;
       }
       else
+      {
         width = seqPanel.getWidth() + getVisibleIdWidth();
+      }
 
     }
     else if (av.getShowAnnotation())
@@ -917,21 +933,26 @@ public class AlignmentPanel extends GAlignmentPanel
     try
     {
 
-    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);
-    else
-      im = new jalview.util.ImageMaker(this,
-                                        jalview.util.ImageMaker.EPS,
-                                       "Create EPS file from alignment",
-                                        width, height, file, alignFrame.getTitle() );
+      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);
+      }
+      else
+      {
+        im = new jalview.util.ImageMaker(this,
+                                         jalview.util.ImageMaker.EPS,
+                                         "Create EPS file from alignment",
+                                         width, height, file,
+                                         alignFrame.getTitle());
+      }
 
       if (av.getWrapAlignment())
       {
-        if(im.getGraphics()!=null)
+        if (im.getGraphics() != null)
         {
           printWrappedAlignment(im.getGraphics(), width, height, 0);
           im.writeImage();
@@ -939,7 +960,7 @@ public class AlignmentPanel extends GAlignmentPanel
       }
       else
       {
-        if(im.getGraphics()!=null)
+        if (im.getGraphics() != null)
         {
           printUnwrapped(im.getGraphics(), width, height, 0);
           im.writeImage();
@@ -967,6 +988,7 @@ public class AlignmentPanel extends GAlignmentPanel
       ex.printStackTrace();
     }
   }
+
   /**
    * DOCUMENT ME!
    */
@@ -1011,92 +1033,107 @@ public class AlignmentPanel extends GAlignmentPanel
           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++)
+          for (res = 0; res < alwidth; res++)
           {
             text = new StringBuffer();
             Object obj = null;
-            if(av.alignment.isNucleotide())
-              obj = ResidueProperties.nucleotideName.get(seq.getCharAt(res)+"" );
+            if (av.alignment.isNucleotide())
+            {
+              obj = ResidueProperties.nucleotideName.get(seq.getCharAt(res) +
+                  "");
+            }
             else
+            {
               obj = ResidueProperties.aa2Triplet.get(
-                    seq.getCharAt(res) + "");
+                  seq.getCharAt(res) + "");
+            }
 
-              if (obj == null)
-                  continue;
+            if (obj == null)
+            {
+              continue;
+            }
 
             String triplet = obj.toString();
             int alIndex = seq.findPosition(res);
             gSize = groups.length;
             for (g = 0; g < gSize; g++)
             {
-              if(text.length()<1)
+              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>");
+              }
             }
 
             if (features != null)
             {
-              if(text.length()<1)
+              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++)
-                {
+              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))
+                    {
+                      text.append("<br>disulfide bond " + features[f].getBegin() +
+                                  ":" +
+                                  features[f].getEnd());
+                    }
+                  }
+                  else
                   {
-                    if (features[f].getType().equals("disulfide bond"))
+                    text.append("<br>");
+                    text.append(features[f].getType());
+                    if (features[f].getDescription() != null &&
+                        !features[f].
+                        getType().equals(features[f].getDescription()))
                     {
-                      if (features[f].getBegin() == seq.findPosition(res)
-                          || features[f].getEnd() == seq.findPosition(res))
-                      {
-                        text.append("<br>disulfide bond " + features[f].getBegin() + ":" +
-                                       features[f].getEnd());
-                      }
+                      text.append(" " + features[f].getDescription());
                     }
-                    else
+
+                    if (features[f].getValue("status") != null)
                     {
-                      text.append("<br>");
-                      text.append(features[f].getType());
-                      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") + ")");
                     }
                   }
-
                 }
-              }
-              if(text.length()>1)
-              {
-                text.append("')\"; onMouseOut=\"toolTip()\";  href=\"#\">");
-                out.println(text.toString());
+
               }
             }
+            if (text.length() > 1)
+            {
+              text.append("')\"; onMouseOut=\"toolTip()\";  href=\"#\">");
+              out.println(text.toString());
+            }
           }
+        }
         out.println("</map></body></html>");
         out.close();
 
@@ -1125,11 +1162,13 @@ public class AlignmentPanel extends GAlignmentPanel
 
     int chunkWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(
         seqPanelWidth
-          );
+        );
 
     int hgap = av.charHeight;
     if (av.scaleAboveWrapped)
+    {
       hgap += av.charHeight;
+    }
 
     int annotationHeight = 0;
     if (av.showAnnotation)
@@ -1143,8 +1182,9 @@ public class AlignmentPanel extends GAlignmentPanel
 
     int maxwidth = av.alignment.getWidth();
     if (av.hasHiddenColumns)
+    {
       maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
-
+    }
 
     int height = ( (maxwidth / chunkWidth) + 1) * cHeight;
 
diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java
index b748c85..ba76858 100755
--- a/src/jalview/gui/AnnotationColourChooser.java
+++ b/src/jalview/gui/AnnotationColourChooser.java
@@ -1,33 +1,32 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 jalview.gui;
 
-import javax.swing.*;
-import java.awt.event.*;
+import java.util.*;
+
 import java.awt.*;
+import java.awt.event.*;
+import javax.swing.*;
+import javax.swing.event.*;
 
+import jalview.datamodel.*;
 import jalview.schemes.*;
-import javax.swing.event.*;
-import java.util.*;
-import jalview.datamodel.SequenceGroup;
-import java.awt.Dimension;
-import javax.swing.BorderFactory;
 
 public class AnnotationColourChooser
     extends JPanel
@@ -51,8 +50,10 @@ public class AnnotationColourChooser
       for (int g = 0; g < allGroups.size(); g++)
       {
         sg = (SequenceGroup) allGroups.get(g);
-        if(sg.cs!=null)
+        if (sg.cs != null)
+        {
           oldgroupColours.put(sg, sg.cs);
+        }
       }
     }
     this.av = av;
@@ -73,7 +74,7 @@ public class AnnotationColourChooser
     {
       public void stateChanged(ChangeEvent evt)
       {
-        if(!adjusting)
+        if (!adjusting)
         {
           thresholdValue.setText( ( (float) slider.getValue() / 1000f) + "");
           valueChanged();
@@ -82,7 +83,9 @@ public class AnnotationColourChooser
     });
 
     if (av.alignment.getAlignmentAnnotation() == null)
+    {
       return;
+    }
 
     if (oldcs instanceof AnnotationColourGradient)
     {
@@ -100,7 +103,9 @@ public class AnnotationColourChooser
     for (int i = 0; i < av.alignment.getAlignmentAnnotation().length; i++)
     {
       if (av.alignment.getAlignmentAnnotation()[i].graph > 0)
+      {
         annotations.addItem(av.alignment.getAlignmentAnnotation()[i].label);
+      }
     }
 
     threshold.addItem("No Threshold");
@@ -137,7 +142,9 @@ public class AnnotationColourChooser
       public void mousePressed(MouseEvent e)
       {
         if (minColour.isEnabled())
+        {
           minColour_actionPerformed();
+        }
       }
     });
     maxColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
@@ -149,7 +156,9 @@ public class AnnotationColourChooser
       public void mousePressed(MouseEvent e)
       {
         if (maxColour.isEnabled())
+        {
           maxColour_actionPerformed();
+        }
       }
     });
     ok.setOpaque(false);
@@ -251,7 +260,9 @@ public class AnnotationColourChooser
                                          "Select Colour for Minimum Value",
                                          minColour.getBackground());
     if (col != null)
+    {
       minColour.setBackground(col);
+    }
     minColour.repaint();
     changeColour();
   }
@@ -262,7 +273,9 @@ public class AnnotationColourChooser
                                          "Select Colour for Maximum Value",
                                          maxColour.getBackground());
     if (col != null)
+    {
       maxColour.setBackground(col);
+    }
     maxColour.repaint();
     changeColour();
   }
@@ -271,7 +284,9 @@ public class AnnotationColourChooser
   {
     // Check if combobox is still adjusting
     if (adjusting)
+    {
       return;
+    }
 
     // We removed the non-graph annotations when filling the combobox
     // so allow for them again here
@@ -279,21 +294,31 @@ public class AnnotationColourChooser
     for (int i = 0; i < av.alignment.getAlignmentAnnotation().length; i++)
     {
       if (av.alignment.getAlignmentAnnotation()[i].graph == 0)
+      {
         nograph++;
+      }
       else
+      {
         graph++;
+      }
 
       if (graph == annotations.getSelectedIndex())
+      {
         break;
+      }
     }
 
     currentAnnotation = av.alignment.getAlignmentAnnotation()[graph + nograph];
 
     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);
@@ -314,7 +339,7 @@ public class AnnotationColourChooser
                                       Color.black));
     }
 
-    if(aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
+    if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
     {
       adjusting = true;
       float range = currentAnnotation.graphMax * 1000 -
@@ -332,16 +357,20 @@ public class AnnotationColourChooser
 
     AnnotationColourGradient acg = null;
     if (currentColours.isSelected())
+    {
       acg = new AnnotationColourGradient(
           currentAnnotation,
           av.getGlobalColourScheme(), aboveThreshold);
+    }
     else
+    {
       acg =
           new AnnotationColourGradient(
               currentAnnotation,
               minColour.getBackground(),
               maxColour.getBackground(),
               aboveThreshold);
+    }
 
     av.setGlobalColourScheme(acg);
 
@@ -359,15 +388,19 @@ public class AnnotationColourChooser
         }
 
         if (currentColours.isSelected())
+        {
           sg.cs = new AnnotationColourGradient(
               currentAnnotation,
               sg.cs, aboveThreshold);
+        }
         else
+        {
           sg.cs = new AnnotationColourGradient(
               currentAnnotation,
               minColour.getBackground(),
               maxColour.getBackground(),
               aboveThreshold);
+        }
 
       }
     }
@@ -397,7 +430,6 @@ public class AnnotationColourChooser
     {}
   }
 
-
   void reset()
   {
     av.setGlobalColourScheme(oldcs);
@@ -408,7 +440,7 @@ public class AnnotationColourChooser
       for (int g = 0; g < allGroups.size(); g++)
       {
         sg = (SequenceGroup) allGroups.get(g);
-        sg.cs = (ColourSchemeI)oldgroupColours.get(sg);
+        sg.cs = (ColourSchemeI) oldgroupColours.get(sg);
       }
     }
   }
@@ -442,18 +474,18 @@ public class AnnotationColourChooser
   public void valueChanged()
   {
     if (currentColours.isSelected()
-        && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
+        && ! (av.getGlobalColourScheme() instanceof AnnotationColourGradient))
     {
       changeColour();
     }
 
-    currentAnnotation.threshold.value = (float)slider.getValue()/1000f;
+    currentAnnotation.threshold.value = (float) slider.getValue() / 1000f;
     ap.repaint();
   }
 
   public void currentColours_actionPerformed(ActionEvent e)
   {
-    if(currentColours.isSelected())
+    if (currentColours.isSelected())
     {
       reset();
     }
diff --git a/src/jalview/gui/AnnotationExporter.java b/src/jalview/gui/AnnotationExporter.java
index 522622d..676611c 100755
--- a/src/jalview/gui/AnnotationExporter.java
+++ b/src/jalview/gui/AnnotationExporter.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -19,18 +19,14 @@
 
 package jalview.gui;
 
+import java.util.*;
+
+import java.awt.*;
+import java.awt.event.*;
 import javax.swing.*;
-import java.awt.event.ActionListener;
-import java.awt.event.ActionEvent;
 
+import jalview.datamodel.*;
 import jalview.io.*;
-import jalview.datamodel.AlignmentAnnotation;
-
-import java.awt.Color;
-import java.awt.FlowLayout;
-import java.util.Vector;
-import javax.swing.BorderFactory;
-
 
 public class AnnotationExporter
     extends JPanel
@@ -38,7 +34,7 @@ public class AnnotationExporter
   JInternalFrame frame;
   AlignmentPanel ap;
   boolean features = true;
-  AlignmentAnnotation [] annotations;
+  AlignmentAnnotation[] annotations;
   Vector sequenceGroups;
 
   public AnnotationExporter()
@@ -68,7 +64,7 @@ public class AnnotationExporter
   }
 
   public void exportAnnotations(AlignmentPanel ap,
-                                AlignmentAnnotation [] annotations,
+                                AlignmentAnnotation[] annotations,
                                 Vector sequenceGroups)
   {
     this.ap = ap;
@@ -81,95 +77,102 @@ 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.setToolTipText("Save");
+    chooser.setFileView(new JalviewFileView());
+    chooser.setDialogTitle(
+        features ? "Save Features to File" : "Save Annotation to File");
+    chooser.setToolTipText("Save");
 
-      int value = chooser.showSaveDialog(this);
+    int value = chooser.showSaveDialog(this);
 
-      if (value == JalviewFileChooser.APPROVE_OPTION)
+    if (value == JalviewFileChooser.APPROVE_OPTION)
+    {
+      String text = "No features found on alignment";
+      if (features)
       {
-        String text = "No features found on alignment";
-        if (features)
+        if (GFFFormat.isSelected())
         {
-          if (GFFFormat.isSelected())
-            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().printGFFFormat(
+              ap.av.alignment.getDataset().getSequencesArray(),
+              ap.av.featuresDisplayed);
         }
         else
         {
-           text = new AnnotationFile().printAnnotations(
-              annotations,
-              sequenceGroups );
+          text = new FeaturesFile().printJalviewFormat(
+              ap.av.alignment.getDataset().getSequencesArray(),
+              ap.av.featuresDisplayed);
         }
+      }
+      else
+      {
+        text = new AnnotationFile().printAnnotations(
+            annotations,
+            sequenceGroups);
+      }
 
-        try
-        {
-          java.io.PrintWriter out = new java.io.PrintWriter(
-              new java.io.FileWriter(chooser.getSelectedFile()));
+      try
+      {
+        java.io.PrintWriter out = new java.io.PrintWriter(
+            new java.io.FileWriter(chooser.getSelectedFile()));
 
-          out.print(text);
-          out.close();
-        }
-        catch (Exception ex)
-        {
-          ex.printStackTrace();
-        }
+        out.print(text);
+        out.close();
+      }
+      catch (Exception ex)
+      {
+        ex.printStackTrace();
       }
+    }
   }
 
   public void toTextbox_actionPerformed(ActionEvent e)
   {
     String text = "No features found on alignment";
-    if(features)
+    if (features)
     {
       if (GFFFormat.isSelected())
+      {
         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);
+            ap.av.featuresDisplayed);
+      }
     }
-    else if(!features)
+    else if (!features)
     {
       text = new AnnotationFile().printAnnotations(
           annotations,
-          sequenceGroups );
+          sequenceGroups);
     }
 
-
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
     cap.setText(text);
     Desktop.addInternalFrame(cap,
-                             (features ?  "Features for - " : "Annotations for - ")
+                             (features ? "Features for - " :
+                              "Annotations for - ")
                              + ap.alignFrame.getTitle(),
                              600,
                              500);
 
-
   }
 
   public void close_actionPerformed(ActionEvent e)
   {
-    try{
+    try
+    {
       frame.setClosed(true);
-    }catch(java.beans.PropertyVetoException ex)
+    }
+    catch (java.beans.PropertyVetoException ex)
     {}
   }
 
-
-
   private void jbInit()
       throws Exception
   {
diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 783c905..3f8478a 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,17 +18,16 @@
  */
 package jalview.gui;
 
-import jalview.datamodel.*;
-import jalview.io.FormatAdapter;
+import java.util.*;
 
 import java.awt.*;
-import java.awt.datatransfer.StringSelection;
+import java.awt.datatransfer.*;
 import java.awt.event.*;
 import java.awt.image.*;
-import java.util.Vector;
-
 import javax.swing.*;
 
+import jalview.datamodel.*;
+import jalview.io.*;
 
 /**
  * DOCUMENT ME!
@@ -36,608 +35,648 @@ import javax.swing.*;
  * @author $author$
  * @version $Revision$
  */
-public class AnnotationLabels extends JPanel implements MouseListener,
+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!
-     */
-    public AnnotationLabels(AlignmentPanel ap)
-    {
-        this.ap = ap;
-        av = ap.av;
-        ToolTipManager.sharedInstance().registerComponent(this);
-
-        java.net.URL url = getClass().getResource("/images/idwidth.gif");
-        Image temp = null;
-
-        if (url != null)
-        {
-            temp = java.awt.Toolkit.getDefaultToolkit().createImage(url);
-        }
-
-        try
-        {
-            MediaTracker mt = new MediaTracker(this);
-            mt.addImage(temp, 0);
-            mt.waitForID(0);
-        }
-        catch (Exception ex)
-        {
-        }
-
-        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);
-        image = (Image) bi;
-
-        addMouseListener(this);
-        addMouseMotionListener(this);
+  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!
+   */
+  public AnnotationLabels(AlignmentPanel ap)
+  {
+    this.ap = ap;
+    av = ap.av;
+    ToolTipManager.sharedInstance().registerComponent(this);
+
+    java.net.URL url = getClass().getResource("/images/idwidth.gif");
+    Image temp = null;
+
+    if (url != null)
+    {
+      temp = java.awt.Toolkit.getDefaultToolkit().createImage(url);
     }
 
-    public AnnotationLabels(AlignViewport av)
+    try
     {
-      this.av = av;
+      MediaTracker mt = new MediaTracker(this);
+      mt.addImage(temp, 0);
+      mt.waitForID(0);
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param y DOCUMENT ME!
-     */
-    public void setScrollOffset(int y)
+    catch (Exception ex)
     {
-        scrollOffset = y;
-        repaint();
     }
 
-    void getSelectedRow(int y)
+    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);
+    image = (Image) bi;
+
+    addMouseListener(this);
+    addMouseMotionListener(this);
+  }
+
+  public AnnotationLabels(AlignViewport av)
+  {
+    this.av = av;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param y DOCUMENT ME!
+   */
+  public void setScrollOffset(int y)
+  {
+    scrollOffset = y;
+    repaint();
+  }
+
+  void getSelectedRow(int y)
+  {
+    int height = 0;
+    AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+
+    if (aa != null)
     {
-      int height = 0;
-      AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
-
-      if(aa!=null)
+      for (int i = 0; i < aa.length; i++)
       {
-        for (int i = 0; i < aa.length; i++)
+        if (!aa[i].visible)
         {
-          if (!aa[i].visible)
-          {
-            continue;
-          }
+          continue;
+        }
 
-          height += aa[i].height;
+        height += aa[i].height;
 
-          if (y < height)
-          {
-            selectedRow = i;
+        if (y < height)
+        {
+          selectedRow = i;
 
-            break;
-          }
+          break;
         }
       }
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void actionPerformed(ActionEvent evt)
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void actionPerformed(ActionEvent evt)
+  {
+    int dif = 0;
+    AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+
+    if (evt.getActionCommand().equals(ADDNEW))
     {
-        int dif = 0;
-        AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
-
-        if (evt.getActionCommand().equals(ADDNEW))
-        {
-            AlignmentAnnotation newAnnotation = new AlignmentAnnotation(null,
-                    null,
-                    new Annotation[ap.av.alignment.getWidth()]);
-
-            if(!editLabelDescription(newAnnotation))
-              return;
-
-            ap.av.alignment.addAnnotation(newAnnotation);
-            ap.av.alignment.setAnnotationIndex(newAnnotation, 0);
-            if (aa != null)
-              dif = aa[aa.length - 1].height;
-        }
-        else if(evt.getActionCommand().equals(EDITNAME))
-        {
-          editLabelDescription(aa[selectedRow]);
-          repaint();
-        }
-        else if (evt.getActionCommand().equals(HIDE))
-        {
-            aa[selectedRow].visible = false;
-
-            if (aa[selectedRow].label.equals("Quality"))
-            {
-                ap.av.quality = null;
-            }
-
-            dif = aa[selectedRow].height * -1;
-        }
-        else if (evt.getActionCommand().equals(DELETE))
-        {
-            ap.av.alignment.deleteAnnotation(aa[selectedRow]);
-            dif = aa[selectedRow].height * -1;
-        }
-        else if (evt.getActionCommand().equals(SHOWALL))
-        {
-            for (int i = 0; i < aa.length; i++)
-            {
-                if (!aa[i].visible)
-                {
-                    dif += aa[i].height;
-                    aa[i].visible = true;
-                }
-            }
-        }
-        else if (evt.getActionCommand().equals(OUTPUT_TEXT))
-        {
-          new AnnotationExporter().exportAnnotations(
-              ap,
-              new AlignmentAnnotation[]
-              {aa[selectedRow]},
-              null
-              );
-        }
-        else if (evt.getActionCommand().equals(COPYCONS_SEQ))
-        {
-          SequenceI cons=av.getConsensusSeq();
-          if (cons!=null)
-            copy_annotseqtoclipboard(cons);
+      AlignmentAnnotation newAnnotation = new AlignmentAnnotation(null,
+          null,
+          new Annotation[ap.av.alignment.getWidth()]);
 
-        }
+      if (!editLabelDescription(newAnnotation))
+      {
+        return;
+      }
 
-        ap.annotationPanel.adjustPanelHeight();
-        ap.annotationScroller.validate();
-        ap.repaint();
+      ap.av.alignment.addAnnotation(newAnnotation);
+      ap.av.alignment.setAnnotationIndex(newAnnotation, 0);
+      if (aa != null)
+      {
+        dif = aa[aa.length - 1].height;
+      }
     }
-
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    boolean editLabelDescription(AlignmentAnnotation annotation)
+    else if (evt.getActionCommand().equals(EDITNAME))
     {
-      EditNameDialog dialog = new EditNameDialog(annotation.label,
-                                                 annotation.description,
-                                                 "       Annotation Name ",
-                                                 "Annotation Description ",
-                                                 "Edit Annotation Name/Description");
+      editLabelDescription(aa[selectedRow]);
+      repaint();
+    }
+    else if (evt.getActionCommand().equals(HIDE))
+    {
+      aa[selectedRow].visible = false;
 
-      if (!dialog.accept)
+      if (aa[selectedRow].label.equals("Quality"))
       {
-        return false;
+        ap.av.quality = null;
       }
 
-        annotation.label = dialog.getName();
-
-        String text = dialog.getDescription();
-        if(text.length()==0)
-          text = null;
-        annotation.description = text;
-
-        return true;
+      dif = aa[selectedRow].height * -1;
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mousePressed(MouseEvent evt)
+    else if (evt.getActionCommand().equals(DELETE))
     {
-        getSelectedRow(evt.getY() - scrollOffset);
-        oldY = evt.getY();
+      ap.av.alignment.deleteAnnotation(aa[selectedRow]);
+      dif = aa[selectedRow].height * -1;
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mouseReleased(MouseEvent evt)
+    else if (evt.getActionCommand().equals(SHOWALL))
     {
-        int start = selectedRow;
-        getSelectedRow(evt.getY() - scrollOffset);
-        int end = selectedRow;
-
-        if(start!=end)
+      for (int i = 0; i < aa.length; i++)
+      {
+        if (!aa[i].visible)
         {
-          //Swap these annotations
-          AlignmentAnnotation startAA = ap.av.alignment.getAlignmentAnnotation()[start];
-          AlignmentAnnotation endAA = ap.av.alignment.getAlignmentAnnotation()[end];
-
-
-          ap.av.alignment.getAlignmentAnnotation()[end] = startAA;
-          ap.av.alignment.getAlignmentAnnotation()[start] = endAA;
+          dif += aa[i].height;
+          aa[i].visible = true;
         }
-
-        resizePanel = false;
-        dragEvent = null;
-        repaint();
-        ap.annotationPanel.repaint();
+      }
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mouseEntered(MouseEvent evt)
+    else if (evt.getActionCommand().equals(OUTPUT_TEXT))
     {
-      if(evt.getY()<10)
-      {
-        resizePanel = true;
-        repaint();
-      }
+      new AnnotationExporter().exportAnnotations(
+          ap,
+          new AlignmentAnnotation[]
+          {aa[selectedRow]},
+          null
+          );
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mouseExited(MouseEvent evt)
+    else if (evt.getActionCommand().equals(COPYCONS_SEQ))
     {
-      if(dragEvent == null)
+      SequenceI cons = av.getConsensusSeq();
+      if (cons != null)
       {
-        resizePanel = false;
-        repaint();
+        copy_annotseqtoclipboard(cons);
       }
+
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mouseDragged(MouseEvent evt)
+    ap.annotationPanel.adjustPanelHeight();
+    ap.annotationScroller.validate();
+    ap.repaint();
+  }
+
+  /**
+   * 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");
+
+    if (!dialog.accept)
     {
-      dragEvent = evt;
-
-      if (resizePanel)
-      {
-        Dimension d = ap.annotationScroller.getPreferredSize();
-        int dif = evt.getY() - oldY;
+      return false;
+    }
 
-        dif /= ap.av.charHeight;
-        dif *= ap.av.charHeight;
+    annotation.label = dialog.getName();
 
-        if ( (d.height - dif) > 20)
-        {
-          ap.annotationScroller.setPreferredSize(new Dimension(d.width,
-              d.height - dif));
-          d = ap.annotationSpaceFillerHolder.getPreferredSize();
-          ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension(
-              d.width, d.height - dif));
-          ap.repaint();
-        }
+    String text = dialog.getDescription();
+    if (text.length() == 0)
+    {
+      text = null;
+    }
+    annotation.description = text;
+
+    return true;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void mousePressed(MouseEvent evt)
+  {
+    getSelectedRow(evt.getY() - scrollOffset);
+    oldY = evt.getY();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void mouseReleased(MouseEvent evt)
+  {
+    int start = selectedRow;
+    getSelectedRow(evt.getY() - scrollOffset);
+    int end = selectedRow;
+
+    if (start != end)
+    {
+      //Swap these annotations
+      AlignmentAnnotation startAA = ap.av.alignment.getAlignmentAnnotation()[
+          start];
+      AlignmentAnnotation endAA = ap.av.alignment.getAlignmentAnnotation()[end];
 
-        ap.addNotify();
-      }
-      else
-        repaint();
+      ap.av.alignment.getAlignmentAnnotation()[end] = startAA;
+      ap.av.alignment.getAlignmentAnnotation()[start] = endAA;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mouseMoved(MouseEvent evt)
+    resizePanel = false;
+    dragEvent = null;
+    repaint();
+    ap.annotationPanel.repaint();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void mouseEntered(MouseEvent evt)
+  {
+    if (evt.getY() < 10)
+    {
+      resizePanel = true;
+      repaint();
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void mouseExited(MouseEvent evt)
+  {
+    if (dragEvent == null)
     {
-      resizePanel = evt.getY()<10;
+      resizePanel = false;
+      repaint();
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void mouseDragged(MouseEvent evt)
+  {
+    dragEvent = evt;
+
+    if (resizePanel)
+    {
+      Dimension d = ap.annotationScroller.getPreferredSize();
+      int dif = evt.getY() - oldY;
 
-      getSelectedRow(evt.getY() - scrollOffset);
+      dif /= ap.av.charHeight;
+      dif *= ap.av.charHeight;
 
-      if(selectedRow>-1
-         && ap.av.alignment.getAlignmentAnnotation().length>selectedRow)
+      if ( (d.height - dif) > 20)
       {
-        String desc = ap.av.alignment.
-            getAlignmentAnnotation()[selectedRow].description;
-
-        if (desc != null && !desc.equals("New description"))
-          setToolTipText(ap.av.alignment.
-                         getAlignmentAnnotation()[selectedRow].description);
-
+        ap.annotationScroller.setPreferredSize(new Dimension(d.width,
+            d.height - dif));
+        d = ap.annotationSpaceFillerHolder.getPreferredSize();
+        ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension(
+            d.width, d.height - dif));
+        ap.repaint();
       }
+
+      ap.addNotify();
+    }
+    else
+    {
       repaint();
     }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void mouseMoved(MouseEvent evt)
+  {
+    resizePanel = evt.getY() < 10;
+
+    getSelectedRow(evt.getY() - scrollOffset);
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mouseClicked(MouseEvent evt)
+    if (selectedRow > -1
+        && ap.av.alignment.getAlignmentAnnotation().length > selectedRow)
     {
-       if(!SwingUtilities.isRightMouseButton(evt))
-         return;
+      String desc = ap.av.alignment.
+          getAlignmentAnnotation()[selectedRow].description;
 
-        AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+      if (desc != null && !desc.equals("New description"))
+      {
+        setToolTipText(ap.av.alignment.
+                       getAlignmentAnnotation()[selectedRow].description);
+      }
 
-        if ((aa == null) || (aa.length == 0))
-        {
-            JPopupMenu pop = new JPopupMenu("Annotations");
-            JMenuItem item = new JMenuItem(ADDNEW);
-            item.addActionListener(this);
-            pop.add(item);
-            pop.show(this, evt.getX(), evt.getY());
+    }
+    repaint();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void mouseClicked(MouseEvent evt)
+  {
+    if (!SwingUtilities.isRightMouseButton(evt))
+    {
+      return;
+    }
 
-            return;
-        }
+    AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
 
+    if ( (aa == null) || (aa.length == 0))
+    {
+      JPopupMenu pop = new JPopupMenu("Annotations");
+      JMenuItem item = new JMenuItem(ADDNEW);
+      item.addActionListener(this);
+      pop.add(item);
+      pop.show(this, evt.getX(), evt.getY());
+
+      return;
+    }
 
-        JPopupMenu pop = new JPopupMenu("Annotations");
-        JMenuItem item = new JMenuItem(ADDNEW);
-        item.addActionListener(this);
-        pop.add(item);
-        item = new JMenuItem(EDITNAME);
-        item.addActionListener(this);
-        pop.add(item);
-        item = new JMenuItem(HIDE);
-        item.addActionListener(this);
-        pop.add(item);
-        item = new JMenuItem(DELETE);
-        item.addActionListener(this);
-        pop.add(item);
-        item = new JMenuItem(SHOWALL);
-        item.addActionListener(this);
-        pop.add(item);
-        item = new JMenuItem(OUTPUT_TEXT);
-        item.addActionListener(this);
-        pop.add(item);
-        // annotation object should be typed
-        if (aa[selectedRow]==ap.av.consensus)
+    JPopupMenu pop = new JPopupMenu("Annotations");
+    JMenuItem item = new JMenuItem(ADDNEW);
+    item.addActionListener(this);
+    pop.add(item);
+    item = new JMenuItem(EDITNAME);
+    item.addActionListener(this);
+    pop.add(item);
+    item = new JMenuItem(HIDE);
+    item.addActionListener(this);
+    pop.add(item);
+    item = new JMenuItem(DELETE);
+    item.addActionListener(this);
+    pop.add(item);
+    item = new JMenuItem(SHOWALL);
+    item.addActionListener(this);
+    pop.add(item);
+    item = new JMenuItem(OUTPUT_TEXT);
+    item.addActionListener(this);
+    pop.add(item);
+    // annotation object should be typed
+    if (aa[selectedRow] == ap.av.consensus)
+    {
+      pop.addSeparator();
+      final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
+          "Ignore Gaps In Consensus",
+          ap.av.getIgnoreGapsConsensus());
+      cbmi.addActionListener(new ActionListener()
+      {
+        public void actionPerformed(ActionEvent e)
         {
-          pop.addSeparator();
-          final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
-              "Ignore Gaps In Consensus",
-              ap.av.getIgnoreGapsConsensus());
-          cbmi.addActionListener(new ActionListener()
-              {public void actionPerformed(ActionEvent e)
-               {
-                 ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
-               }
-              });
-          pop.add(cbmi);
-          final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ);
-          consclipbrd.addActionListener(this);
-          pop.add(consclipbrd);
+          ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
         }
+      });
+      pop.add(cbmi);
+      final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ);
+      consclipbrd.addActionListener(this);
+      pop.add(consclipbrd);
+    }
 
-        pop.show(this, evt.getX(), evt.getY());
-    }
-    /**
-     * do a single sequence copy to jalview and the system clipboard
-     *
-     * @param sq sequence to be copied to clipboard
-     */
-    protected void copy_annotseqtoclipboard(SequenceI sq)
-    {
-      SequenceI [] seqs = new SequenceI[] { sq };
-      String[] omitHidden = null;
-      SequenceI [] dseqs=new SequenceI[] { sq.getDatasetSequence()};
-      if (dseqs[0]==null) {
-        dseqs[0] = new Sequence(sq);
-        dseqs[0].setSequence(
-            jalview.analysis.AlignSeq.extractGaps(
-                jalview.util.Comparison.GapChars,
-                sq.getSequenceAsString()));
-
-        sq.setDatasetSequence(dseqs[0]);
-      }
-      Alignment ds=new Alignment(dseqs);
-      if (av.hasHiddenColumns)
-      {
-        omitHidden = av.getColumnSelection().getVisibleSequenceStrings(0, sq.getLength(), seqs);
-      }
+    pop.show(this, evt.getX(), evt.getY());
+  }
+
+  /**
+   * do a single sequence copy to jalview and the system clipboard
+   *
+   * @param sq sequence to be copied to clipboard
+   */
+  protected void copy_annotseqtoclipboard(SequenceI sq)
+  {
+    SequenceI[] seqs = new SequenceI[]
+        {
+        sq};
+    String[] omitHidden = null;
+    SequenceI[] dseqs = new SequenceI[]
+        {
+        sq.getDatasetSequence()};
+    if (dseqs[0] == null)
+    {
+      dseqs[0] = new Sequence(sq);
+      dseqs[0].setSequence(
+          jalview.analysis.AlignSeq.extractGaps(
+              jalview.util.Comparison.GapChars,
+              sq.getSequenceAsString()));
 
-      String output = new FormatAdapter().formatSequences(
-          "Fasta",
-          seqs,
-          omitHidden);
+      sq.setDatasetSequence(dseqs[0]);
+    }
+    Alignment ds = new Alignment(dseqs);
+    if (av.hasHiddenColumns)
+    {
+      omitHidden = av.getColumnSelection().getVisibleSequenceStrings(0,
+          sq.getLength(), seqs);
+    }
 
+    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)
+    Vector hiddenColumns = null;
+    if (av.hasHiddenColumns)
+    {
+      hiddenColumns = new Vector();
+      for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)
       {
-        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]});
-        }
+        hiddenColumns.addElement(new int[]
+                                 {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};
     }
-    /**
-     * DOCUMENT ME!
-     *
-     * @param g1 DOCUMENT ME!
-     */
-    public void paintComponent(Graphics g)
+
+    Desktop.jalviewClipboard = new Object[]
+        {
+        seqs,
+        ds, // what is the dataset of a consensus sequence ? need to flag sequence as special.
+        hiddenColumns};
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param g1 DOCUMENT ME!
+   */
+  public void paintComponent(Graphics g)
+  {
+
+    int width = getWidth();
+    if (width == 0)
     {
+      width = ap.calculateIdWidth().width + 4;
+    }
 
-        int width = getWidth();
-        if(width==0)
-         width = ap.calculateIdWidth().width + 4;
+    Graphics2D g2 = (Graphics2D) g;
+    if (av.antiAlias)
+    {
+      g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+                          RenderingHints.VALUE_ANTIALIAS_ON);
+    }
 
-       Graphics2D g2 = (Graphics2D) g;
-       if(av.antiAlias)
-        g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
-            RenderingHints.VALUE_ANTIALIAS_ON);
+    drawComponent(g2, width);
 
-       drawComponent(g2, width);
+  }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param g DOCUMENT ME!
+   */
+  public void drawComponent(Graphics g, int width)
+  {
+    if (av.getFont().getSize() < 10)
+    {
+      g.setFont(font);
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param g DOCUMENT ME!
-     */
-    public void drawComponent(Graphics g, int width)
+    else
     {
-        if(av.getFont().getSize()<10)
-          g.setFont(font);
-        else
-          g.setFont(av.getFont());
+      g.setFont(av.getFont());
+    }
 
-        FontMetrics fm = g.getFontMetrics(g.getFont());
-        g.setColor(Color.white);
-        g.fillRect(0, 0, getWidth(), getHeight());
+    FontMetrics fm = g.getFontMetrics(g.getFont());
+    g.setColor(Color.white);
+    g.fillRect(0, 0, getWidth(), getHeight());
+
+    g.translate(0, scrollOffset);
+    g.setColor(Color.black);
+
+    AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+    int fontHeight = g.getFont().getSize();
+    int y = fontHeight;
+    int x = 0;
+    int graphExtras = 0;
+
+    if (aa != null)
+    {
+      for (int i = 0; i < aa.length; i++)
+      {
+        if (!aa[i].visible)
+        {
+          continue;
+        }
 
-        g.translate(0, scrollOffset);
-        g.setColor(Color.black);
+        x = width - fm.stringWidth(aa[i].label) - 3;
 
-        AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
-        int fontHeight = g.getFont().getSize();
-        int y = fontHeight;
-        int x = 0;
-        int graphExtras = 0;
+        if (aa[i].graph > 0 && aa[i].graphHeight > 0)
+        {
+          graphExtras = y;
 
+          y += (aa[i].height / 3);
 
+          if (aa[i].graphGroup < 0)
+          {
+            graphExtras = y + fontHeight;
+          }
+        }
 
-        if (aa != null)
+        if (aa[i].graphGroup > -1)
         {
-            for (int i = 0; i < aa.length; i++)
+          int groupSize = 0;
+          for (int gg = 0; gg < aa.length; gg++)
+          {
+            if (aa[gg].graphGroup == aa[i].graphGroup)
+            {
+              groupSize++;
+            }
+          }
+
+          if (groupSize * (fontHeight + 8) < aa[i].height)
+          {
+            graphExtras += (aa[i].height - (groupSize * (fontHeight + 8))) / 2;
+          }
+
+          for (int gg = 0; gg < aa.length; gg++)
+          {
+            if (aa[gg].graphGroup == aa[i].graphGroup)
             {
-                if (!aa[i].visible)
-                {
-                    continue;
-                }
-
-                x = width - fm.stringWidth(aa[i].label) - 3;
-
-                if (aa[i].graph>0 && aa[i].graphHeight>0)
-                {
-                    graphExtras = y;
-
-                    y += (aa[i].height / 3);
-
-                    if(aa[i].graphGroup<0)
-                        graphExtras = y + fontHeight;
-                }
-
-                if(aa[i].graphGroup>-1)
-                {
-                  int groupSize = 0;
-                  for (int gg = 0; gg < aa.length; gg++)
-                  {
-                    if (aa[gg].graphGroup == aa[i].graphGroup)
-                      groupSize++;
-                  }
-
-                  if(groupSize * (fontHeight+8) < aa[i].height)
-                    graphExtras += (aa[i].height -( groupSize * (fontHeight+8)) )/2;
-
-                 for(int gg=0; gg<aa.length; gg++)
-                 {
-                   if(aa[gg].graphGroup==aa[i].graphGroup)
-                   {
-                     x = width - fm.stringWidth(aa[gg].label) - 3;
-                     g.drawString(aa[gg].label, x, graphExtras );
-                     if(aa[gg].annotations[0]!=null)
-                       g.setColor(aa[gg].annotations[0].colour);
-
-                     g.drawLine( x, graphExtras+3,
-                                 x+fm.stringWidth(aa[gg].label),
-                                 graphExtras+3);
-
-                     g.setColor(Color.black);
-                     graphExtras += fontHeight+8;
-                   }
-                 }
-                }
-                else
-                  g.drawString(aa[i].label, x, y);
-
-                if (aa[i].graph>0)
-                {
-                /*  if (aa[i].graphLines != null)
-                  {
-                    for (int gl = 0; gl < aa[i].graphLines.size(); gl++)
-                    {
-                       x = width - fm.stringWidth(aa[i].getGraphLine(gl).label) - 3;
-                      g.drawString(aa[i].getGraphLine(gl).label, x, graphExtras);
-                      g.setColor(aa[i].getGraphLine(gl).colour);
-                      Graphics2D g2 = (Graphics2D) g;
-                      g2.setStroke(new BasicStroke(1,
-                          BasicStroke.CAP_SQUARE,
-                          BasicStroke.JOIN_ROUND, 3f,
-                          new float[]
-                          {5f, 3f}, 0f));
-
-                      graphExtras += 3;
-
-                      g.drawLine(x, graphExtras,
-                                 x+fm.stringWidth(aa[i].label),
-                                 graphExtras);
-                      g2.setStroke(new BasicStroke());
-                    }
-                  }*/
-                    y += ((2 * aa[i].height) / 3);
-                }
-                else
-                {
-                    y += aa[i].height;
-                }
+              x = width - fm.stringWidth(aa[gg].label) - 3;
+              g.drawString(aa[gg].label, x, graphExtras);
+              if (aa[gg].annotations[0] != null)
+              {
+                g.setColor(aa[gg].annotations[0].colour);
+              }
+
+              g.drawLine(x, graphExtras + 3,
+                         x + fm.stringWidth(aa[gg].label),
+                         graphExtras + 3);
+
+              g.setColor(Color.black);
+              graphExtras += fontHeight + 8;
             }
+          }
+        }
+        else
+        {
+          g.drawString(aa[i].label, x, y);
         }
 
-        if (resizePanel)
+        if (aa[i].graph > 0)
         {
-          g.drawImage(image, 2, 0 - scrollOffset, this);
+          /*  if (aa[i].graphLines != null)
+            {
+              for (int gl = 0; gl < aa[i].graphLines.size(); gl++)
+              {
+                 x = width - fm.stringWidth(aa[i].getGraphLine(gl).label) - 3;
+                g.drawString(aa[i].getGraphLine(gl).label, x, graphExtras);
+                g.setColor(aa[i].getGraphLine(gl).colour);
+                Graphics2D g2 = (Graphics2D) g;
+                g2.setStroke(new BasicStroke(1,
+                    BasicStroke.CAP_SQUARE,
+                    BasicStroke.JOIN_ROUND, 3f,
+                    new float[]
+                    {5f, 3f}, 0f));
+
+                graphExtras += 3;
+
+                g.drawLine(x, graphExtras,
+                           x+fm.stringWidth(aa[i].label),
+                           graphExtras);
+                g2.setStroke(new BasicStroke());
+              }
+            }*/
+          y += ( (2 * aa[i].height) / 3);
         }
-        else if (dragEvent != null && aa!=null)
+        else
         {
-          g.setColor(Color.lightGray);
-          g.drawString(aa[selectedRow].label, dragEvent.getX(), dragEvent.getY() - scrollOffset);
+          y += aa[i].height;
         }
+      }
+    }
 
+    if (resizePanel)
+    {
+      g.drawImage(image, 2, 0 - scrollOffset, this);
+    }
+    else if (dragEvent != null && aa != null)
+    {
+      g.setColor(Color.lightGray);
+      g.drawString(aa[selectedRow].label, dragEvent.getX(),
+                   dragEvent.getY() - scrollOffset);
+    }
 
-        if ((aa == null) || (aa.length < 1))
-        {
-            g.drawString("Right click", 2, 8);
-            g.drawString("to add annotation", 2, 18);
-        }
+    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 0f6901d..895d196 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,14 +18,12 @@
  */
 package jalview.gui;
 
-import jalview.datamodel.*;
-
 import java.awt.*;
 import java.awt.event.*;
 import java.awt.image.*;
-
 import javax.swing.*;
 
+import jalview.datamodel.*;
 
 /**
  * DOCUMENT ME!
@@ -33,1261 +31,1323 @@ import javax.swing.*;
  * @author $author$
  * @version $Revision$
  */
-public class AnnotationPanel extends JPanel implements MouseListener,
+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
-    int graphStretch = -1;
-    int graphStretchY = -1;
-    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!
-     */
-    public AnnotationPanel(AlignmentPanel ap)
+  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
+  int graphStretch = -1;
+  int graphStretchY = -1;
+  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!
+   */
+  public AnnotationPanel(AlignmentPanel ap)
+  {
+
+    if (System.getProperty("os.name").startsWith("Mac"))
     {
-
-    if(System.getProperty("os.name").startsWith("Mac"))
       MAC = true;
-
-        ToolTipManager.sharedInstance().registerComponent(this);
-        ToolTipManager.sharedInstance().setInitialDelay(0);
-        ToolTipManager.sharedInstance().setDismissDelay(10000);
-        this.ap = ap;
-        av = ap.av;
-        this.setLayout(null);
-        addMouseListener(this);
-        addMouseMotionListener(this);
-        ap.annotationScroller.getVerticalScrollBar().addAdjustmentListener(this);
-    }
-
-    public AnnotationPanel(AlignViewport av)
-    {
-      this.av = av;
-    }
-
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void adjustmentValueChanged(AdjustmentEvent evt)
-    {
-        ap.alabels.setScrollOffset(-evt.getValue());
     }
 
-    /**
-     * DOCUMENT ME!
-     */
-    public int adjustPanelHeight()
+    ToolTipManager.sharedInstance().registerComponent(this);
+    ToolTipManager.sharedInstance().setInitialDelay(0);
+    ToolTipManager.sharedInstance().setDismissDelay(10000);
+    this.ap = ap;
+    av = ap.av;
+    this.setLayout(null);
+    addMouseListener(this);
+    addMouseMotionListener(this);
+    ap.annotationScroller.getVerticalScrollBar().addAdjustmentListener(this);
+  }
+
+  public AnnotationPanel(AlignViewport av)
+  {
+    this.av = av;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void adjustmentValueChanged(AdjustmentEvent evt)
+  {
+    ap.alabels.setScrollOffset( -evt.getValue());
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public int adjustPanelHeight()
+  {
+    // setHeight of panels
+    AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+    int height = 0;
+
+    if (aa != null)
     {
-        // setHeight of panels
-        AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
-        int height = 0;
-
-        if (aa != null)
+      for (int i = 0; i < aa.length; i++)
+      {
+        if (!aa[i].visible)
         {
-            for (int i = 0; i < aa.length; i++)
-            {
-                if (!aa[i].visible)
-                {
-                    continue;
-                }
-
-                aa[i].height = 0;
-
-                if (aa[i].hasText)
-                {
-                    aa[i].height += av.charHeight;
-                }
-
-                if (aa[i].hasIcons)
-                {
-                    aa[i].height += 16;
-                }
+          continue;
+        }
 
-                if (aa[i].graph>0)
-                {
-                    aa[i].height += aa[i].graphHeight;
-                }
+        aa[i].height = 0;
 
-                if (aa[i].height == 0)
-                {
-                    aa[i].height = 20;
-                }
+        if (aa[i].hasText)
+        {
+          aa[i].height += av.charHeight;
+        }
 
-                height += aa[i].height;
-            }
+        if (aa[i].hasIcons)
+        {
+          aa[i].height += 16;
         }
-        else
+
+        if (aa[i].graph > 0)
         {
-            height = 20;
+          aa[i].height += aa[i].graphHeight;
         }
 
-        this.setPreferredSize(new Dimension(1, height));
+        if (aa[i].height == 0)
+        {
+          aa[i].height = 20;
+        }
 
-        return height;
+        height += aa[i].height;
+      }
     }
-
-
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void actionPerformed(ActionEvent evt)
+    else
     {
-        AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
-        Annotation[] anot = aa[activeRow].annotations;
+      height = 20;
+    }
 
-        if (anot.length < av.getColumnSelection().getMax())
-        {
-          Annotation[] temp = new Annotation[av.getColumnSelection().getMax()+2 ];
-          System.arraycopy(anot, 0, temp, 0, anot.length);
-          anot = temp;
-          aa[activeRow].annotations = anot;
-        }
+    this.setPreferredSize(new Dimension(1, height));
 
+    return height;
+  }
 
-        if (evt.getActionCommand().equals(REMOVE))
-        {
-            for (int i = 0; i < av.getColumnSelection().size(); i++)
-            {
-                anot[av.getColumnSelection().columnAt(i)] = null;
-            }
-        }
-        else if (evt.getActionCommand().equals(LABEL))
-        {
-            String label = JOptionPane.showInputDialog(this, "Enter Label ",
-                    "Enter label", JOptionPane.QUESTION_MESSAGE);
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void actionPerformed(ActionEvent evt)
+  {
+    AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+    Annotation[] anot = aa[activeRow].annotations;
 
-            if (label == null)
-            {
-                return;
-            }
+    if (anot.length < av.getColumnSelection().getMax())
+    {
+      Annotation[] temp = new Annotation[av.getColumnSelection().getMax() + 2];
+      System.arraycopy(anot, 0, temp, 0, anot.length);
+      anot = temp;
+      aa[activeRow].annotations = anot;
+    }
 
-            if ((label.length() > 0) && !aa[activeRow].hasText)
-            {
-                aa[activeRow].hasText = true;
-            }
+    if (evt.getActionCommand().equals(REMOVE))
+    {
+      for (int i = 0; i < av.getColumnSelection().size(); i++)
+      {
+        anot[av.getColumnSelection().columnAt(i)] = null;
+      }
+    }
+    else if (evt.getActionCommand().equals(LABEL))
+    {
+      String label = JOptionPane.showInputDialog(this, "Enter Label ",
+                                                 "Enter label",
+                                                 JOptionPane.QUESTION_MESSAGE);
 
-            for (int i = 0; i < av.getColumnSelection().size(); i++)
-            {
-                int index = av.getColumnSelection().columnAt(i);
+      if (label == null)
+      {
+        return;
+      }
 
-                if (anot[index] == null)
-                {
-                    anot[index] = new Annotation(label, "", ' ', 0);
-                }
+      if ( (label.length() > 0) && !aa[activeRow].hasText)
+      {
+        aa[activeRow].hasText = true;
+      }
 
-                anot[index].displayCharacter = label;
-            }
-        }
-        else if (evt.getActionCommand().equals(COLOUR))
+      for (int i = 0; i < av.getColumnSelection().size(); i++)
+      {
+        int index = av.getColumnSelection().columnAt(i);
+
+        if (anot[index] == null)
         {
-            Color col = JColorChooser.showDialog(this,
-                    "Choose foreground colour", Color.black);
+          anot[index] = new Annotation(label, "", ' ', 0);
+        }
 
-            for (int i = 0; i < av.getColumnSelection().size(); i++)
-            {
-                int index = av.getColumnSelection().columnAt(i);
+        anot[index].displayCharacter = label;
+      }
+    }
+    else if (evt.getActionCommand().equals(COLOUR))
+    {
+      Color col = JColorChooser.showDialog(this,
+                                           "Choose foreground colour",
+                                           Color.black);
 
-                if (anot[index] == null)
-                {
-                    anot[index] = new Annotation("", "", ' ', 0);
-                }
+      for (int i = 0; i < av.getColumnSelection().size(); i++)
+      {
+        int index = av.getColumnSelection().columnAt(i);
 
-                anot[index].colour = col;
-            }
-        }
-        else // HELIX OR SHEET
+        if (anot[index] == null)
         {
-            char type = 0;
-            String symbol = "\u03B1";
+          anot[index] = new Annotation("", "", ' ', 0);
+        }
 
-            if (evt.getActionCommand().equals(HELIX))
-            {
-                type = 'H';
-            }
-            else if (evt.getActionCommand().equals(SHEET))
-            {
-                type = 'E';
-                symbol = "\u03B2";
-            }
+        anot[index].colour = col;
+      }
+    }
+    else // HELIX OR SHEET
+    {
+      char type = 0;
+      String symbol = "\u03B1";
 
-            if (!aa[activeRow].hasIcons)
-            {
-                aa[activeRow].hasIcons = true;
-            }
+      if (evt.getActionCommand().equals(HELIX))
+      {
+        type = 'H';
+      }
+      else if (evt.getActionCommand().equals(SHEET))
+      {
+        type = 'E';
+        symbol = "\u03B2";
+      }
 
-            String label = JOptionPane.showInputDialog("Enter a label for the structure?",
-                    symbol);
+      if (!aa[activeRow].hasIcons)
+      {
+        aa[activeRow].hasIcons = true;
+      }
 
-            if (label == null)
-            {
-                return;
-            }
+      String label = JOptionPane.showInputDialog(
+          "Enter a label for the structure?",
+          symbol);
 
-            if ((label.length() > 0) && !aa[activeRow].hasText)
-            {
-                aa[activeRow].hasText = true;
-            }
+      if (label == null)
+      {
+        return;
+      }
 
-            for (int i = 0; i < av.getColumnSelection().size(); i++)
-            {
-                int index = av.getColumnSelection().columnAt(i);
+      if ( (label.length() > 0) && !aa[activeRow].hasText)
+      {
+        aa[activeRow].hasText = true;
+      }
 
-                if (anot[index] == null)
-                {
-                    anot[index] = new Annotation(label, "", type, 0);
-                }
+      for (int i = 0; i < av.getColumnSelection().size(); i++)
+      {
+        int index = av.getColumnSelection().columnAt(i);
 
-                anot[index].secondaryStructure = type;
-                anot[index].displayCharacter = label;
-            }
+        if (anot[index] == null)
+        {
+          anot[index] = new Annotation(label, "", type, 0);
         }
 
-        adjustPanelHeight();
-        repaint();
-
-        return;
+        anot[index].secondaryStructure = type;
+        anot[index].displayCharacter = label;
+      }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mousePressed(MouseEvent evt)
-    {
-
-        AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
-        if(aa==null)
-          return;
+    adjustPanelHeight();
+    repaint();
 
+    return;
+  }
 
-        int height = 0;
-        activeRow = -1;
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void mousePressed(MouseEvent evt)
+  {
 
+    AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+    if (aa == null)
+    {
+      return;
+    }
 
-        for (int i = 0; i < aa.length; i++)
-        {
-            if (aa[i].visible)
-            {
-              height += aa[i].height;
-            }
-
-            if (evt.getY() < height)
-            {
-                if (aa[i].editable)
-                {
-                    activeRow = i;
-                }
-                else if(aa[i].graph>0)
-                {
-                    //Stretch Graph
-                    graphStretch = i;
-                    graphStretchY = evt.getY();
-                }
-
-                break;
-            }
-        }
+    int height = 0;
+    activeRow = -1;
 
+    for (int i = 0; i < aa.length; i++)
+    {
+      if (aa[i].visible)
+      {
+        height += aa[i].height;
+      }
 
-        if (SwingUtilities.isRightMouseButton(evt) && activeRow!=-1)
+      if (evt.getY() < height)
+      {
+        if (aa[i].editable)
         {
-            if (av.getColumnSelection() == null)
-            {
-                return;
-            }
-
-            JPopupMenu pop = new JPopupMenu("Structure type");
-            JMenuItem item = new JMenuItem(HELIX);
-            item.addActionListener(this);
-            pop.add(item);
-            item = new JMenuItem(SHEET);
-            item.addActionListener(this);
-            pop.add(item);
-            item = new JMenuItem(LABEL);
-            item.addActionListener(this);
-            pop.add(item);
-            item = new JMenuItem(COLOUR);
-            item.addActionListener(this);
-            pop.add(item);
-            item = new JMenuItem(REMOVE);
-            item.addActionListener(this);
-            pop.add(item);
-            pop.show(this, evt.getX(), evt.getY());
-
-            return;
+          activeRow = i;
         }
-
-        if (aa == null)
+        else if (aa[i].graph > 0)
         {
-            return;
+          //Stretch Graph
+          graphStretch = i;
+          graphStretchY = evt.getY();
         }
 
-        int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+        break;
+      }
+    }
 
-        if(av.hasHiddenColumns)
-          res = av.getColumnSelection().adjustForHiddenColumns(res);
+    if (SwingUtilities.isRightMouseButton(evt) && activeRow != -1)
+    {
+      if (av.getColumnSelection() == null)
+      {
+        return;
+      }
 
-        min = res;
-        max = res;
+      JPopupMenu pop = new JPopupMenu("Structure type");
+      JMenuItem item = new JMenuItem(HELIX);
+      item.addActionListener(this);
+      pop.add(item);
+      item = new JMenuItem(SHEET);
+      item.addActionListener(this);
+      pop.add(item);
+      item = new JMenuItem(LABEL);
+      item.addActionListener(this);
+      pop.add(item);
+      item = new JMenuItem(COLOUR);
+      item.addActionListener(this);
+      pop.add(item);
+      item = new JMenuItem(REMOVE);
+      item.addActionListener(this);
+      pop.add(item);
+      pop.show(this, evt.getX(), evt.getY());
+
+      return;
+    }
 
-        if (av.getColumnSelection().contains(res))
-          av.getColumnSelection().removeElement(res);
-        else
-        {
-            av.getColumnSelection().addElement(res);
-            SequenceGroup sg = new SequenceGroup();
+    if (aa == null)
+    {
+      return;
+    }
 
-            for (int i = 0; i < av.alignment.getSequences().size(); i++)
-            {
-                sg.addSequence(av.alignment.getSequenceAt(i), false);
-            }
+    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
 
-            sg.setStartRes(res);
-            sg.setEndRes(res);
-            av.setSelectionGroup(sg);
-        }
+    if (av.hasHiddenColumns)
+    {
+      res = av.getColumnSelection().adjustForHiddenColumns(res);
+    }
 
-        ap.repaint();
+    min = res;
+    max = res;
 
+    if (av.getColumnSelection().contains(res))
+    {
+      av.getColumnSelection().removeElement(res);
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mouseReleased(MouseEvent evt)
+    else
     {
-      graphStretch = -1;
-      graphStretchY = -1;
-      mouseDragging = false;
+      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);
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mouseEntered(MouseEvent evt)
+    ap.repaint();
+
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void mouseReleased(MouseEvent evt)
+  {
+    graphStretch = -1;
+    graphStretchY = -1;
+    mouseDragging = false;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void mouseEntered(MouseEvent evt)
+  {
+    if (mouseDragging)
     {
-      if(mouseDragging)
-        ap.seqPanel.scrollCanvas(null);
+      ap.seqPanel.scrollCanvas(null);
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mouseExited(MouseEvent evt)
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void mouseExited(MouseEvent evt)
+  {
+    if (mouseDragging)
     {
-      if(mouseDragging)
-        ap.seqPanel.scrollCanvas(evt);
+      ap.seqPanel.scrollCanvas(evt);
     }
-
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mouseDragged(MouseEvent evt)
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void mouseDragged(MouseEvent evt)
+  {
+    if (graphStretch > -1)
     {
-      if(graphStretch>-1)
+      av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight +=
+          graphStretchY - evt.getY();
+      if (av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight < 0)
       {
-        av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY - evt.getY();
-        if(av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight <0)
-          av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight = 0;
-        graphStretchY = evt.getY();
-        adjustPanelHeight();
-        ap.repaint();
+        av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight = 0;
       }
-      else
+      graphStretchY = evt.getY();
+      adjustPanelHeight();
+      ap.repaint();
+    }
+    else
+    {
+      mouseDragging = true;
+
+      int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+
+      if (av.hasHiddenColumns)
       {
-        mouseDragging = true;
+        res = av.getColumnSelection().adjustForHiddenColumns(res);
+      }
 
-        int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+      SequenceGroup sg = av.getSelectionGroup();
 
-        if(av.hasHiddenColumns)
-          res = av.getColumnSelection().adjustForHiddenColumns(res);
+      if (res < min)
+      {
+        min = res;
+      }
 
-        SequenceGroup sg = av.getSelectionGroup();
+      if (res > max)
+      {
+        max = res;
+      }
 
-        if (res < min)
+      if (sg != null)
+      {
+        if (!av.getColumnSelection().contains(res))
         {
-            min = res;
+          av.getColumnSelection().addElement(res);
         }
 
-        if (res > max)
+        if (res > sg.getStartRes())
         {
-            max = res;
+          sg.setEndRes(res);
         }
-
-        if (sg != null)
+        else if (res < sg.getStartRes())
         {
-            if (!av.getColumnSelection().contains(res))
-            {
-                av.getColumnSelection().addElement(res);
-            }
-
-            if (res > sg.getStartRes())
-            {
-                sg.setEndRes(res);
-            }
-            else if (res < sg.getStartRes())
-            {
-                sg.setStartRes(res);
-            }
-
-            for (int i = min; i <= max; i++)
-            {
-                if ((i < sg.getStartRes()) || (i > sg.getEndRes()))
-                {
-                    av.getColumnSelection().removeElement(i);
-                }
-                else
-                {
-                    av.getColumnSelection().addElement(i);
-                }
-            }
+          sg.setStartRes(res);
+        }
 
-            ap.repaint();
+        for (int i = min; i <= max; i++)
+        {
+          if ( (i < sg.getStartRes()) || (i > sg.getEndRes()))
+          {
+            av.getColumnSelection().removeElement(i);
+          }
+          else
+          {
+            av.getColumnSelection().addElement(i);
+          }
         }
 
+        ap.repaint();
       }
-    }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mouseMoved(MouseEvent evt)
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void mouseMoved(MouseEvent evt)
+  {
+    AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+
+    if (aa == null)
     {
-        AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
-
-        if (aa == null)
-        {
-          this.setToolTipText(null);
-            return;
-        }
+      this.setToolTipText(null);
+      return;
+    }
 
-        int row = -1;
-        int height = 0;
+    int row = -1;
+    int height = 0;
 
-        for (int i = 0; i < aa.length; i++)
-        {
-            if (aa[i].visible)
-            {
-                height += aa[i].height;
-            }
+    for (int i = 0; i < aa.length; i++)
+    {
+      if (aa[i].visible)
+      {
+        height += aa[i].height;
+      }
 
-            if (evt.getY() < height)
-            {
-                row = i;
+      if (evt.getY() < height)
+      {
+        row = i;
 
-                break;
-            }
-        }
+        break;
+      }
+    }
 
-        if(row==-1)
-       {
-         this.setToolTipText(null);
-         return;
-       }
+    if (row == -1)
+    {
+      this.setToolTipText(null);
+      return;
+    }
 
-        int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
 
-        if(av.hasHiddenColumns)
-          res = av.getColumnSelection().adjustForHiddenColumns(res);
+    if (av.hasHiddenColumns)
+    {
+      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[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)
-                  tip.append(aa[gg].label+" "+aa[gg].annotations[res].description+"<br>" );
-              }
-              if(tip.length()!=6)
-              {
-                tip.setLength(tip.length() - 4);
-                this.setToolTipText(tip.toString() + "</html>");
-              }
-            }
-            else if(aa[row].annotations[res] != 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));
+          if (aa[gg].graphGroup == aa[row].graphGroup && aa[gg].annotations[res] != null)
+          {
+            tip.append(aa[gg].label + " " + aa[gg].annotations[res].description +
+                       "<br>");
+          }
+        }
+        if (tip.length() != 6)
+        {
+          tip.setLength(tip.length() - 4);
+          this.setToolTipText(tip.toString() + "</html>");
+        }
+      }
+      else if (aa[row].annotations[res] != null
+               && aa[row].annotations[res].description != null)
+      {
+        this.setToolTipText(aa[row].annotations[res].description);
+      }
 
-              if (aa[row].annotations[res].description != null)
-                text.append("  " + aa[row].annotations[res].description);
+      if (aa[row].annotations[res] != null)
+      {
+        StringBuffer text = new StringBuffer("Sequence position " +
+                                             (res + 1));
 
-              ap.alignFrame.statusBar.setText(text.toString());
-            }
+        if (aa[row].annotations[res].description != null)
+        {
+          text.append("  " + aa[row].annotations[res].description);
         }
-        else
-          this.setToolTipText(null);
-    }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mouseClicked(MouseEvent evt)
+        ap.alignFrame.statusBar.setText(text.toString());
+      }
+    }
+    else
     {
+      this.setToolTipText(null);
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param g DOCUMENT ME!
-     */
-    public void paintComponent(Graphics g)
+  }
+
+  /**
+   * 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 (image != null)
     {
-      g.setColor(Color.white);
-      g.fillRect(0, 0, getWidth(), getHeight());
-
-      if(image!=null)
-      {if (fastPaint
-            || (getVisibleRect().width != g.getClipBounds().width)
-            || (getVisibleRect().height != g.getClipBounds().height))
-        {
-          g.drawImage(image, 0, 0, this);
-          fastPaint = false;
-          return;
-        }
+      if (fastPaint
+          || (getVisibleRect().width != g.getClipBounds().width)
+          || (getVisibleRect().height != g.getClipBounds().height))
+      {
+        g.drawImage(image, 0, 0, this);
+        fastPaint = false;
+        return;
       }
-      imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;
+    }
+    imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;
 
-      if (image == null || imgWidth != image.getWidth()
-          || image.getHeight(this) != getHeight())
-      {
-        image = new BufferedImage(imgWidth, ap.annotationPanel.getHeight(),
-                                  BufferedImage.TYPE_INT_RGB);
-        gg = (Graphics2D) image.getGraphics();
+    if (image == null || imgWidth != image.getWidth()
+        || image.getHeight(this) != getHeight())
+    {
+      image = new BufferedImage(imgWidth, ap.annotationPanel.getHeight(),
+                                BufferedImage.TYPE_INT_RGB);
+      gg = (Graphics2D) image.getGraphics();
 
-        if(av.antiAlias)
+      if (av.antiAlias)
+      {
         gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
                             RenderingHints.VALUE_ANTIALIAS_ON);
-
-        gg.setFont(av.getFont());
-        fm = gg.getFontMetrics();
-        gg.setColor(Color.white);
-        gg.fillRect(0, 0, imgWidth, image.getHeight());
       }
 
-
-      drawComponent(gg, av.startRes, av.endRes + 1);
-      g.drawImage(image, 0, 0, this);
+      gg.setFont(av.getFont());
+      fm = gg.getFontMetrics();
+      gg.setColor(Color.white);
+      gg.fillRect(0, 0, imgWidth, image.getHeight());
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param horizontal DOCUMENT ME!
-     */
-    public void fastPaint(int horizontal)
+    drawComponent(gg, av.startRes, av.endRes + 1);
+    g.drawImage(image, 0, 0, this);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param horizontal DOCUMENT ME!
+   */
+  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;
-        }
+      repaint();
+      return;
+    }
 
-        gg.copyArea(0, 0, imgWidth, getHeight(), -horizontal * av.charWidth, 0);
+    gg.copyArea(0, 0, imgWidth, getHeight(), -horizontal * av.charWidth, 0);
 
-        int sr = av.startRes;
-        int er = av.endRes + 1;
-        int transX = 0;
+    int sr = av.startRes;
+    int er = av.endRes + 1;
+    int transX = 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;
-        }
+    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;
+    }
 
-        gg.translate(transX, 0);
+    gg.translate(transX, 0);
 
-        drawComponent(gg, sr, er);
+    drawComponent(gg, sr, er);
 
-        gg.translate(-transX, 0);
+    gg.translate( -transX, 0);
 
-        fastPaint = true;
+    fastPaint = true;
 
-        repaint();
+    repaint();
 
-    }
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param g DOCUMENT ME!
-     * @param startRes DOCUMENT ME!
-     * @param endRes DOCUMENT ME!
-     */
-    public void drawComponent(Graphics g, int startRes, int endRes)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param g DOCUMENT ME!
+   * @param startRes DOCUMENT ME!
+   * @param endRes DOCUMENT ME!
+   */
+  public void drawComponent(Graphics g, int startRes, int endRes)
+  {
+    if (av.updatingConsensus || av.updatingConservation)
     {
-      if(av.updatingConsensus || av.updatingConservation)
+      if (image == null)
       {
-        if(image==null)
-         {
-           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())
-        {
-          fadedImage = new BufferedImage(
-              imgWidth, image.getHeight(),
-              BufferedImage.TYPE_INT_RGB);
+        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())
+      {
+        fadedImage = new BufferedImage(
+            imgWidth, image.getHeight(),
+            BufferedImage.TYPE_INT_RGB);
 
-          Graphics2D fadedG = (Graphics2D) fadedImage.getGraphics();
+        Graphics2D fadedG = (Graphics2D) fadedImage.getGraphics();
 
-          fadedG.setColor(Color.white);
+        fadedG.setColor(Color.white);
         fadedG.fillRect(0, 0, imgWidth, image.getHeight());
 
-          fadedG.setComposite(
-              AlphaComposite.getInstance(
-                  AlphaComposite.SRC_OVER, .3f));
-          fadedG.drawImage(image, 0, 0, this);
-
-        }
+        fadedG.setComposite(
+            AlphaComposite.getInstance(
+                AlphaComposite.SRC_OVER, .3f));
+        fadedG.drawImage(image, 0, 0, this);
 
       }
-      else
-        fadedImage = null;
 
+    }
+    else
+    {
+      fadedImage = null;
+    }
 
-      g.setColor(Color.white);
-      g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight());
+    g.setColor(Color.white);
+    g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight());
 
-      g.setFont(av.getFont());
-      if (fm == null)
-        fm = g.getFontMetrics();
+    g.setFont(av.getFont());
+    if (fm == null)
+    {
+      fm = g.getFontMetrics();
+    }
 
+    if ( (av.alignment.getAlignmentAnnotation() == null) ||
+        (av.alignment.getAlignmentAnnotation().length < 1))
+    {
+      g.setColor(Color.white);
+      g.fillRect(0, 0, getWidth(), getHeight());
+      g.setColor(Color.black);
+      if (av.validCharWidth)
+      {
+        g.drawString("Alignment has no annotations", 20, 15);
+      }
 
+      return;
+    }
 
+    AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
 
-        if ( (av.alignment.getAlignmentAnnotation() == null) ||
-                (av.alignment.getAlignmentAnnotation().length < 1))
-        {
-            g.setColor(Color.white);
-            g.fillRect(0, 0, getWidth(), getHeight());
-            g.setColor(Color.black);
-            if(av.validCharWidth)
-              g.drawString("Alignment has no annotations", 20, 15);
+    int x = 0, y = 0;
+    int column = 0;
+    char lastSS;
+    int lastSSX;
+    int iconOffset = av.charHeight / 2;
+    boolean validRes = false;
 
-            return;
-        }
+    boolean[] graphGroupDrawn = new boolean[aa.length];
 
+    //\u03B2 \u03B1
+    for (int i = 0; i < aa.length; i++)
+    {
+      AlignmentAnnotation row = aa[i];
 
-        AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+      if (!row.visible)
+      {
+        continue;
+      }
 
-        int x = 0, y = 0;
-        int column=0;
-        char lastSS;
-        int lastSSX;
-        int iconOffset = av.charHeight / 2;
-        boolean validRes = false;
+      lastSS = ' ';
+      lastSSX = 0;
 
-        boolean [] graphGroupDrawn = new boolean[aa.length];
+      if (row.graph > 0)
+      {
+        if (row.graphGroup > -1 && graphGroupDrawn[row.graphGroup])
+        {
+          continue;
+        }
 
+        // this is so that we draw the characters below the graph
+        y += row.height;
 
-        //\u03B2 \u03B1
-        for (int i = 0; i < aa.length; i++)
+        if (row.hasText)
         {
-            AlignmentAnnotation row = aa[i];
+          y -= av.charHeight;
+        }
+      }
 
-            if (!row.visible)
-            {
-                continue;
-            }
+      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.setColor(Color.black);
+        // g.drawString("Calculating Consensus....",20, y-row.height/2);
 
-            lastSS = ' ';
-            lastSSX = 0;
+        continue;
+      }
+      else if (av.updatingConservation && aa[i].label.equals("Conservation"))
+      {
 
-            if (row.graph>0)
-            {
-                if(row.graphGroup>-1 && graphGroupDrawn[ row.graphGroup ] )
-                  continue;
+        y += av.charHeight;
+        g.drawImage(fadedImage,
+                    0, y - row.height, imgWidth, y,
+                    0, y - row.height, imgWidth, y, this);
 
-                // this is so that we draw the characters below the graph
-                y += row.height;
+        g.setColor(Color.black);
+        //  g.drawString("Calculating Conservation.....",20, y-row.height/2);
 
-                if (row.hasText)
-                {
-                    y -= av.charHeight;
-                }
-            }
+        continue;
+      }
+      else if (av.updatingConservation && aa[i].label.equals("Quality"))
+      {
 
-            if (av.updatingConsensus && aa[i]==av.consensus)
-            {
-              y += av.charHeight;
+        y += av.charHeight;
+        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.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;
+      }
 
-              continue;
-            }
-            else if (av.updatingConservation && aa[i].label.equals("Conservation"))
-            {
+      if (row.hasText)
+      {
+        iconOffset = av.charHeight / 2 + 4;
+      }
+      else
+      {
+        iconOffset = 0;
+      }
+
+      x = 0;
+      while (x < endRes - startRes)
+      {
+        if (av.hasHiddenColumns)
+        {
+          column = av.getColumnSelection().adjustForHiddenColumns(startRes + x);
+          if (column > row.annotations.length - 1)
+          {
+            break;
+          }
+        }
+        else
+        {
+          column = startRes + x;
+        }
 
-              y += av.charHeight;
-              g.drawImage(fadedImage,
-                          0, y - row.height, imgWidth, y,
-                          0, y - row.height, imgWidth, y, this);
+        if ( (row.annotations.length <= column) ||
+            (row.annotations[column] == null))
+        {
+          validRes = false;
+        }
+        else
+        {
+          validRes = true;
+        }
 
-              g.setColor(Color.black);
-            //  g.drawString("Calculating Conservation.....",20, y-row.height/2);
+        if (activeRow == i)
+        {
+          g.setColor(Color.red);
 
-              continue;
-            }
-            else if (av.updatingConservation && aa[i].label.equals("Quality"))
+          if (av.getColumnSelection() != null)
+          {
+            for (int n = 0; n < av.getColumnSelection().size(); n++)
             {
+              int v = av.getColumnSelection().columnAt(n);
 
-              y += av.charHeight;
-              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);
-
-              continue;
+              if (v == column)
+              {
+                g.fillRect(x * av.charWidth, y,
+                           av.charWidth, av.charHeight);
+              }
             }
+          }
+        }
 
+        if (av.validCharWidth && validRes &&
+            (row.annotations[column].displayCharacter.length() > 0))
+        {
 
-            if (row.hasText)
-            {
-                iconOffset = av.charHeight / 2 + 4;
-            }
-            else
-            {
-                iconOffset = 0;
-            }
+          int charOffset = (av.charWidth -
+                            fm.charWidth(row.annotations[column].
+                                         displayCharacter.charAt(
+                                             0))) / 2;
+          g.setColor(row.annotations[column].colour);
+
+          if (column == 0 || row.graph > 0)
+          {
+            g.drawString(row.annotations[column].displayCharacter,
+                         (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 == ' ')))
+          {
+            g.drawString(row.annotations[column].displayCharacter,
+                         x * av.charWidth + charOffset,
+                         y + iconOffset);
+          }
+        }
 
-            x = 0;
-            while (x < endRes-startRes)
+        if (row.hasIcons)
+        {
+          if (!validRes ||
+              (row.annotations[column].secondaryStructure != lastSS))
+          {
+            switch (lastSS)
             {
-              if (av.hasHiddenColumns)
-              {
-                column = av.getColumnSelection().adjustForHiddenColumns(startRes+x);
-                if (column > row.annotations.length-1)
+              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;
                 }
-              }
-              else
-                column = startRes+x;
 
+                int sCol = (lastSSX / av.charWidth) + startRes;
+                int x1 = lastSSX;
+                int x2 = (x * av.charWidth);
 
-                if ((row.annotations.length <= column) ||
-                        (row.annotations[column] == null))
-                {
-                    validRes = false;
-                }
-                else
+                if (sCol == 0 ||
+                    row.annotations[sCol - 1] == null ||
+                    row.annotations[sCol - 1].secondaryStructure != 'H')
                 {
-                    validRes = true;
+                  g.fillArc(lastSSX, y + 4 + iconOffset, av.charWidth, 8, 90,
+                            180);
+                  x1 += av.charWidth / 2;
                 }
 
-
-                if (activeRow == i)
+                if (row.annotations[column] == null ||
+                    row.annotations[column].secondaryStructure != 'H')
                 {
-                    g.setColor(Color.red);
-
-                    if (av.getColumnSelection() != null)
-                    {
-                        for (int n = 0; n < av.getColumnSelection().size(); n++)
-                        {
-                            int v = av.getColumnSelection().columnAt(n);
-
-                            if (v == column)
-                            {
-                                g.fillRect(x * av.charWidth, y,
-                                    av.charWidth, av.charHeight);
-                            }
-                        }
-                    }
+                  g.fillArc( (x * av.charWidth) - av.charWidth,
+                            y + 4 + iconOffset, av.charWidth, 8, 270, 180);
+                  x2 -= av.charWidth / 2;
                 }
 
-                if (av.validCharWidth && validRes &&
-                        (row.annotations[column].displayCharacter.length() > 0))
-                {
+                g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
+                break;
 
-                    int charOffset = (av.charWidth -
-                        fm.charWidth(row.annotations[column].displayCharacter.charAt(
-                                0))) / 2;
-                    g.setColor(row.annotations[column].colour);
-
-                    if (column == 0 || row.graph>0)
-                    {
-                        g.drawString(row.annotations[column].displayCharacter,
-                                     (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==' ')))
-                    {
-                        g.drawString(row.annotations[column].displayCharacter,
-                                     x*av.charWidth+charOffset,
-                                     y + iconOffset );
-                    }
-                }
+              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);
 
-                if (row.hasIcons)
-                {
-                    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);
-                              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)
-                        {
-                            lastSS = row.annotations[column].secondaryStructure;
-                        }
-                        else
-                        {
-                            lastSS = ' ';
-                        }
-
-                        lastSSX = (x*av.charWidth);
-                    }
-                }
+                break;
 
+              default:
+                g.setColor(Color.gray);
+                g.fillRect(lastSSX, y + 6 + iconOffset,
+                           (x * av.charWidth) - lastSSX, 2);
 
-            column++;
-            x++;
+                break;
             }
 
-            if(column>=row.annotations.length)
-                column = row.annotations.length-1;
+            if (validRes)
+            {
+              lastSS = row.annotations[column].secondaryStructure;
+            }
+            else
+            {
+              lastSS = ' ';
+            }
 
-          //  x ++;
+            lastSSX = (x * av.charWidth);
+          }
+        }
 
-            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;
-                  }
-
-                  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);
+        column++;
+        x++;
+      }
 
-                  break;
+      if (column >= row.annotations.length)
+      {
+        column = row.annotations.length - 1;
+      }
 
-                case 'E':
-                  g.setColor(SHEET_COLOUR);
-
-                  if (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;
+      //  x ++;
 
-                default:
-                  g.setColor(Color.gray);
-                  g.fillRect(lastSSX, y + 6 + iconOffset,
-                             (x*av.charWidth) - lastSSX, 2);
+      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;
+            }
 
-                  break;
-              }
-          }
+            int sCol = (lastSSX / av.charWidth) + startRes;
+            int x1 = lastSSX;
+            int x2 = (x * av.charWidth);
 
-            if (row.graph>0 && row.graphHeight>0)
+            if (sCol == 0 ||
+                row.annotations[sCol - 1] == null ||
+                row.annotations[sCol - 1].secondaryStructure != 'H')
             {
-                if(row.graph == AlignmentAnnotation.LINE_GRAPH )
-                {
-                  if(row.graphGroup>-1 && !graphGroupDrawn[row.graphGroup])
-                   {
-                     float groupmax=-999999, groupmin=9999999;
-                     for(int gg=0; gg<aa.length; gg++)
-                     {
-                       if(aa[gg].graphGroup!=row.graphGroup)
-                         continue;
-
-                       if(aa[gg]!=row)
-                         aa[gg].visible = false;
-
-                       if(aa[gg].graphMax>groupmax)
-                         groupmax = aa[gg].graphMax;
-                       if(aa[gg].graphMin<groupmin)
-                         groupmin = aa[gg].graphMin;
-                     }
-
-                     for (int gg = 0; gg < aa.length; gg++)
-                     {
-                       if (aa[gg].graphGroup == row.graphGroup)
-                       {
-                         drawLineGraph(g, aa[gg], startRes, endRes, y,
-                                       groupmin, groupmax,
-                                       row.graphHeight);
-                       }
-                     }
-
-                     graphGroupDrawn[ row.graphGroup ] = true;
-                   }
-                   else
-                     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);
+              g.fillArc(lastSSX, y + 4 + iconOffset, av.charWidth, 8, 90, 180);
+              x1 += av.charWidth / 2;
             }
 
-            if (row.graph>0 && row.hasText)
+            if (row.annotations[column] == null ||
+                row.annotations[column].secondaryStructure != 'H')
             {
-                y += av.charHeight;
+              g.fillArc( (x * av.charWidth) - av.charWidth,
+                        y + 4 + iconOffset, av.charWidth, 8, 270,
+                        180);
+              x2 -= av.charWidth / 2;
             }
 
-            if (row.graph==0)
+            g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
+
+            break;
+
+          case 'E':
+            g.setColor(SHEET_COLOUR);
+
+            if (row.annotations[endRes] == null
+                || row.annotations[endRes].secondaryStructure != 'E')
             {
-                y += aa[i].height;
+              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);
+
+            break;
         }
-    }
+      }
 
-    public void drawLineGraph(Graphics g, AlignmentAnnotation aa,
-                              int sRes, int eRes,
-                              int y,
-                              float min, float max,
-                              int graphHeight)
-    {
-      if(sRes>aa.annotations.length)
-        return;
+      if (row.graph > 0 && row.graphHeight > 0)
+      {
+        if (row.graph == AlignmentAnnotation.LINE_GRAPH)
+        {
+          if (row.graphGroup > -1 && !graphGroupDrawn[row.graphGroup])
+          {
+            float groupmax = -999999, groupmin = 9999999;
+            for (int gg = 0; gg < aa.length; gg++)
+            {
+              if (aa[gg].graphGroup != row.graphGroup)
+              {
+                continue;
+              }
 
+              if (aa[gg] != row)
+              {
+                aa[gg].visible = false;
+              }
 
-      int x = 0;
+              if (aa[gg].graphMax > groupmax)
+              {
+                groupmax = aa[gg].graphMax;
+              }
+              if (aa[gg].graphMin < groupmin)
+              {
+                groupmin = aa[gg].graphMin;
+              }
+            }
 
-      //Adjustment for fastpaint to left
-      if(eRes<av.endRes)
-        eRes++;
+            for (int gg = 0; gg < aa.length; gg++)
+            {
+              if (aa[gg].graphGroup == row.graphGroup)
+              {
+                drawLineGraph(g, aa[gg], startRes, endRes, y,
+                              groupmin, groupmax,
+                              row.graphHeight);
+              }
+            }
 
-      eRes = Math.min(eRes, aa.annotations.length);
+            graphGroupDrawn[row.graphGroup] = true;
+          }
+          else
+          {
+            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);
+        }
+      }
 
-      if(sRes==0)
+      if (row.graph > 0 && row.hasText)
       {
-        x++;
+        y += av.charHeight;
       }
 
-      int y1=y, y2=y;
-      float range = max - min;
+      if (row.graph == 0)
+      {
+        y += aa[i].height;
+      }
+    }
+  }
+
+  public void drawLineGraph(Graphics g, AlignmentAnnotation aa,
+                            int sRes, int eRes,
+                            int y,
+                            float min, float max,
+                            int graphHeight)
+  {
+    if (sRes > aa.annotations.length)
+    {
+      return;
+    }
 
-      ////Draw origin
-      if(min<0)
-        y2 = y - (int)((0-min / range)*graphHeight);
+    int x = 0;
 
-      g.setColor(Color.gray);
-      g.drawLine(x-av.charWidth,y2,(eRes-sRes+1)*av.charWidth,y2);
+    //Adjustment for fastpaint to left
+    if (eRes < av.endRes)
+    {
+      eRes++;
+    }
 
-      eRes = Math.min(eRes, aa.annotations.length);
+    eRes = Math.min(eRes, aa.annotations.length);
 
-      int column;
-      int aaMax = aa.annotations.length-1;
+    if (sRes == 0)
+    {
+      x++;
+    }
 
-      while( x < eRes - sRes )
-      {
-        column = sRes + x;
-        if(av.hasHiddenColumns)
-        {
-          column = av.getColumnSelection().adjustForHiddenColumns(column);
-        }
+    int y1 = y, y2 = y;
+    float range = max - min;
 
-        if (column > aaMax)
-        {
-          break;
-        }
+    ////Draw origin
+    if (min < 0)
+    {
+      y2 = y - (int) ( (0 - min / range) * graphHeight);
+    }
 
-        if(aa.annotations[column]==null || aa.annotations[column-1]==null)
-        {
-          x++;
-          continue;
-        }
+    g.setColor(Color.gray);
+    g.drawLine(x - av.charWidth, y2, (eRes - sRes + 1) * av.charWidth, y2);
 
+    eRes = Math.min(eRes, aa.annotations.length);
 
-          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);
+    int column;
+    int aaMax = aa.annotations.length - 1;
 
-          g.drawLine(x*av.charWidth-av.charWidth/2, y1, x*av.charWidth+av.charWidth/2, y2);
-          x ++;
-       }
+    while (x < eRes - sRes)
+    {
+      column = sRes + x;
+      if (av.hasHiddenColumns)
+      {
+        column = av.getColumnSelection().adjustForHiddenColumns(column);
+      }
 
-       if(aa.threshold!=null)
-       {
-           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));
+      if (column > aaMax)
+      {
+        break;
+      }
 
-           y2 = (int)(y - ((aa.threshold.value-min) / range)*graphHeight);
-           g.drawLine(0,y2,(eRes-sRes)*av.charWidth,y2);
-           g2.setStroke(new BasicStroke());
+      if (aa.annotations[column] == null || aa.annotations[column - 1] == null)
+      {
+        x++;
+        continue;
       }
+
+      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);
+
+      g.drawLine(x * av.charWidth - av.charWidth / 2, y1,
+                 x * av.charWidth + av.charWidth / 2, y2);
+      x++;
     }
 
-    public void drawBarGraph(Graphics g, AlignmentAnnotation aa,
-                             int sRes, int eRes,
-                             float min, float max,
-                             int y)
+    if (aa.threshold != null)
     {
-      if(sRes>aa.annotations.length)
-        return;
+      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));
+
+      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)
+  {
+    if (sRes > aa.annotations.length)
+    {
+      return;
+    }
 
-      eRes = Math.min(eRes, aa.annotations.length);
+    eRes = Math.min(eRes, aa.annotations.length);
 
-      int x=0, y1=y, y2=y;
+    int x = 0, y1 = y, y2 = y;
 
-      float range = max - min;
+    float range = max - min;
 
-      if(min<0)
-        y2 = y - (int)((0-min / (range))*aa.graphHeight);
+    if (min < 0)
+    {
+      y2 = y - (int) ( (0 - min / (range)) * aa.graphHeight);
+    }
 
-      g.setColor(Color.gray);
+    g.setColor(Color.gray);
 
-      g.drawLine(x,y2,(eRes-sRes)*av.charWidth,y2);
+    g.drawLine(x, y2, (eRes - sRes) * av.charWidth, y2);
 
-      int column;
-      int aaMax = aa.annotations.length-1;
+    int column;
+    int aaMax = aa.annotations.length - 1;
 
-      while( x < eRes-sRes )
+    while (x < eRes - sRes)
+    {
+      column = sRes + x;
+      if (av.hasHiddenColumns)
       {
-        column = sRes + x;
-        if(av.hasHiddenColumns)
-        {
-          column = av.getColumnSelection().adjustForHiddenColumns(column);
-        }
-
-        if(column > aaMax)
-        {
-            break;
-        }
-
-        if (aa.annotations[column] == null)
-        {
-          x ++;
-          continue;
-        }
+        column = av.getColumnSelection().adjustForHiddenColumns(column);
+      }
 
-          g.setColor(aa.annotations[column].colour);
-          y1 = y - (int) (((aa.annotations[column].value-min) / (range)) * aa.graphHeight);
+      if (column > aaMax)
+      {
+        break;
+      }
 
-          if(y1-y2>0)
-            g.fillRect(x*av.charWidth, y2, av.charWidth, y1-y2 );
-          else
-            g.fillRect(x*av.charWidth, y1, av.charWidth, y2-y1 );
+      if (aa.annotations[column] == null)
+      {
+        x++;
+        continue;
+      }
 
-          x ++ ;
+      g.setColor(aa.annotations[column].colour);
+      y1 = y -
+          (int) ( ( (aa.annotations[column].value - min) / (range)) * aa.graphHeight);
 
+      if (y1 - y2 > 0)
+      {
+        g.fillRect(x * av.charWidth, y2, av.charWidth, y1 - y2);
       }
-      if(aa.threshold!=null)
+      else
       {
-          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));
-
-          y2 = (int)(y - ((aa.threshold.value-min) / range)*aa.graphHeight);
-          g.drawLine(0,y2,(eRes-sRes)*av.charWidth,y2);
-          g2.setStroke(new BasicStroke());
+        g.fillRect(x * av.charWidth, y1, av.charWidth, y2 - y1);
       }
-    }
 
-    // used by overview window
-    public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, int y, int sRes, int eRes)
+      x++;
+
+    }
+    if (aa.threshold != null)
     {
-      eRes = Math.min(eRes, aa.annotations.length);
-      g.setColor(Color.white);
-      g.fillRect(0, 0, width, y);
-      g.setColor(new Color(0, 0, 180));
+      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));
+
+      y2 = (int) (y - ( (aa.threshold.value - min) / range) * aa.graphHeight);
+      g.drawLine(0, y2, (eRes - sRes) * av.charWidth, y2);
+      g2.setStroke(new BasicStroke());
+    }
+  }
 
-      int x = 0, height;
+  // used by overview window
+  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);
+    g.fillRect(0, 0, width, y);
+    g.setColor(new Color(0, 0, 180));
 
-      for (int j = sRes; j < eRes; j++)
-      {
-        if (aa.annotations[j] != null)
-        {
-          g.setColor(aa.annotations[j].colour);
+    int x = 0, height;
 
-          height = (int) ( (aa.annotations[j].value / aa.graphMax) * y);
-          if (height > y)
-            height = y;
+    for (int j = sRes; j < eRes; j++)
+    {
+      if (aa.annotations[j] != null)
+      {
+        g.setColor(aa.annotations[j].colour);
 
-          g.fillRect(x, y - height, av.charWidth, height);
+        height = (int) ( (aa.annotations[j].value / aa.graphMax) * y);
+        if (height > y)
+        {
+          height = y;
         }
-          x += av.charWidth;
+
+        g.fillRect(x, y - height, av.charWidth, height);
       }
+      x += av.charWidth;
     }
+  }
 
 }
diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java
index 4773c26..a3fa7c7 100755
--- a/src/jalview/gui/CutAndPasteTransfer.java
+++ b/src/jalview/gui/CutAndPasteTransfer.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,18 +18,14 @@
  */
 package jalview.gui;
 
-import jalview.datamodel.*;
-
-import jalview.io.*;
-
-import jalview.jbgui.*;
-
 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!
@@ -37,7 +33,8 @@ import javax.swing.*;
  * @author $author$
  * @version $Revision$
  */
-public class CutAndPasteTransfer extends GCutAndPasteTransfer
+public class CutAndPasteTransfer
+    extends GCutAndPasteTransfer
 {
 
   AlignViewport viewport;
@@ -54,208 +51,215 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
 
   }
 
-    /**
-     * DOCUMENT ME!
-     */
-    public void setForInput(AlignViewport viewport)
+  /**
+   * DOCUMENT ME!
+   */
+  public void setForInput(AlignViewport viewport)
+  {
+    this.viewport = viewport;
+    if (viewport != null)
     {
-      this.viewport = viewport;
-      if(viewport!=null)
-        ok.setText("Add");
-
-      getContentPane().add(inputButtonPanel, java.awt.BorderLayout.SOUTH);
+      ok.setText("Add");
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String getText()
-    {
-        return textarea.getText();
-    }
+    getContentPane().add(inputButtonPanel, java.awt.BorderLayout.SOUTH);
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param text DOCUMENT ME!
-     */
-    public void setText(String text)
-    {
-        textarea.setText(text);
-    }
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public String getText()
+  {
+    return textarea.getText();
+  }
 
-    public void appendText(String text)
-    {
-      textarea.append(text);
-    }
+  /**
+   * 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"));
+  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");
+    chooser.setAcceptAllFileFilterUsed(false);
+    chooser.setFileView(new JalviewFileView());
+    chooser.setDialogTitle("Save Text to File");
+    chooser.setToolTipText("Save");
 
-      int value = chooser.showSaveDialog(this);
+    int value = chooser.showSaveDialog(this);
 
-      if (value == JalviewFileChooser.APPROVE_OPTION)
+    if (value == JalviewFileChooser.APPROVE_OPTION)
+    {
+      try
       {
-        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();
-        }
+        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);
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void copyItem_actionPerformed(ActionEvent e)
+    if (contents == null)
     {
-        textarea.getSelectedText();
-        Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
-        c.setContents(new StringSelection(textarea.getSelectedText()), null);
+      return;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void pasteMenu_actionPerformed(ActionEvent e)
+    try
     {
-        Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
-        Transferable contents = c.getContents(this);
+      textarea.append( (String) contents.getTransferData(
+          DataFlavor.stringFlavor));
+    }
+    catch (Exception ex)
+    {
+    }
+  }
 
-        if (contents == null)
+  /**
+   * 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++)
         {
-            return;
+          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
         {
-            textarea.append((String) contents.getTransferData(
-                    DataFlavor.stringFlavor));
+          af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
         }
         catch (Exception ex)
         {
         }
+      }
     }
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void ok_actionPerformed(ActionEvent e)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void cancel_actionPerformed(ActionEvent e)
+  {
+    try
+    {
+      this.setClosed(true);
+    }
+    catch (Exception ex)
     {
-        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)
+  public void textarea_mousePressed(MouseEvent e)
+  {
+    if (SwingUtilities.isRightMouseButton(e))
     {
-        try
+      JPopupMenu popup = new JPopupMenu("Edit");
+      JMenuItem item = new JMenuItem("Copy");
+      item.addActionListener(new ActionListener()
+      {
+        public void actionPerformed(ActionEvent e)
         {
-            this.setClosed(true);
+          copyItem_actionPerformed(e);
         }
-        catch (Exception ex)
+      });
+      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);
 
-    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 58580eb..7f41d3c 100755
--- a/src/jalview/gui/DasSourceBrowser.java
+++ b/src/jalview/gui/DasSourceBrowser.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,22 +18,20 @@
  */
 package jalview.gui;
 
-import jalview.jbgui.*;
-import javax.swing.table.AbstractTableModel;
-import javax.swing.event.*;
-import jalview.util.TableSorter;
-import java.awt.event.*;
-import javax.swing.*;
 import java.util.*;
 
+import java.awt.*;
+import java.awt.event.*;
+import javax.swing.*;
+import javax.swing.event.*;
+import javax.swing.table.*;
 
-import org.biojava.dasobert.dasregistry.DasCoordinateSystem;
-import org.biojava.dasobert.dasregistry.DasSource;
-import org.biojava.dasobert.dasregistry.Das1Source;
-import java.awt.BorderLayout;
+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;
 
@@ -41,23 +39,23 @@ public class DasSourceBrowser extends GDasSourceBrowser
 
   Vector selectedSources;
 
-  public static String DEFAULT_REGISTRY = "http://www.dasregistry.org/das1/sources/";
+  public static String DEFAULT_REGISTRY =
+      "http://www.dasregistry.org/das1/sources/";
 
   boolean loadingDasSources = false;
 
-
   public DasSourceBrowser()
   {
     String registry = jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",
         DEFAULT_REGISTRY);
 
-    if(registry.indexOf("/registry/das1/sources/")>-1)
+    if (registry.indexOf("/registry/das1/sources/") > -1)
     {
       jalview.bin.Cache.setProperty("DAS_REGISTRY_URL", DEFAULT_REGISTRY);
       registry = DEFAULT_REGISTRY;
     }
 
-    registryURL.setText( registry );
+    registryURL.setText(registry);
 
     setSelectedFromProperties();
 
@@ -84,18 +82,20 @@ public class DasSourceBrowser extends GDasSourceBrowser
     });
 
     table.addMouseListener(new MouseAdapter()
+    {
+      public void mouseClicked(MouseEvent evt)
+      {
+        if (evt.getClickCount() == 2
+            || SwingUtilities.isRightMouseButton(evt))
         {
-          public void mouseClicked(MouseEvent evt)
-          {
-            if(evt.getClickCount()==2
-               || SwingUtilities.isRightMouseButton(evt))
-              editRemoveLocalSource(evt);
-          }
-        });
+          editRemoveLocalSource(evt);
+        }
+      }
+    });
 
-    if(dasSources!=null)
+    if (dasSources != null)
     {
-       init();
+      init();
     }
   }
 
@@ -123,14 +123,14 @@ public class DasSourceBrowser extends GDasSourceBrowser
     setCapabilities(dasSources);
 
     javax.swing.SwingUtilities.invokeLater(new Runnable()
-        {
-          public void run()
-          {
-            TableSorter sorter = (TableSorter)table.getModel();
-            sorter.setSortingStatus(1, TableSorter.DESCENDING);
-            sorter.setSortingStatus(1, TableSorter.NOT_SORTED);
-          }
-        });
+    {
+      public void run()
+      {
+        TableSorter sorter = (TableSorter) table.getModel();
+        sorter.setSortingStatus(1, TableSorter.DESCENDING);
+        sorter.setSortingStatus(1, TableSorter.NOT_SORTED);
+      }
+    });
 
     progressBar.setIndeterminate(false);
     progressBar.setVisible(false);
@@ -138,7 +138,6 @@ public class DasSourceBrowser extends GDasSourceBrowser
     refresh.setVisible(true);
   }
 
-
   public void refreshTableData(Object[][] data)
   {
     TableSorter sorter = new TableSorter(new DASTableModel(data));
@@ -164,7 +163,9 @@ public class DasSourceBrowser extends GDasSourceBrowser
     for (int i = 0; i < dSize; i++)
     {
       if (!dasSources[i].getNickname().equals(nickName))
+      {
         continue;
+      }
 
       DasSource ds = dasSources[i];
 
@@ -175,37 +176,41 @@ public class DasSourceBrowser extends GDasSourceBrowser
       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++)
+      for (int s = 0; s < dasSources[i].getLabels().length; s++)
       {
-        text.append( dasSources[i].getLabels()[s]);
-        if(s<dasSources[i].getLabels().length-1)
+        text.append(dasSources[i].getLabels()[s]);
+        if (s < dasSources[i].getLabels().length - 1)
+        {
           text.append(",");
+        }
         text.append(" ");
       }
       text.append("<br>");
 
-
-
       text.append("<font color=\"#0000FF\">Capabilities:</font> ");
       String[] scap = dasSources[i].getCapabilities();
       for (int j = 0; j < scap.length; j++)
       {
         text.append(scap[j]);
         if (j < scap.length - 1)
+        {
           text.append(", ");
+        }
       }
       text.append("<br>");
 
@@ -216,9 +221,13 @@ public class DasSourceBrowser extends GDasSourceBrowser
         text.append("(" + dcs[j].getUniqueId() + ") "
                     + dcs[j].getCategory() + ", " + dcs[j].getName());
         if (dcs[j].getNCBITaxId() != 0)
+        {
           text.append(", " + dcs[j].getNCBITaxId());
+        }
         if (dcs[j].getOrganismName().length() > 0)
+        {
           text.append(", " + dcs[j].getOrganismName());
+        }
 
         text.append("<br>");
       }
@@ -226,8 +235,7 @@ public class DasSourceBrowser extends GDasSourceBrowser
       text.append("<font color=\"#0000FF\">Description:</font> " +
                   dasSources[i].getDescription() + "<br>");
 
-
-      if (dasSources[i].getHelperurl()!=null
+      if (dasSources[i].getHelperurl() != null
           && dasSources[i].getHelperurl().length() > 0)
       {
         text.append("<font color=\"#0000FF\"><a href=\"" +
@@ -250,7 +258,6 @@ public class DasSourceBrowser extends GDasSourceBrowser
     });
   }
 
-
   public void run()
   {
     loadingDasSources = true;
@@ -275,15 +282,15 @@ public class DasSourceBrowser extends GDasSourceBrowser
     Vector selected = new Vector();
     for (int r = 0; r < selectedSources.size(); r++)
     {
-        for (int i = 0; i < dasSources.length; i++)
+      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;
-          }
+          selected.addElement(dasSources[i]);
+          break;
         }
+      }
     }
 
     return selected;
@@ -291,10 +298,10 @@ public class DasSourceBrowser extends GDasSourceBrowser
 
   public DasSource[] getDASSource()
   {
-    if(dasSources==null)
+    if (dasSources == null)
     {
-     dasSources = jalview.io.DasSequenceFeatureFetcher.getDASSources();
-     appendLocalSources();
+      dasSources = jalview.io.DasSequenceFeatureFetcher.getDASSources();
+      appendLocalSources();
     }
 
     return dasSources;
@@ -327,10 +334,14 @@ public class DasSourceBrowser extends GDasSourceBrowser
       for (int j = 0; j < dcs.length; j++)
       {
         if (!type.contains(dcs[j].getCategory()))
+        {
           type.addElement(dcs[j].getCategory());
+        }
 
         if (!authority.contains(dcs[j].getName()))
+        {
           authority.addElement(dcs[j].getName());
+        }
       }
 
       String[] slabels = ds.getLabels();
@@ -363,11 +374,11 @@ public class DasSourceBrowser extends GDasSourceBrowser
   {
     String url = "http://localhost:8080/", nickname = "";
 
-    if(!newSource)
+    if (!newSource)
     {
       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);
@@ -383,209 +394,220 @@ public class DasSourceBrowser extends GDasSourceBrowser
     pane12.add(urltf, BorderLayout.EAST);
     panel.add(pane12, BorderLayout.SOUTH);
 
-
     int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
         panel, "Enter Nickname & URL of Local DAS Source",
         JOptionPane.OK_CANCEL_OPTION);
 
-       if (reply != JOptionPane.OK_OPTION )
-       {
-           return;
-       }
-
-       if(!urltf.getText().endsWith("/"))
-         urltf.setText(urltf.getText()+"/");
-
-       Das1Source local = new Das1Source();
-
-       local.setUrl(urltf.getText());
-       local.setNickname(nametf.getText());
+    if (reply != JOptionPane.OK_OPTION)
+    {
+      return;
+    }
 
+    if (!urltf.getText().endsWith("/"))
+    {
+      urltf.setText(urltf.getText() + "/");
+    }
 
-       if(localSources==null)
-         localSources = new Hashtable();
+    Das1Source local = new Das1Source();
 
-       localSources.put(local.getNickname(), local);
+    local.setUrl(urltf.getText());
+    local.setNickname(nametf.getText());
 
-       if(!newSource && !nickname.equals(nametf.getText()))
-       {
-         localSources.remove(nickname);
-       }
+    if (localSources == null)
+    {
+      localSources = new Hashtable();
+    }
 
-       int size = dasSources.length;
-       int adjust = newSource ? 1 : 0;
+    localSources.put(local.getNickname(), local);
 
-       Object[][] data = new Object[size+adjust][2];
-       for (int i = 0; i < size; i++)
-       {
-         if(!newSource && dasSources[i].getNickname().equals(nickname))
-         {
-           ((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()));
-         }
-       }
+    if (!newSource && !nickname.equals(nametf.getText()))
+    {
+      localSources.remove(nickname);
+    }
 
-       if(newSource)
-       {
-         data[size][0] = local.getNickname();
-         data[size][1] = new Boolean(true);
-         selectedSources.add(local.getNickname());
-       }
+    int size = dasSources.length;
+    int adjust = newSource ? 1 : 0;
 
-       DasSource [] tmp = new DasSource[size+adjust];
+    Object[][] data = new Object[size + adjust][2];
+    for (int i = 0; i < size; i++)
+    {
+      if (!newSource && dasSources[i].getNickname().equals(nickname))
+      {
+        ( (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()));
+      }
+    }
 
-       System.arraycopy(dasSources, 0, tmp, 0, size);
+    if (newSource)
+    {
+      data[size][0] = local.getNickname();
+      data[size][1] = new Boolean(true);
+      selectedSources.add(local.getNickname());
+    }
 
-       if(newSource)
-         tmp[size] = local;
+    DasSource[] tmp = new DasSource[size + adjust];
 
-       dasSources = tmp;
+    System.arraycopy(dasSources, 0, tmp, 0, size);
 
-       refreshTableData(data);
+    if (newSource)
+    {
+      tmp[size] = local;
+    }
 
-       SwingUtilities.invokeLater(new Runnable()
-       {
-         public void run()
-         {
-           scrollPane.getVerticalScrollBar().setValue(
-               scrollPane.getVerticalScrollBar().getMaximum()
-               );
-         }
-       });
+    dasSources = tmp;
 
-       displayFullDetails(local.getNickname());
-     }
+    refreshTableData(data);
 
-    public void editRemoveLocalSource(MouseEvent evt)
+    SwingUtilities.invokeLater(new Runnable()
     {
-      int selectedRow = table.getSelectionModel().getMinSelectionIndex();
-      if(selectedRow==-1)
-        return;
-
-      String nickname = table.getValueAt(selectedRow, 0).toString();
-
-      if (!localSources.containsKey(nickname))
+      public void run()
       {
-        JOptionPane.showInternalMessageDialog(Desktop.desktop,
-        "You can only edit or remove local DAS Sources!",
-         "Public DAS source - not editable",
-         JOptionPane.WARNING_MESSAGE);
-        return;
+        scrollPane.getVerticalScrollBar().setValue(
+            scrollPane.getVerticalScrollBar().getMaximum()
+            );
       }
+    });
 
+    displayFullDetails(local.getNickname());
+  }
 
-      Object[] options = {"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]);
+  public void editRemoveLocalSource(MouseEvent evt)
+  {
+    int selectedRow = table.getSelectionModel().getMinSelectionIndex();
+    if (selectedRow == -1)
+    {
+      return;
+    }
 
-      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++)
+    String nickname = table.getValueAt(selectedRow, 0).toString();
+
+    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);
+      return;
+    }
+
+    Object[] options =
+        {
+        "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]);
+
+    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++)
+        {
+          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()
-           {
-             public void run()
-             {
-               scrollPane.getVerticalScrollBar().setValue(
-                   scrollPane.getVerticalScrollBar().getMaximum()
-                   );
-             }
-           });
+        }
+        dasSources = tmp;
+        refreshTableData(data);
+        SwingUtilities.invokeLater(new Runnable()
+        {
+          public void run()
+          {
+            scrollPane.getVerticalScrollBar().setValue(
+                scrollPane.getVerticalScrollBar().getMaximum()
+                );
+          }
+        });
 
-          break;
-      }
+        break;
     }
+  }
 
-    void appendLocalSources()
+  void appendLocalSources()
+  {
+    if (localSources == null)
     {
-      if(localSources==null)
-        return;
+      return;
+    }
 
-      int size = dasSources!=null ? dasSources.length : 0;
-      int lsize = localSources.size();
+    int size = dasSources != null ? dasSources.length : 0;
+    int lsize = localSources.size();
 
-      Object[][] data = new Object[size+lsize][2];
-      for (int i = 0; i < size; i++)
-      {
-        data[i][0] = dasSources[i].getNickname();
-        data[i][1] = new Boolean(selectedSources.contains(dasSources[i].
-            getNickname()));
-      }
+    Object[][] data = new Object[size + lsize][2];
+    for (int i = 0; i < size; i++)
+    {
+      data[i][0] = dasSources[i].getNickname();
+      data[i][1] = new Boolean(selectedSources.contains(dasSources[i].
+          getNickname()));
+    }
 
-      DasSource [] tmp = new DasSource[size+lsize];
-      if(dasSources!=null)
-        System.arraycopy(dasSources, 0, tmp, 0, size);
+    DasSource[] tmp = new DasSource[size + lsize];
+    if (dasSources != null)
+    {
+      System.arraycopy(dasSources, 0, tmp, 0, size);
+    }
 
-      Enumeration en = localSources.keys();
-      int index = size;
-      while(en.hasMoreElements())
-      {
-        String key = en.nextElement().toString();
-        data[index][0] = key;
-        data[index][1] = new Boolean(false);
-        tmp[index] = new Das1Source();
-        tmp[index].setNickname(key);
-        tmp[index].setUrl( ((DasSource)localSources.get(key)).getUrl() );
-
-        index++;
-      }
+    Enumeration en = localSources.keys();
+    int index = size;
+    while (en.hasMoreElements())
+    {
+      String key = en.nextElement().toString();
+      data[index][0] = key;
+      data[index][1] = new Boolean(false);
+      tmp[index] = new Das1Source();
+      tmp[index].setNickname(key);
+      tmp[index].setUrl( ( (DasSource) localSources.get(key)).getUrl());
+
+      index++;
+    }
 
-      dasSources = tmp;
+    dasSources = tmp;
 
-      refreshTableData(data);
+    refreshTableData(data);
   }
 
   public void valueChanged(ListSelectionEvent evt)
   {
     //Called when the MainTable selection changes
-    if (evt.getValueIsAdjusting() )
+    if (evt.getValueIsAdjusting())
     {
       return;
     }
 
-
     displayFullDetails(null);
 
     // Filter the displayed data sources
     int dSize = dasSources.length;
 
-
     ArrayList names = new ArrayList();
     ArrayList selected = new ArrayList();
     DasSource ds;
@@ -593,7 +615,9 @@ public class DasSourceBrowser extends GDasSourceBrowser
     //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"};
+    Object[] dummyFeatureList = new Object[]
+        {
+        "features"};
 
     for (int i = 0; i < dSize; i++)
     {
@@ -610,21 +634,20 @@ public class DasSourceBrowser extends GDasSourceBrowser
         //IS ADDED FROM THE REGISTRY
         names.add(ds.getNickname());
         selected.add(new Boolean(
-              selectedSources.contains(ds.getNickname())));
+            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(),
+        if (selectedInList(filter1.getSelectedValues(),
                            new String[]
                            {dcs[j].getName()})
             && selectedInList(filter2.getSelectedValues(),
@@ -650,17 +673,21 @@ public class DasSourceBrowser extends GDasSourceBrowser
     refreshTableData(data);
   }
 
-  boolean selectedInList(Object [] selection, String[] items)
+  boolean selectedInList(Object[] selection, String[] items)
   {
     for (int i = 0; i < selection.length; i++)
     {
-      if (selection[i].equals("Any") )
+      if (selection[i].equals("Any"))
+      {
         return true;
+      }
 
       for (int j = 0; j < items.length; j++)
       {
         if (selection[i].equals(items[j]))
+        {
           return true;
+        }
       }
     }
 
@@ -669,33 +696,35 @@ public class DasSourceBrowser extends GDasSourceBrowser
 
   void setSelectedFromProperties()
   {
-     String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE", "uniprot");
-     StringTokenizer st = new StringTokenizer(active, "\t");
-     selectedSources = new Vector();
-     while(st.hasMoreTokens())
-     {
-       selectedSources.addElement(st.nextToken());
-     }
-
-     String local = jalview.bin.Cache.getProperty("DAS_LOCAL_SOURCE");
-     if(local!=null)
-     {
-       if(localSources == null)
-         localSources = new Hashtable();
-
-       st = new StringTokenizer(local, "\t");
-       while(st.hasMoreTokens())
-       {
-         String token = st.nextToken();
-         int bar = token.indexOf("|");
-         Das1Source source = new Das1Source();
-
-         source.setUrl(token.substring(bar + 1));
-         source.setNickname(token.substring(0, bar));
-
-         localSources.put(source.getNickname(), source);
-       }
-     }
+    String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE", "uniprot");
+    StringTokenizer st = new StringTokenizer(active, "\t");
+    selectedSources = new Vector();
+    while (st.hasMoreTokens())
+    {
+      selectedSources.addElement(st.nextToken());
+    }
+
+    String local = jalview.bin.Cache.getProperty("DAS_LOCAL_SOURCE");
+    if (local != null)
+    {
+      if (localSources == null)
+      {
+        localSources = new Hashtable();
+      }
+
+      st = new StringTokenizer(local, "\t");
+      while (st.hasMoreTokens())
+      {
+        String token = st.nextToken();
+        int bar = token.indexOf("|");
+        Das1Source source = new Das1Source();
+
+        source.setUrl(token.substring(bar + 1));
+        source.setNickname(token.substring(0, bar));
+
+        localSources.put(source.getNickname(), source);
+      }
+    }
   }
 
   public void reset_actionPerformed(ActionEvent e)
@@ -706,31 +735,35 @@ public class DasSourceBrowser extends GDasSourceBrowser
   public void saveProperties(Properties properties)
   {
     if (registryURL.getText() == null || registryURL.getText().length() < 1)
+    {
       properties.remove("DAS_REGISTRY_URL");
+    }
     else
+    {
       properties.setProperty("DAS_REGISTRY_URL", registryURL.getText());
+    }
 
     StringBuffer sb = new StringBuffer();
-    for(int r=0; r<table.getModel().getRowCount(); r++)
+    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");
+        sb.append(table.getValueAt(r, 0) + "\t");
       }
     }
 
-    properties.setProperty("DAS_ACTIVE_SOURCE", sb.toString() );
+    properties.setProperty("DAS_ACTIVE_SOURCE", sb.toString());
 
-    if(localSources!=null)
+    if (localSources != null)
     {
       sb = new StringBuffer();
       Enumeration en = localSources.keys();
-      while(en.hasMoreElements())
+      while (en.hasMoreElements())
       {
         String token = en.nextElement().toString();
-        sb.append(token+"|"
-                  + ((DasSource)localSources.get(token)).getUrl()
-                  +"\t");
+        sb.append(token + "|"
+                  + ( (DasSource) localSources.get(token)).getUrl()
+                  + "\t");
       }
 
       properties.setProperty("DAS_LOCAL_SOURCE", sb.toString());
@@ -747,7 +780,9 @@ public class DasSourceBrowser extends GDasSourceBrowser
       this.data = data;
     }
 
-    private String[] columnNames = new String[]  {"Nickname", "Use Source"};
+    private String[] columnNames = new String[]
+        {
+        "Nickname", "Use Source"};
 
     private Object[][] data;
 
@@ -803,16 +838,18 @@ public class DasSourceBrowser extends GDasSourceBrowser
       data[row][col] = value;
       fireTableCellUpdated(row, col);
 
-      String name = getValueAt(row,0).toString();
-      boolean selected = ((Boolean)value).booleanValue();
+      String name = getValueAt(row, 0).toString();
+      boolean selected = ( (Boolean) value).booleanValue();
 
-      if(selectedSources.contains(name) && !selected)
+      if (selectedSources.contains(name) && !selected)
+      {
         selectedSources.remove(name);
+      }
 
-      if(!selectedSources.contains(name) && selected)
+      if (!selectedSources.contains(name) && selected)
+      {
         selectedSources.add(name);
+      }
     }
   }
 }
-
-
diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 6d8f125..e5f288a 100755
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -27,670 +27,720 @@ import java.util.*;
 
 import javax.swing.*;
 
-
 /**
  * DOCUMENT ME!
  *
  * @author $author$
  * @version $Revision$
  */
-public class Desktop extends jalview.jbgui.GDesktop
-    implements DropTargetListener, ClipboardOwner
+public class Desktop
+    extends jalview.jbgui.GDesktop implements DropTargetListener,
+    ClipboardOwner
 {
-    /** DOCUMENT ME!! */
-    public static Desktop instance;
-    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;
-
-    /**
-     * Creates a new Desktop object.
-     */
-    public Desktop()
+  /** DOCUMENT ME!! */
+  public static Desktop instance;
+  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;
+
+  /**
+   * Creates a new Desktop object.
+   */
+  public Desktop()
+  {
+    instance = this;
+    doVamsasClientCheck();
+    Image image = null;
+
+    try
     {
-        instance = this;
-        doVamsasClientCheck();
-        Image image = null;
+      java.net.URL url = getClass().getResource("/images/logo.gif");
 
-        try
-        {
-            java.net.URL url = getClass().getResource("/images/logo.gif");
-
-            if (url != null)
-            {
-                image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
+      if (url != null)
+      {
+        image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
 
-                MediaTracker mt = new MediaTracker(this);
-                mt.addImage(image, 0);
-                mt.waitForID(0);
-                setIconImage(image);
-            }
-        }
-        catch (Exception ex)
-        {
-        }
+        MediaTracker mt = new MediaTracker(this);
+        mt.addImage(image, 0);
+        mt.waitForID(0);
+        setIconImage(image);
+      }
+    }
+    catch (Exception ex)
+    {
+    }
 
-        setTitle("Jalview "+jalview.bin.Cache.getProperty("VERSION"));
-        setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
-        desktop = new JDesktopPane();
-        desktop.setBackground(Color.white);
-        getContentPane().setLayout(new BorderLayout());
-        getContentPane().add(desktop, BorderLayout.CENTER);
-        desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);
-
-        // This line prevents Windows Look&Feel resizing all new windows to maximum
-        // if previous window was maximised
-        desktop.setDesktopManager(new DefaultDesktopManager());
-
-        Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
-        String x = jalview.bin.Cache.getProperty("SCREEN_X");
-        String y = jalview.bin.Cache.getProperty("SCREEN_Y");
-        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))
-        {
-            setBounds(Integer.parseInt(x), Integer.parseInt(y),
+    setTitle("Jalview " + jalview.bin.Cache.getProperty("VERSION"));
+    setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
+    desktop = new JDesktopPane();
+    desktop.setBackground(Color.white);
+    getContentPane().setLayout(new BorderLayout());
+    getContentPane().add(desktop, BorderLayout.CENTER);
+    desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);
+
+    // This line prevents Windows Look&Feel resizing all new windows to maximum
+    // if previous window was maximised
+    desktop.setDesktopManager(new DefaultDesktopManager());
+
+    Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
+    String x = jalview.bin.Cache.getProperty("SCREEN_X");
+    String y = jalview.bin.Cache.getProperty("SCREEN_Y");
+    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))
+    {
+      setBounds(Integer.parseInt(x), Integer.parseInt(y),
                 Integer.parseInt(width), Integer.parseInt(height));
-        }
-        else
-        {
-            setBounds((int) (screenSize.width - 900) / 2,
+    }
+    else
+    {
+      setBounds( (int) (screenSize.width - 900) / 2,
                 (int) (screenSize.height - 650) / 2, 900, 650);
-        }
-
-        this.addWindowListener(new WindowAdapter()
-            {
-                public void windowClosing(WindowEvent evt)
-                {
-                    quit();
-                }
-            });
+    }
 
-        this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
+    this.addWindowListener(new WindowAdapter()
+    {
+      public void windowClosing(WindowEvent evt)
+      {
+        quit();
+      }
+    });
 
-        /////////Add a splashscreen on startup
-        /////////Add a splashscreen on startup
-        JInternalFrame frame = new JInternalFrame();
+    this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
 
-        SplashScreen splash = new SplashScreen(frame, image);
-        frame.setContentPane(splash);
-        frame.setLayer(JLayeredPane.PALETTE_LAYER);
-        frame.setLocation((int) ((getWidth() - 750) / 2),
-            (int) ((getHeight() - 160) / 2));
+    /////////Add a splashscreen on startup
+    /////////Add a splashscreen on startup
+    JInternalFrame frame = new JInternalFrame();
 
-        addInternalFrame(frame, "", 750, 160, false);
+    SplashScreen splash = new SplashScreen(frame, image);
+    frame.setContentPane(splash);
+    frame.setLayer(JLayeredPane.PALETTE_LAYER);
+    frame.setLocation( (int) ( (getWidth() - 750) / 2),
+                      (int) ( (getHeight() - 160) / 2));
 
-        discoverer=new jalview.ws.Discoverer(); // Only gets started if gui is displayed.
-    }
+    addInternalFrame(frame, "", 750, 160, false);
 
-    private void doVamsasClientCheck() {
-      if (jalview.bin.Cache.vamsasJarsPresent()) {
-        VamsasMenu.setVisible(true);
-        vamsasLoad.setVisible(true);
-      }
+    discoverer = new jalview.ws.Discoverer(); // Only gets started if gui is displayed.
+  }
 
+  private void doVamsasClientCheck()
+  {
+    if (jalview.bin.Cache.vamsasJarsPresent())
+    {
+      VamsasMenu.setVisible(true);
+      vamsasLoad.setVisible(true);
     }
 
-    /**
-     * 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)
+  }
+
+  /**
+   * 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)
+  {
+    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!
+   */
+  public static synchronized void addInternalFrame(final JInternalFrame frame,
+      String title, int w, int h, boolean resizable)
+  {
+
+    frame.setTitle(title);
+    if (frame.getWidth() < 1 || frame.getHeight() < 1)
     {
-        addInternalFrame(frame, title, w, h, true);
+      frame.setSize(w, h);
     }
+    // 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"))
+    {
+      return;
+    }
+
+    openFrameCount++;
+
+    frame.setVisible(true);
+    frame.setClosable(true);
+    frame.setResizable(resizable);
+    frame.setMaximizable(resizable);
+    frame.setIconifiable(resizable);
+    frame.setFrameIcon(null);
 
-    /**
-     * 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)
+    if (frame.getX() < 1 && frame.getY() < 1)
     {
+      frame.setLocation(xOffset * openFrameCount,
+                        yOffset * ( (openFrameCount - 1) % 10) + yOffset);
+    }
 
-      frame.setTitle(title);
-      if(frame.getWidth()<1 || frame.getHeight()<1)
+    final JMenuItem menuItem = new JMenuItem(title);
+    frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+    {
+      public void internalFrameActivated(javax.swing.event.
+                                         InternalFrameEvent evt)
       {
-        frame.setSize(w, h);
+        JInternalFrame itf = desktop.getSelectedFrame();
+        if (itf != null)
+        {
+          itf.requestFocus();
+        }
+
       }
-      // 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"))
+
+      public void internalFrameClosed(
+          javax.swing.event.InternalFrameEvent evt)
       {
-        return;
+        PaintRefresher.RemoveComponent(frame);
+        openFrameCount--;
+        windowMenu.remove(menuItem);
+        JInternalFrame itf = desktop.getSelectedFrame();
+        if (itf != null)
+        {
+          itf.requestFocus();
+        }
       }
+      ;
+    });
 
+    menuItem.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        try
+        {
+          frame.setSelected(true);
+          frame.setIcon(false);
+        }
+        catch (java.beans.PropertyVetoException ex)
+        {
 
-        openFrameCount++;
-
-        frame.setVisible(true);
-        frame.setClosable(true);
-        frame.setResizable(resizable);
-        frame.setMaximizable(resizable);
-        frame.setIconifiable(resizable);
-        frame.setFrameIcon(null);
-
-        if (frame.getX()<1 && frame.getY()<1)
-       {
-         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();
-
-              }
+        }
+      }
+    });
 
+    windowMenu.add(menuItem);
 
-                public void internalFrameClosed(
-                    javax.swing.event.InternalFrameEvent evt)
-                {
-                    PaintRefresher.RemoveComponent(frame);
-                    openFrameCount--;
-                    windowMenu.remove(menuItem);
-                    JInternalFrame itf = desktop.getSelectedFrame();
-                       if (itf != null)
-                        itf.requestFocus();
-                }
-                ;
-            });
-
-        menuItem.addActionListener(new ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    try
-                    {
-                        frame.setSelected(true);
-                        frame.setIcon(false);
-                    }
-                    catch (java.beans.PropertyVetoException ex)
-                    {
-
-                    }
-                }
-            });
-
-        windowMenu.add(menuItem);
-
-        desktop.add(frame);
-        frame.toFront();
-        try{
-          frame.setSelected(true);
-          frame.requestFocus();
-        }catch(java.beans.PropertyVetoException ve)
-        {   }
+    desktop.add(frame);
+    frame.toFront();
+    try
+    {
+      frame.setSelected(true);
+      frame.requestFocus();
     }
+    catch (java.beans.PropertyVetoException ve)
+    {}
+  }
 
-    public void lostOwnership(Clipboard clipboard, Transferable contents)
+  public void lostOwnership(Clipboard clipboard, Transferable contents)
+  {
+    if (!internalCopy)
     {
-      if (!internalCopy)
-        Desktop.jalviewClipboard = null;
-
-      internalCopy = false;
+      Desktop.jalviewClipboard = null;
     }
 
-    public void dragEnter(DropTargetDragEvent evt)
-    {}
+    internalCopy = false;
+  }
 
-    public void dragExit(DropTargetEvent evt)
-    {}
+  public void dragEnter(DropTargetDragEvent evt)
+  {}
 
-    public void dragOver(DropTargetDragEvent evt)
-    {}
+  public void dragExit(DropTargetEvent evt)
+  {}
 
-    public void dropActionChanged(DropTargetDragEvent evt)
-    {}
+  public void dragOver(DropTargetDragEvent evt)
+  {}
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void drop(DropTargetDropEvent evt)
-    {
-        Transferable t = evt.getTransferable();
-        java.util.List files = null;
+  public void dropActionChanged(DropTargetDragEvent evt)
+  {}
 
-        try
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  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");
+      if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
+      {
+        //Works on Windows and MacOSX
+        evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
+        files = (java.util.List) t.getTransferData(DataFlavor.
+            javaFileListFlavor);
+      }
+      else if (t.isDataFlavorSupported(uriListFlavor))
+      {
+        // This is used by Unix drag system
+        evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
+        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(); )
         {
-          DataFlavor uriListFlavor = new DataFlavor("text/uri-list;class=java.lang.String");
-          if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
+          String s = st.nextToken();
+          if (s.startsWith("#"))
           {
-            //Works on Windows and MacOSX
-            evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
-            files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);
+            // the line is a comment (as per the RFC 2483)
+            continue;
           }
-          else if (t.isDataFlavorSupported(uriListFlavor))
-          {
-            // This is used by Unix drag system
-            evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
-            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(); )
-            {
-              String s = st.nextToken();
-              if (s.startsWith("#"))
-              {
-                // the line is a comment (as per the RFC 2483)
-                continue;
-              }
 
-              java.net.URI uri = new java.net.URI(s);
-              java.io.File file = new java.io.File(uri);
-              files.add(file);
-            }
-          }
+          java.net.URI uri = new java.net.URI(s);
+          java.io.File file = new java.io.File(uri);
+          files.add(file);
         }
-        catch (Exception e)
-        {      }
+      }
+    }
+    catch (Exception e)
+    {}
 
-        if (files != null)
+    if (files != null)
+    {
+      try
+      {
+        for (int i = 0; i < files.size(); i++)
         {
-          try
-          {
-            for (int i = 0; i < files.size(); i++)
-            {
-              String file = files.get(i).toString();
-              String protocol = FormatAdapter.FILE;
-              String format = null;
-
-              if (file.endsWith(".jar"))
-              {
-                format = "Jalview";
+          String file = files.get(i).toString();
+          String protocol = FormatAdapter.FILE;
+          String format = null;
 
-              }
-              else
-              {
-                format = new IdentifyFile().Identify(file,
-                                                          protocol);
-              }
-
-
-              new FileLoader().LoadFile(file, protocol, format);
+          if (file.endsWith(".jar"))
+          {
+            format = "Jalview";
 
-            }
           }
-          catch (Exception ex)
-          {      }
-        }
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport)
-    {
-        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("Open local file");
-        chooser.setToolTipText("Open");
-
-        int value = chooser.showOpenDialog(this);
-
-        if (value == JalviewFileChooser.APPROVE_OPTION)
-        {
-            String choice = chooser.getSelectedFile().getPath();
-            jalview.bin.Cache.setProperty("LAST_DIRECTORY",
-                chooser.getSelectedFile().getParent());
+          else
+          {
+            format = new IdentifyFile().Identify(file,
+                                                 protocol);
+          }
 
-            String format = null;
-            if (chooser.getSelectedFormat().equals("Jalview"))
-            {
-                format = "Jalview";
-            }
-            else
-            {
-                format = new IdentifyFile().Identify(choice, FormatAdapter.FILE);
-            }
+          new FileLoader().LoadFile(file, protocol, format);
 
-            if (viewport != null)
-              new FileLoader().LoadFile(viewport, choice, FormatAdapter.FILE, format);
-            else
-              new FileLoader().LoadFile(choice, FormatAdapter.FILE, format);
         }
+      }
+      catch (Exception ex)
+      {}
     }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport)
+  {
+    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("Open local file");
+    chooser.setToolTipText("Open");
 
+    int value = chooser.showOpenDialog(this);
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void inputURLMenuItem_actionPerformed(AlignViewport viewport)
+    if (value == JalviewFileChooser.APPROVE_OPTION)
     {
-      // This construct allows us to have a wider textfield
-      // for viewing
-      JLabel label = new JLabel("Enter URL of Input File");
-      final JComboBox history = new JComboBox();
+      String choice = chooser.getSelectedFile().getPath();
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+                                    chooser.getSelectedFile().getParent());
 
-      JPanel panel = new JPanel(new GridLayout(2,1));
-      panel.add(label);
-      panel.add(history);
-      history.setPreferredSize(new Dimension(400,20));
-      history.setEditable(true);
-      history.addItem("http://www.");
-
-      String historyItems = jalview.bin.Cache.getProperty("RECENT_URL");
-
-      StringTokenizer st;
-
-      if (historyItems != null)
+      String format = null;
+      if (chooser.getSelectedFormat().equals("Jalview"))
       {
-        st = new StringTokenizer(historyItems, "\t");
-
-        while (st.hasMoreTokens())
-        {
-          history.addItem(st.nextElement());
-        }
+        format = "Jalview";
+      }
+      else
+      {
+        format = new IdentifyFile().Identify(choice, FormatAdapter.FILE);
       }
 
-       int reply = JOptionPane.showInternalConfirmDialog(desktop,
-          panel, "Input Alignment From URL",
-          JOptionPane.OK_CANCEL_OPTION );
-
-
-        if (reply != JOptionPane.OK_OPTION )
-        {
-            return;
-        }
-
-        String url = history.getSelectedItem().toString();
-
-        if (url.toLowerCase().endsWith(".jar"))
-        {
-          if (viewport != null)
-            new FileLoader().LoadFile(viewport, url, FormatAdapter.URL, "Jalview");
-          else
-            new FileLoader().LoadFile(url, FormatAdapter.URL, "Jalview");
-        }
-        else
-        {
-          String format = new IdentifyFile().Identify(url, FormatAdapter.URL);
-
-          if (format.equals("URL NOT FOUND"))
-          {
-            JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                                                  "Couldn't locate " + url,
-                                                  "URL not found",
-                                                  JOptionPane.WARNING_MESSAGE);
-
-            return;
-          }
+      if (viewport != null)
+      {
+        new FileLoader().LoadFile(viewport, choice, FormatAdapter.FILE, format);
+      }
+      else
+      {
+        new FileLoader().LoadFile(choice, FormatAdapter.FILE, format);
+      }
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void inputURLMenuItem_actionPerformed(AlignViewport viewport)
+  {
+    // This construct allows us to have a wider textfield
+    // for viewing
+    JLabel label = new JLabel("Enter URL of Input File");
+    final JComboBox history = new JComboBox();
+
+    JPanel panel = new JPanel(new GridLayout(2, 1));
+    panel.add(label);
+    panel.add(history);
+    history.setPreferredSize(new Dimension(400, 20));
+    history.setEditable(true);
+    history.addItem("http://www.");
+
+    String historyItems = jalview.bin.Cache.getProperty("RECENT_URL");
+
+    StringTokenizer st;
+
+    if (historyItems != null)
+    {
+      st = new StringTokenizer(historyItems, "\t");
 
-          if (viewport != null)
-            new FileLoader().LoadFile(viewport, url, FormatAdapter.URL, format);
-          else
-            new FileLoader().LoadFile(url, FormatAdapter.URL, format);
-        }
+      while (st.hasMoreTokens())
+      {
+        history.addItem(st.nextElement());
+      }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void inputTextboxMenuItem_actionPerformed(AlignViewport viewport)
+    int reply = JOptionPane.showInternalConfirmDialog(desktop,
+        panel, "Input Alignment From URL",
+        JOptionPane.OK_CANCEL_OPTION);
+
+    if (reply != JOptionPane.OK_OPTION)
     {
-        CutAndPasteTransfer cap = new CutAndPasteTransfer();
-        cap.setForInput(viewport);
-        Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500);
+      return;
     }
 
-    /*
-     * Exit the program
-     */
-    public void quit()
+    String url = history.getSelectedItem().toString();
+
+    if (url.toLowerCase().endsWith(".jar"))
     {
-        jalview.bin.Cache.setProperty("SCREEN_X", getBounds().x + "");
-        jalview.bin.Cache.setProperty("SCREEN_Y", getBounds().y + "");
-        jalview.bin.Cache.setProperty("SCREEN_WIDTH", getWidth() + "");
-        jalview.bin.Cache.setProperty("SCREEN_HEIGHT", getHeight() + "");
-        System.exit(0);
+      if (viewport != null)
+      {
+        new FileLoader().LoadFile(viewport, url, FormatAdapter.URL, "Jalview");
+      }
+      else
+      {
+        new FileLoader().LoadFile(url, FormatAdapter.URL, "Jalview");
+      }
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void aboutMenuItem_actionPerformed(ActionEvent e)
+    else
     {
-      StringBuffer message = new StringBuffer("JalView version " +
-                                              jalview.bin.Cache.getProperty(
-          "VERSION") +
-                                              "; last updated: " +
-                                              jalview.bin.
-                                              Cache.getDefault("BUILD_DATE", "unknown"));
+      String format = new IdentifyFile().Identify(url, FormatAdapter.URL);
 
-      if (!jalview.bin.Cache.getProperty("LATEST_VERSION").equals(
-          jalview.bin.Cache.getProperty("VERSION")))
+      if (format.equals("URL NOT FOUND"))
       {
-        message.append("\n\n!! Jalview version "
-                       + jalview.bin.Cache.getProperty("LATEST_VERSION")
-                       + " is available for download from http://www.jalview.org !!\n");
+        JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                                              "Couldn't locate " + url,
+                                              "URL not found",
+                                              JOptionPane.WARNING_MESSAGE);
 
+        return;
       }
 
-      message.append( "\nAuthors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton." +
-            "\nCurrent development managed by Andrew Waterhouse; Barton Group, University of Dundee." +
-            "\nFor all issues relating to Jalview, email help@jalview.org" +
-            "\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,
+      if (viewport != null)
+      {
+        new FileLoader().LoadFile(viewport, url, FormatAdapter.URL, format);
+      }
+      else
+      {
+        new FileLoader().LoadFile(url, FormatAdapter.URL, format);
+      }
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void inputTextboxMenuItem_actionPerformed(AlignViewport viewport)
+  {
+    CutAndPasteTransfer cap = new CutAndPasteTransfer();
+    cap.setForInput(viewport);
+    Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500);
+  }
+
+  /*
+   * Exit the program
+   */
+  public void quit()
+  {
+    jalview.bin.Cache.setProperty("SCREEN_X", getBounds().x + "");
+    jalview.bin.Cache.setProperty("SCREEN_Y", getBounds().y + "");
+    jalview.bin.Cache.setProperty("SCREEN_WIDTH", getWidth() + "");
+    jalview.bin.Cache.setProperty("SCREEN_HEIGHT", getHeight() + "");
+    System.exit(0);
+  }
+
+  /**
+   * 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"));
+
+    if (!jalview.bin.Cache.getProperty("LATEST_VERSION").equals(
+        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.toString(), "About Jalview",
-            JOptionPane.INFORMATION_MESSAGE);
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void documentationMenuItem_actionPerformed(ActionEvent e)
+    message.append("\nAuthors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton." +
+                   "\nCurrent development managed by Andrew Waterhouse; Barton Group, University of Dundee." +
+                   "\nFor all issues relating to Jalview, email help@jalview.org" +
+                   "\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);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void documentationMenuItem_actionPerformed(ActionEvent e)
+  {
+    try
     {
-        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);
+      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)
-        {     }
+      javax.help.HelpBroker hb = hs.createHelpBroker();
+      hb.setCurrentID("home");
+      hb.setDisplayed(true);
     }
+    catch (Exception ex)
+    {}
+  }
 
-    public void closeAll_actionPerformed(ActionEvent e)
+  public void closeAll_actionPerformed(ActionEvent e)
+  {
+    JInternalFrame[] frames = desktop.getAllFrames();
+    for (int i = 0; i < frames.length; i++)
     {
-      JInternalFrame [] frames = desktop.getAllFrames();
-      for(int i=0; i<frames.length; i++)
+      try
       {
-        try{
         frames[i].setClosed(true);
-      }catch(java.beans.PropertyVetoException ex){}
       }
+      catch (java.beans.PropertyVetoException ex)
+      {}
     }
-
-    public void raiseRelated_actionPerformed(ActionEvent e)
+  }
+
+  public void raiseRelated_actionPerformed(ActionEvent e)
+  {
+    reorderAssociatedWindows(false, false);
+  }
+
+  public void minimizeAssociated_actionPerformed(ActionEvent e)
+  {
+    reorderAssociatedWindows(true, false);
+  }
+
+  void closeAssociatedWindows()
+  {
+    reorderAssociatedWindows(false, true);
+  }
+
+  void reorderAssociatedWindows(boolean minimize, boolean close)
+  {
+    JInternalFrame[] frames = desktop.getAllFrames();
+    if (frames == null || frames.length < 1)
     {
-      reorderAssociatedWindows(false, false);
+      return;
     }
 
-    public void minimizeAssociated_actionPerformed(ActionEvent e)
+    AlignViewport source = null, target = null;
+    if (frames[0] instanceof AlignFrame)
     {
-      reorderAssociatedWindows(true, false);
+      source = ( (AlignFrame) frames[0]).getCurrentView();
     }
-
-    void closeAssociatedWindows()
+    else if (frames[0] instanceof TreePanel)
     {
-      reorderAssociatedWindows(false, true);
+      source = ( (TreePanel) frames[0]).getViewPort();
     }
-
-    void reorderAssociatedWindows(boolean minimize, boolean close)
+    else if (frames[0] instanceof PCAPanel)
     {
-      JInternalFrame[] frames = desktop.getAllFrames();
-      if (frames == null || frames.length<1)
-        return;
-
-      AlignViewport source = null, target = null;
-      if (frames[0] instanceof AlignFrame)
-        source = ( (AlignFrame) frames[0]).getCurrentView();
-      else if (frames[0] instanceof TreePanel)
-        source = ( (TreePanel) frames[0]).getViewPort();
-      else if (frames[0] instanceof PCAPanel)
-        source = ( (PCAPanel) frames[0]).av;
-      else if (frames[0].getContentPane() instanceof PairwiseAlignPanel)
-        source = ((PairwiseAlignPanel)frames[0].getContentPane()).av;
+      source = ( (PCAPanel) frames[0]).av;
+    }
+    else if (frames[0].getContentPane() instanceof PairwiseAlignPanel)
+    {
+      source = ( (PairwiseAlignPanel) frames[0].getContentPane()).av;
+    }
 
+    if (source != null)
+    {
+      for (int i = 0; i < frames.length; i++)
+      {
+        target = null;
+        if (frames[i] == null)
+        {
+          continue;
+        }
+        if (frames[i] instanceof AlignFrame)
+        {
+          target = ( (AlignFrame) frames[i]).getCurrentView();
+        }
+        else if (frames[i] instanceof TreePanel)
+        {
+          target = ( (TreePanel) frames[i]).getViewPort();
+        }
+        else if (frames[i] instanceof PCAPanel)
+        {
+          target = ( (PCAPanel) frames[i]).av;
+        }
+        else if (frames[i].getContentPane() instanceof PairwiseAlignPanel)
+        {
+          target = ( (PairwiseAlignPanel) frames[i].getContentPane()).av;
+        }
 
-      if (source != null)
-        for (int i = 0; i < frames.length; i++)
+        if (source == target)
         {
-          target = null;
-          if(frames[i]==null)
-          {
-            continue;
-          }
-          if (frames[i] instanceof AlignFrame)
-            target = ( (AlignFrame) frames[i]).getCurrentView();
-          else if (frames[i] instanceof TreePanel)
-            target = ( (TreePanel) frames[i]).getViewPort();
-          else if (frames[i] instanceof PCAPanel)
-            target = ( (PCAPanel) frames[i]).av;
-          else if (frames[i].getContentPane() instanceof PairwiseAlignPanel)
-            target = ( (PairwiseAlignPanel) frames[i].getContentPane()).av;
-
-          if (source == target)
+          try
           {
-            try
+            if (close)
             {
-              if (close)
-                frames[i].setClosed(true);
-              else
+              frames[i].setClosed(true);
+            }
+            else
+            {
+              frames[i].setIcon(minimize);
+              if (!minimize)
               {
-                frames[i].setIcon(minimize);
-                if (!minimize)
-                {
-                  frames[i].toFront();
-                }
+                frames[i].toFront();
               }
-
             }
-            catch (java.beans.PropertyVetoException ex)
-            {       }
+
           }
+          catch (java.beans.PropertyVetoException ex)
+          {}
         }
+      }
     }
-
-
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void preferences_actionPerformed(ActionEvent e)
-    {
-        new Preferences();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void saveState_actionPerformed(ActionEvent e)
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void preferences_actionPerformed(ActionEvent e)
+  {
+    new Preferences();
+  }
+
+  /**
+   * 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");
+
+    chooser.setFileView(new JalviewFileView());
+    chooser.setDialogTitle("Save State");
+
+    int value = chooser.showSaveDialog(this);
+
+    if (value == JalviewFileChooser.APPROVE_OPTION)
     {
-        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");
-
-        int value = chooser.showSaveDialog(this);
-
-        if (value == JalviewFileChooser.APPROVE_OPTION)
-        {
-            java.io.File choice = chooser.getSelectedFile();
-            jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
-            new Jalview2XML().SaveState(choice);
-        }
+      java.io.File choice = chooser.getSelectedFile();
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
+      new Jalview2XML().SaveState(choice);
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void loadState_actionPerformed(ActionEvent 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");
+    chooser.setFileView(new JalviewFileView());
+    chooser.setDialogTitle("Restore state");
+
+    int value = chooser.showOpenDialog(this);
+
+    if (value == JalviewFileChooser.APPROVE_OPTION)
     {
-        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");
-
-        int value = chooser.showOpenDialog(this);
-
-        if (value == JalviewFileChooser.APPROVE_OPTION)
-        {
-            String choice = chooser.getSelectedFile().getAbsolutePath();
-            jalview.bin.Cache.setProperty("LAST_DIRECTORY",
-                chooser.getSelectedFile().getParent());
-            new Jalview2XML().LoadJalviewAlign(choice);
-        }
+      String choice = chooser.getSelectedFile().getAbsolutePath();
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+                                    chooser.getSelectedFile().getParent());
+      new Jalview2XML().LoadJalviewAlign(choice);
     }
+  }
 
   /*  public void vamsasLoad_actionPerformed(ActionEvent e)
     {
@@ -714,184 +764,201 @@ public class Desktop extends jalview.jbgui.GDesktop
     }*/
 
 
-    public void inputSequence_actionPerformed(ActionEvent e)
-    {
-      new SequenceFetcher(null);
-    }
+  public void inputSequence_actionPerformed(ActionEvent e)
+  {
+    new SequenceFetcher(null);
+  }
 
-    JPanel progressPanel;
+  JPanel progressPanel;
 
-    public void startLoading(final String fileName)
+  public void startLoading(final String fileName)
+  {
+    if (fileLoadingCount == 0)
     {
-      if (fileLoadingCount == 0)
-      {
-        progressPanel = new JPanel(new BorderLayout());
-        JProgressBar progressBar = new JProgressBar();
-        progressBar.setIndeterminate(true);
+      progressPanel = new JPanel(new BorderLayout());
+      JProgressBar progressBar = new JProgressBar();
+      progressBar.setIndeterminate(true);
 
-        progressPanel.add(new JLabel("Loading File: " + fileName + "   "),
-                          BorderLayout.WEST);
+      progressPanel.add(new JLabel("Loading File: " + fileName + "   "),
+                        BorderLayout.WEST);
 
-        progressPanel.add(progressBar, BorderLayout.CENTER);
+      progressPanel.add(progressBar, BorderLayout.CENTER);
 
-        instance.getContentPane().add(progressPanel, BorderLayout.SOUTH);
-      }
-      fileLoadingCount++;
-      validate();
+      instance.getContentPane().add(progressPanel, BorderLayout.SOUTH);
     }
-
-    public void stopLoading()
+    fileLoadingCount++;
+    validate();
+  }
+
+  public void stopLoading()
+  {
+    fileLoadingCount--;
+    if (fileLoadingCount < 1)
     {
-      fileLoadingCount--;
-      if (fileLoadingCount < 1)
+      if (progressPanel != null)
       {
-        if(progressPanel!=null)
-        {
-          this.getContentPane().remove(progressPanel);
-          progressPanel = null;
-        }
-        fileLoadingCount = 0;
+        this.getContentPane().remove(progressPanel);
+        progressPanel = null;
       }
-      validate();
+      fileLoadingCount = 0;
     }
-
-    public static int getViewCount(String viewId)
+    validate();
+  }
+
+  public static int getViewCount(String viewId)
+  {
+    int count = 0;
+    JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+    for (int t = 0; t < frames.length; t++)
     {
-      int count = 0;
-      JInternalFrame[] frames = Desktop.desktop.getAllFrames();
-      for (int t = 0; t < frames.length; t++)
+      if (frames[t] instanceof AlignFrame)
       {
-        if (frames[t] instanceof AlignFrame)
+        AlignFrame af = (AlignFrame) frames[t];
+        for (int a = 0; a < af.alignPanels.size(); a++)
         {
-          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 ++;
+            count++;
           }
         }
       }
-
-      return count;
     }
 
-    public void explodeViews(AlignFrame af)
+    return count;
+  }
+
+  public void explodeViews(AlignFrame af)
+  {
+    int size = af.alignPanels.size();
+    if (size < 2)
     {
-      int size = af.alignPanels.size();
-      if(size<2)
-        return;
+      return;
+    }
 
-      for(int i=0; i<size; i++)
+    for (int i = 0; i < size; i++)
+    {
+      AlignmentPanel ap = (AlignmentPanel) af.alignPanels.elementAt(i);
+      AlignFrame newaf = new AlignFrame(ap);
+      if (ap.av.explodedPosition != null)
       {
-        AlignmentPanel ap = (AlignmentPanel)af.alignPanels.elementAt(i);
-        AlignFrame newaf = new AlignFrame(ap);
-        if(ap.av.explodedPosition!=null)
-          newaf.setBounds(ap.av.explodedPosition);
-
-        ap.av.gatherViewsHere = false;
-
-        addInternalFrame(newaf, af.getTitle(),
-                         AlignFrame.DEFAULT_WIDTH,
-                         AlignFrame.DEFAULT_HEIGHT);
+        newaf.setBounds(ap.av.explodedPosition);
       }
 
-      af.alignPanels.clear();
-      af.closeMenuItem_actionPerformed(true);
+      ap.av.gatherViewsHere = false;
 
+      addInternalFrame(newaf, af.getTitle(),
+                       AlignFrame.DEFAULT_WIDTH,
+                       AlignFrame.DEFAULT_HEIGHT);
     }
 
-    public void gatherViews(AlignFrame source)
-    {
-      source.viewport.gatherViewsHere = true;
-      source.viewport.explodedPosition = source.getBounds();
-      JInternalFrame[] frames = desktop.getAllFrames();
-      String viewId = source.viewport.sequenceSetID;
+    af.alignPanels.clear();
+    af.closeMenuItem_actionPerformed(true);
+
+  }
+
+  public void gatherViews(AlignFrame source)
+  {
+    source.viewport.gatherViewsHere = true;
+    source.viewport.explodedPosition = source.getBounds();
+    JInternalFrame[] frames = desktop.getAllFrames();
+    String viewId = source.viewport.sequenceSetID;
 
-      for (int t = 0; t < frames.length; t++)
+    for (int t = 0; t < frames.length; t++)
+    {
+      if (frames[t] instanceof AlignFrame && frames[t] != source)
       {
-        if (frames[t] instanceof AlignFrame && frames[t] != source)
+        AlignFrame af = (AlignFrame) frames[t];
+        boolean gatherThis = false;
+        for (int a = 0; a < af.alignPanels.size(); a++)
         {
-          AlignFrame af = (AlignFrame) frames[t];
-          boolean gatherThis = false;
-          for (int a = 0; a < af.alignPanels.size(); a++)
+          AlignmentPanel ap = (AlignmentPanel) af.alignPanels.elementAt(a);
+          if (viewId.equals(ap.av.getSequenceSetId()))
           {
-            AlignmentPanel ap = (AlignmentPanel) af.alignPanels.elementAt(a);
-            if (viewId.equals(ap.av.getSequenceSetId()))
-            {
-              gatherThis = true;
-              ap.av.gatherViewsHere = false;
-              ap.av.explodedPosition = af.getBounds();
-              source.addAlignmentPanel(ap, false);
-            }
+            gatherThis = true;
+            ap.av.gatherViewsHere = false;
+            ap.av.explodedPosition = af.getBounds();
+            source.addAlignmentPanel(ap, false);
           }
+        }
 
-          if (gatherThis)
-          {
-            af.alignPanels.clear();
-            af.closeMenuItem_actionPerformed(true);
-          }
+        if (gatherThis)
+        {
+          af.alignPanels.clear();
+          af.closeMenuItem_actionPerformed(true);
         }
       }
-
     }
 
-    jalview.gui.VamsasClient v_client=null;
-    public void vamsasLoad_actionPerformed(ActionEvent e)
+  }
+
+  jalview.gui.VamsasClient v_client = null;
+  public void vamsasLoad_actionPerformed(ActionEvent e)
+  {
+    if (v_client == null)
     {
-      if (v_client==null) {
-        // Start a session.
-        JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
-            getProperty("LAST_DIRECTORY"));
+      // Start a session.
+      JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+          getProperty("LAST_DIRECTORY"));
 
-        chooser.setFileView(new JalviewFileView());
-        chooser.setDialogTitle("Load Vamsas file");
-        chooser.setToolTipText("Import");
+      chooser.setFileView(new JalviewFileView());
+      chooser.setDialogTitle("Load Vamsas file");
+      chooser.setToolTipText("Import");
 
-        int value = chooser.showOpenDialog(this);
+      int value = chooser.showOpenDialog(this);
 
-        if (value == JalviewFileChooser.APPROVE_OPTION)
-        {
-          v_client = new jalview.gui.VamsasClient(this,
-              chooser.getSelectedFile());
-          this.vamsasLoad.setText("Session Update");
-          this.vamsasStop.setVisible(true);
-          v_client.initial_update();
-          v_client.startWatcher();
-        }
-      } else {
-        // store current data in session.
-        v_client.push_update();
+      if (value == JalviewFileChooser.APPROVE_OPTION)
+      {
+        v_client = new jalview.gui.VamsasClient(this,
+                                                chooser.getSelectedFile());
+        this.vamsasLoad.setText("Session Update");
+        this.vamsasStop.setVisible(true);
+        v_client.initial_update();
+        v_client.startWatcher();
       }
     }
-    public void vamsasStop_actionPerformed(ActionEvent e) {
-      if (v_client!=null) {
-        v_client.end_session();
-        v_client=null;
-        this.vamsasStop.setVisible(false);
-        this.vamsasLoad.setText("Start Vamsas Session...");
-      }
+    else
+    {
+      // store current data in session.
+      v_client.push_update();
     }
-    /**
-     * hide vamsas user gui bits when a vamsas document event is being handled.
-     * @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"));
-      vamsasLoad.setVisible(!b);
-      vamsasStop.setVisible(!b);
+  }
 
+  public void vamsasStop_actionPerformed(ActionEvent e)
+  {
+    if (v_client != null)
+    {
+      v_client.end_session();
+      v_client = null;
+      this.vamsasStop.setVisible(false);
+      this.vamsasLoad.setText("Start Vamsas Session...");
     }
-    /**
-     * 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);
-    }
+  }
+
+  /**
+   * hide vamsas user gui bits when a vamsas document event is being handled.
+   * @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"));
+    vamsasLoad.setVisible(!b);
+    vamsasStop.setVisible(!b);
+
+  }
+
+  /**
+   * 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);
+  }
 
 }
-
diff --git a/src/jalview/gui/EPSOptions.java b/src/jalview/gui/EPSOptions.java
index 543215f..dc7b650 100755
--- a/src/jalview/gui/EPSOptions.java
+++ b/src/jalview/gui/EPSOptions.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,10 +18,9 @@
  */
 package jalview.gui;
 
-import javax.swing.*;
 import java.awt.*;
-import java.awt.event.ActionListener;
-import java.awt.event.ActionEvent;
+import java.awt.event.*;
+import javax.swing.*;
 
 public class EPSOptions
     extends JPanel
@@ -46,8 +45,10 @@ public class EPSOptions
     bg.add(text);
 
     JOptionPane pane = new JOptionPane(null,
-        JOptionPane.DEFAULT_OPTION, JOptionPane.DEFAULT_OPTION,
-       null, new Object[]{this});
+                                       JOptionPane.DEFAULT_OPTION,
+                                       JOptionPane.DEFAULT_OPTION,
+                                       null, new Object[]
+                                       {this});
 
     dialog = pane.createDialog(Desktop.desktop, "EPS Rendering options");
     dialog.setVisible(true);
@@ -109,9 +110,13 @@ public class EPSOptions
   public void ok_actionPerformed(ActionEvent e)
   {
     if (lineart.isSelected())
+    {
       value = "Lineart";
+    }
     else
+    {
       value = "Text";
+    }
 
     if (!askAgain.isSelected())
     {
diff --git a/src/jalview/gui/EditNameDialog.java b/src/jalview/gui/EditNameDialog.java
index 2b1ee72..b6cc5a5 100644
--- a/src/jalview/gui/EditNameDialog.java
+++ b/src/jalview/gui/EditNameDialog.java
@@ -29,7 +29,6 @@ public class EditNameDialog
   JButton cancel = new JButton("Cancel");
   boolean accept = false;
 
-
   public String getName()
   {
     return id.getText();
@@ -38,9 +37,13 @@ public class EditNameDialog
   public String getDescription()
   {
     if (description.getText().length() < 1)
+    {
       return null;
+    }
     else
+    {
       return description.getText();
+    }
   }
 
   public EditNameDialog(String name,
@@ -49,7 +52,7 @@ public class EditNameDialog
                         String label2,
                         String title)
   {
-    JLabel idlabel = new JLabel( label1);
+    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));
@@ -65,14 +68,13 @@ public class EditNameDialog
     panel2.add(description, BorderLayout.CENTER);
     panel.add(panel2, BorderLayout.SOUTH);
 
-
-     int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+    int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
         panel, title,
-        JOptionPane.OK_CANCEL_OPTION );
+        JOptionPane.OK_CANCEL_OPTION);
 
-     if (reply == JOptionPane.OK_OPTION)
-     {
-       accept = true;
-     }
+    if (reply == JOptionPane.OK_OPTION)
+    {
+      accept = true;
+    }
   }
 }
diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index 12876ed..634dbed 100755
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,17 +18,14 @@
  */
 package jalview.gui;
 
-import jalview.datamodel.*;
-
-import java.awt.*;
-
 import java.util.*;
 
+import java.awt.*;
+import java.awt.event.*;
 import java.awt.image.*;
 import javax.swing.*;
-import javax.swing.JOptionPane;
-import java.awt.event.*;
 
+import jalview.datamodel.*;
 
 /**
  * DOCUMENT ME!
@@ -38,696 +35,754 @@ import java.awt.event.*;
  */
 public class FeatureRenderer
 {
-    AlignViewport av;
-    Color resBoxColour;
-    float transparency = 1.0f;
-    FontMetrics fm;
-    int charOffset;
-
-    Hashtable featureColours = new Hashtable();
-
-
-    // A higher level for grouping features of a
-   // particular type
-    Hashtable featureGroups = null;
-
-    // This is actually an Integer held in the hashtable,
-    // Retrieved using the key feature type
-    Object currentColour;
-
-    String [] renderOrder;
-
-    /**
-     * Creates a new FeatureRenderer object.
-     *
-     * @param av DOCUMENT ME!
-     */
-    public FeatureRenderer(AlignViewport av)
+  AlignViewport av;
+  Color resBoxColour;
+  float transparency = 1.0f;
+  FontMetrics fm;
+  int charOffset;
+
+  Hashtable featureColours = new Hashtable();
+
+  // A higher level for grouping features of a
+  // particular type
+  Hashtable featureGroups = null;
+
+  // This is actually an Integer held in the hashtable,
+  // Retrieved using the key feature type
+  Object currentColour;
+
+  String[] renderOrder;
+
+  /**
+   * Creates a new FeatureRenderer object.
+   *
+   * @param av DOCUMENT ME!
+   */
+  public FeatureRenderer(AlignViewport av)
+  {
+    this.av = av;
+  }
+
+  public void transferSettings(FeatureRenderer fr)
+  {
+    renderOrder = fr.renderOrder;
+    featureGroups = fr.featureGroups;
+    featureColours = fr.featureColours;
+    transparency = fr.transparency;
+  }
+
+  BufferedImage offscreenImage;
+  boolean offscreenRender = false;
+  public Color findFeatureColour(Color initialCol, SequenceI seq, int res)
+  {
+    return new Color(findFeatureColour(initialCol.getRGB(),
+                                       seq, res));
+  }
+
+  /**
+   * This is used by the Molecule Viewer and Overview to
+   * get the accurate colourof the rendered sequence
+   */
+  public int findFeatureColour(int initialCol, SequenceI seq, int column)
+  {
+    if (!av.showSequenceFeatures)
     {
-        this.av = av;
+      return initialCol;
     }
 
-    public void transferSettings(FeatureRenderer fr)
+    if (seq != lastSeq)
     {
-      renderOrder = fr.renderOrder;
-      featureGroups = fr.featureGroups;
-      featureColours = fr.featureColours;
-      transparency =  fr.transparency;
+      lastSeq = seq;
+      sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures();
+      if (sequenceFeatures == null)
+      {
+        return initialCol;
+      }
+
+      sfSize = sequenceFeatures.length;
     }
 
-    BufferedImage offscreenImage;
-    boolean offscreenRender = false;
-    public Color findFeatureColour(Color initialCol, SequenceI seq, int res)
+    if (jalview.util.Comparison.isGap(lastSeq.getCharAt(column)))
     {
-      return new Color( findFeatureColour (initialCol.getRGB(),
-                        seq, res ));
+      return Color.white.getRGB();
     }
 
-    /**
-     * This is used by the Molecule Viewer and Overview to
-     * get the accurate colourof the rendered sequence
-     */
-    public int findFeatureColour(int initialCol, SequenceI seq, int column)
+    //Only bother making an offscreen image if transparency is applied
+    if (transparency != 1.0f && offscreenImage == null)
     {
-      if(!av.showSequenceFeatures)
-        return initialCol;
-
-      if(seq!=lastSeq)
-      {
-        lastSeq = seq;
-        sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures();
-        if(sequenceFeatures==null)
-          return initialCol;
-
-        sfSize = sequenceFeatures.length;
-      }
-
-      if(jalview.util.Comparison.isGap(lastSeq.getCharAt(column)))
-        return Color.white.getRGB();
+      offscreenImage = new BufferedImage(1, 1, BufferedImage.TYPE_INT_ARGB);
+    }
 
+    currentColour = null;
 
-      //Only bother making an offscreen image if transparency is applied
-      if(transparency!=1.0f && offscreenImage==null)
-      {
-        offscreenImage = new BufferedImage(1,1,BufferedImage.TYPE_INT_ARGB);
-      }
+    offscreenRender = true;
 
-      currentColour = null;
+    if (offscreenImage != null)
+    {
+      offscreenImage.setRGB(0, 0, initialCol);
+      drawSequence(offscreenImage.getGraphics(),
+                   lastSeq,
+                   column, column, 0);
 
-      offscreenRender = true;
+      return offscreenImage.getRGB(0, 0);
+    }
+    else
+    {
+      drawSequence(null,
+                   lastSeq,
+                   lastSeq.findPosition(column),
+                   -1, -1);
 
-      if(offscreenImage!=null)
+      if (currentColour == null)
       {
-        offscreenImage.setRGB(0,0,initialCol);
-        drawSequence(offscreenImage.getGraphics(),
-                     lastSeq,
-                     column,column,0);
-
-        return offscreenImage.getRGB(0,0);
+        return initialCol;
       }
       else
       {
-        drawSequence(null,
-                    lastSeq,
-                    lastSeq.findPosition(column),
-                    -1, -1);
-
-        if (currentColour == null)
-          return initialCol;
-        else
-          return  ((Integer)currentColour).intValue();
+        return ( (Integer) currentColour).intValue();
       }
-
-
     }
 
+  }
+
+  /**
+   * 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;
+
+  public void drawSequence(Graphics g, SequenceI seq,
+                           int start, int end, int y1)
+  {
+    if (seq.getDatasetSequence().getSequenceFeatures() == null
+        || seq.getDatasetSequence().getSequenceFeatures().length == 0)
+    {
+      return;
+    }
 
-    /**
-     * 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;
+    if (g != null)
+    {
+      fm = g.getFontMetrics();
+    }
 
-    public void drawSequence(Graphics g, SequenceI seq,
-                             int start, int end, int y1)
+    if (av.featuresDisplayed == null
+        || renderOrder == null
+        || newFeatureAdded)
     {
-      if ( seq.getDatasetSequence().getSequenceFeatures() == null
-          || seq.getDatasetSequence().getSequenceFeatures().length==0)
+      findAllFeatures();
+      if (av.featuresDisplayed.size() < 1)
+      {
         return;
+      }
 
-      if(g!=null)
-        fm = g.getFontMetrics();
-
+      sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
+      sfSize = sequenceFeatures.length;
+    }
 
-      if (av.featuresDisplayed == null
-          || renderOrder==null
-          || newFeatureAdded)
-       {
-         findAllFeatures();
-         if(av.featuresDisplayed.size()<1)
-           return;
+    if (lastSeq == null || seq != lastSeq)
+    {
+      lastSeq = seq;
+      sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
+      sfSize = sequenceFeatures.length;
+    }
 
-         sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
-         sfSize = sequenceFeatures.length;
-       }
+    if (transparency != 1 && g != null)
+    {
+      Graphics2D g2 = (Graphics2D) g;
+      g2.setComposite(
+          AlphaComposite.getInstance(
+              AlphaComposite.SRC_OVER, transparency));
+    }
 
-       if(lastSeq==null || seq!=lastSeq)
-      {
-        lastSeq = seq;
-        sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
-        sfSize = sequenceFeatures.length;
-      }
+    if (!offscreenRender)
+    {
+      spos = lastSeq.findPosition(start);
+      epos = lastSeq.findPosition(end);
+    }
 
+    String type;
+    for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++)
+    {
+      type = renderOrder[renderIndex];
 
-      if (transparency != 1 && g!=null)
+      if (type == null || !av.featuresDisplayed.containsKey(type))
       {
-        Graphics2D g2 = (Graphics2D) g;
-        g2.setComposite(
-            AlphaComposite.getInstance(
-                AlphaComposite.SRC_OVER, transparency));
+        continue;
       }
 
-      if(!offscreenRender)
+      // loop through all features in sequence to find
+      // current feature to render
+      for (sfindex = 0; sfindex < sfSize; sfindex++)
       {
-        spos = lastSeq.findPosition(start);
-        epos = lastSeq.findPosition(end);
-      }
-
-
-      String type;
-      for(int renderIndex=0; renderIndex<renderOrder.length; renderIndex++)
-       {
-        type =  renderOrder[renderIndex];
-
-        if(type==null || !av.featuresDisplayed.containsKey(type))
+        if (sequenceFeatures.length <= sfindex)
+        {
+          continue;
+        }
+        if (!sequenceFeatures[sfindex].type.equals(type))
+        {
           continue;
+        }
 
-        // loop through all features in sequence to find
-        // current feature to render
-        for (sfindex = 0; sfindex < sfSize; sfindex++)
+        if (featureGroups != null
+            && sequenceFeatures[sfindex].featureGroup != null
+            &&
+            featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)
+            &&
+            ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].
+                                            featureGroup)).
+            booleanValue())
         {
-          if(sequenceFeatures.length<=sfindex)
-          {
-            continue;
-          }
-          if (!sequenceFeatures[sfindex].type.equals(type))
-            continue;
-
-          if (featureGroups != null
-              && sequenceFeatures[sfindex].featureGroup != null
-              &&
-              featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)
-              &&
-              ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].featureGroup)).
-              booleanValue())
-          {
-            continue;
-          }
+          continue;
+        }
 
-          if (!offscreenRender && (sequenceFeatures[sfindex].getBegin() > epos
-                            || sequenceFeatures[sfindex].getEnd() < spos))
-            continue;
+        if (!offscreenRender && (sequenceFeatures[sfindex].getBegin() > epos
+                                 || sequenceFeatures[sfindex].getEnd() < spos))
+        {
+          continue;
+        }
 
-          if (offscreenRender && offscreenImage==null)
-          {
-            if (sequenceFeatures[sfindex].begin <= start &&
-                sequenceFeatures[sfindex].end  >= start)
-            {
-              currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].
-                 type);
-            }
-          }
-          else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))
+        if (offscreenRender && offscreenImage == null)
+        {
+          if (sequenceFeatures[sfindex].begin <= start &&
+              sequenceFeatures[sfindex].end >= start)
           {
-
-            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);
-
+            currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].
+                type);
           }
-          else
-            renderFeature(g, seq,
-                          seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
-                          seq.findIndex(sequenceFeatures[sfindex].end) - 1,
-                          getColour(sequenceFeatures[sfindex].type),
-                          start, end, y1);
+        }
+        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);
 
         }
+        else
+        {
+          renderFeature(g, seq,
+                        seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
+                        seq.findIndex(sequenceFeatures[sfindex].end) - 1,
+                        getColour(sequenceFeatures[sfindex].type),
+                        start, end, y1);
+        }
 
       }
 
-        if(transparency!=1.0f && g!=null)
-        {
-          Graphics2D g2 = (Graphics2D) g;
-          g2.setComposite(
-              AlphaComposite.getInstance(
-                  AlphaComposite.SRC_OVER, 1.0f));
-        }
     }
 
+    if (transparency != 1.0f && g != null)
+    {
+      Graphics2D g2 = (Graphics2D) g;
+      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)
+  {
 
-    char s;
-    int i;
-    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 < start)
+      { // fix for if the feature we have starts before the sequence start,
+        fstart = start; // but the feature end is still valid!!
+      }
 
-      if (((fstart <= end) && (fend >= start)))
+      if (fend >= end)
       {
-        if (fstart < start)
-        { // fix for if the feature we have starts before the sequence start,
-          fstart = start; // but the feature end is still valid!!
-        }
+        fend = end;
+      }
+      int pady = (y1 + av.charHeight) - av.charHeight / 5;
+      for (i = fstart; i <= fend; i++)
+      {
+        s = seq.getCharAt(i);
 
-        if (fend >= end)
+        if (jalview.util.Comparison.isGap(s))
         {
-          fend = end;
+          continue;
         }
-          int pady = (y1 + av.charHeight) - av.charHeight / 5;
-          for (i = fstart; i <= fend; i++)
-          {
-            s = seq.getCharAt(i);
-
-            if (jalview.util.Comparison.isGap(s))
-            {
-              continue;
-            }
 
-            g.setColor(featureColour);
+        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)
-              continue;
+        if (offscreenRender || !av.validCharWidth)
+        {
+          continue;
+        }
 
-            g.setColor(Color.white);
-            charOffset = (av.charWidth - fm.charWidth(s)) / 2;
-            g.drawString(String.valueOf(s),
-                         charOffset + (av.charWidth * (i - start)),
-                         pady);
+        g.setColor(Color.white);
+        charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+        g.drawString(String.valueOf(s),
+                     charOffset + (av.charWidth * (i - start)),
+                     pady);
 
-          }
       }
     }
+  }
 
+  boolean newFeatureAdded = false;
 
-    boolean newFeatureAdded = false;
+  public void featuresAdded()
+  {
+    findAllFeatures();
+  }
 
-    public void featuresAdded()
+  boolean findingFeatures = false;
+  synchronized void findAllFeatures()
+  {
+    newFeatureAdded = false;
+
+    if (findingFeatures)
     {
-      findAllFeatures();
+      newFeatureAdded = true;
+      return;
     }
 
-   boolean findingFeatures = false;
-   synchronized void findAllFeatures()
-   {
-      newFeatureAdded = false;
-
-      if(findingFeatures)
-      {
-        newFeatureAdded = true;
-        return;
-      }
+    findingFeatures = true;
+    jalview.schemes.UserColourScheme ucs = new
+        jalview.schemes.UserColourScheme();
 
-      findingFeatures = true;
-      jalview.schemes.UserColourScheme ucs = new
-          jalview.schemes.UserColourScheme();
+    if (av.featuresDisplayed == null)
+    {
+      av.featuresDisplayed = new Hashtable();
+    }
 
-      if(av.featuresDisplayed==null)
-        av.featuresDisplayed = new Hashtable();
+    av.featuresDisplayed.clear();
 
-      av.featuresDisplayed.clear();
+    Vector allfeatures = new Vector();
+    for (int i = 0; i < av.alignment.getHeight(); i++)
+    {
+      SequenceFeature[] features
+          = av.alignment.getSequenceAt(i).getDatasetSequence().
+          getSequenceFeatures();
 
-      Vector allfeatures = new Vector();
-      for (int i = 0; i < av.alignment.getHeight(); i++)
+      if (features == null)
       {
-        SequenceFeature [] features
-            = av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();
-
-        if (features == null)
-          continue;
+        continue;
+      }
 
-        int index = 0;
-        while (index < features.length)
+      int index = 0;
+      while (index < features.length)
+      {
+        if (!av.featuresDisplayed.containsKey(features[index].getType()))
         {
-          if (!av.featuresDisplayed.containsKey(features[index].getType()))
+          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 (getColour(features[index].getType()) == null)
             {
-              // 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 (getColour(features[index].getType()) == null)
-              {
-                 featureColours.put(features[index].getType(),
-                                   ucs.createColourFromName(features[index].
-                    getType()));
-              }
-
-              av.featuresDisplayed.put(features[index].getType(),
-                                       new Integer(getColour(features[index].
-                  getType()).getRGB()));
-              allfeatures.addElement(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()));
+            allfeatures.addElement(features[index].getType());
           }
-          index++;
         }
+        index++;
       }
+    }
+
+    renderOrder = new String[allfeatures.size()];
+    Enumeration en = allfeatures.elements();
+    int i = allfeatures.size() - 1;
+    while (en.hasMoreElements())
+    {
+      renderOrder[i] = en.nextElement().toString();
+      i--;
+    }
 
-      renderOrder = new String[allfeatures.size()];
-      Enumeration en = allfeatures.elements();
-      int i = allfeatures.size()-1;
-      while(en.hasMoreElements())
+    findingFeatures = false;
+  }
+
+  public Color getColour(String featureType)
+  {
+    Color colour = (Color) featureColours.get(featureType);
+    return colour;
+  }
+
+  static String lastFeatureAdded;
+  static String lastFeatureGroupAdded;
+  static String lastDescriptionAdded;
+
+  public boolean createNewFeatures(SequenceI[] sequences,
+                                   SequenceFeature[] features)
+  {
+    return amendFeatures(sequences, features, true, null);
+  }
+
+  int featureIndex = 0;
+  boolean amendFeatures(final SequenceI[] sequences,
+                        final SequenceFeature[] features,
+                        boolean newFeatures,
+                        final AlignmentPanel ap)
+  {
+    JPanel bigPanel = new JPanel(new BorderLayout());
+    final JComboBox name = new JComboBox();
+    final JComboBox source = new JComboBox();
+    final JTextArea description = new JTextArea(3, 25);
+    final JSpinner start = new JSpinner();
+    final JSpinner end = new JSpinner();
+    start.setPreferredSize(new Dimension(80, 20));
+    end.setPreferredSize(new Dimension(80, 20));
+    final JPanel colour = new JPanel();
+    colour.setBorder(BorderFactory.createEtchedBorder());
+    colour.setMaximumSize(new Dimension(40, 10));
+    colour.addMouseListener(new MouseAdapter()
+    {
+      public void mousePressed(MouseEvent evt)
       {
-        renderOrder[i] = en.nextElement().toString();
-        i--;
+        colour.setBackground(
+            JColorChooser.showDialog(Desktop.desktop,
+                                     "Select Feature Colour",
+                                     colour.getBackground()));
       }
+    });
+
+    JPanel panel = new JPanel(new GridLayout(3, 2));
+    panel.add(new JLabel("Sequence Feature Name: ", JLabel.RIGHT));
+    panel.add(name);
+    panel.add(new JLabel("Feature Group: ", JLabel.RIGHT));
+    panel.add(source);
+    panel.add(new JLabel("Feature Colour: ", JLabel.RIGHT));
+    JPanel tmp = new JPanel();
+    tmp.add(colour);
+    colour.setPreferredSize(new Dimension(150, 15));
+    panel.add(tmp);
+    name.setEditable(true);
+    source.setEditable(true);
+
+    bigPanel.add(panel, BorderLayout.NORTH);
+    panel = new JPanel();
+    panel.add(new JLabel("Description: ", JLabel.RIGHT));
+    description.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    description.setLineWrap(true);
+    panel.add(new JScrollPane(description));
+
+    if (!newFeatures)
+    {
+      bigPanel.add(panel, BorderLayout.SOUTH);
 
-      findingFeatures = false;
+      panel = new JPanel();
+      panel.add(new JLabel(" Start:", JLabel.RIGHT));
+      panel.add(start);
+      panel.add(new JLabel("  End:", JLabel.RIGHT));
+      panel.add(end);
+      bigPanel.add(panel, BorderLayout.CENTER);
     }
-
-    public Color getColour(String featureType)
+    else
     {
-      Color colour = (Color)featureColours.get(featureType);
-      return colour;
+      bigPanel.add(panel, BorderLayout.CENTER);
     }
 
-
-    static String lastFeatureAdded;
-    static String lastFeatureGroupAdded;
-    static String lastDescriptionAdded;
-
-    public boolean createNewFeatures(SequenceI[] sequences,
-                                  SequenceFeature [] features)
+    if (lastFeatureAdded == null)
     {
-      return amendFeatures(sequences, features, true, null);
+      if (features[0].type != null)
+      {
+        lastFeatureAdded = features[0].type;
+      }
+      else
+      {
+        lastFeatureAdded = "feature_1";
+      }
     }
 
-    int featureIndex = 0;
-    boolean amendFeatures(final SequenceI[] sequences,
-                          final SequenceFeature[] features,
-                          boolean newFeatures,
-                          final AlignmentPanel ap)
+    if (lastFeatureGroupAdded == null)
     {
-      JPanel bigPanel = new JPanel(new BorderLayout());
-      final JComboBox name = new JComboBox();
-      final JComboBox source = new JComboBox();
-      final JTextArea description = new JTextArea(3,25);
-      final JSpinner start = new JSpinner();
-      final JSpinner end = new JSpinner();
-      start.setPreferredSize(new Dimension(80,20));
-      end.setPreferredSize(new Dimension(80,20));
-      final JPanel colour = new JPanel();
-      colour.setBorder(BorderFactory.createEtchedBorder());
-      colour.setMaximumSize(new Dimension(40,10));
-      colour.addMouseListener(new MouseAdapter()
-          {
-            public void mousePressed(MouseEvent evt)
-            {
-              colour.setBackground(
-                  JColorChooser.showDialog(Desktop.desktop,
-                                           "Select Feature Colour",
-                                           colour.getBackground()));
-            }
-          });
-
-      JPanel panel = new JPanel(new GridLayout(3, 2));
-      panel.add(new JLabel("Sequence Feature Name: ",JLabel.RIGHT));
-      panel.add(name);
-      panel.add(new JLabel("Feature Group: ", JLabel.RIGHT));
-      panel.add(source);
-      panel.add(new JLabel("Feature Colour: ", JLabel.RIGHT));
-      JPanel tmp = new JPanel();
-      tmp.add(colour);
-      colour.setPreferredSize(new Dimension(150,15));
-      panel.add(tmp);
-      name.setEditable(true);
-      source.setEditable(true);
-
-      bigPanel.add(panel, BorderLayout.NORTH);
-      panel = new JPanel();
-      panel.add(new JLabel("Description: ", JLabel.RIGHT));
-      description.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-      description.setLineWrap(true);
-      panel.add(new JScrollPane(description));
-
-      if(!newFeatures)
+      if (features[0].featureGroup != null)
       {
-        bigPanel.add(panel, BorderLayout.SOUTH);
-
-        panel = new JPanel();
-        panel.add(new JLabel(" Start:", JLabel.RIGHT));
-        panel.add(start);
-        panel.add(new JLabel("  End:", JLabel.RIGHT));
-        panel.add(end);
-        bigPanel.add(panel, BorderLayout.CENTER);
+        lastFeatureGroupAdded = features[0].featureGroup;
       }
       else
-        bigPanel.add(panel, BorderLayout.CENTER);
-
-      if (lastFeatureAdded == null)
-        if (features[0].type != null)
-          lastFeatureAdded = features[0].type;
-        else
-          lastFeatureAdded = "feature_1";
-
-      if (lastFeatureGroupAdded == null)
-        if (features[0].featureGroup != null)
-          lastFeatureGroupAdded = features[0].featureGroup;
-        else
-          lastFeatureAdded = "Jalview";
-
+      {
+        lastFeatureAdded = "Jalview";
+      }
+    }
 
-      Enumeration en;
-      if (featureGroups != null)
+    Enumeration en;
+    if (featureGroups != null)
+    {
+      en = featureGroups.keys();
+      while (en.hasMoreElements())
       {
-        en = featureGroups.keys();
-        while (en.hasMoreElements())
-        {
-          source.addItem(en.nextElement().toString());
-        }
+        source.addItem(en.nextElement().toString());
       }
+    }
 
-      if (newFeatures)
+    if (newFeatures)
+    {
+      if (av.featuresDisplayed != null)
       {
-        if(av.featuresDisplayed != null)
+        en = av.featuresDisplayed.keys();
+        while (en.hasMoreElements())
         {
-          en = av.featuresDisplayed.keys();
-          while (en.hasMoreElements())
-          {
-            name.addItem(en.nextElement().toString());
-          }
+          name.addItem(en.nextElement().toString());
         }
+      }
 
-        name.setSelectedItem(lastFeatureAdded);
-        source.setSelectedItem(lastFeatureGroupAdded);
-        description.setText(
-            lastDescriptionAdded == null ?
-            features[0].description : lastDescriptionAdded);
-
-        if (getColour(lastFeatureAdded) != null)
-        {
-          colour.setBackground(getColour(lastFeatureAdded));
-        }
-        else
-        {
-          colour.setBackground(new Color(60, 160, 115));
-        }
+      name.setSelectedItem(lastFeatureAdded);
+      source.setSelectedItem(lastFeatureGroupAdded);
+      description.setText(
+          lastDescriptionAdded == null ?
+          features[0].description : lastDescriptionAdded);
 
+      if (getColour(lastFeatureAdded) != null)
+      {
+        colour.setBackground(getColour(lastFeatureAdded));
+      }
+      else
+      {
+        colour.setBackground(new Color(60, 160, 115));
       }
-      else if (!newFeatures)
+
+    }
+    else if (!newFeatures)
+    {
+      featureIndex = 0;
+      for (int f = 0; f < features.length; f++)
       {
-        featureIndex = 0;
-        for(int f=0; f<features.length; f++)
-        {
-          name.addItem(features[f].getType().toString());
-        }
+        name.addItem(features[f].getType().toString());
+      }
 
-        description.setText(features[0].getDescription());
-        source.setSelectedItem(features[0].getFeatureGroup());
-        start.setValue(new Integer(features[0].getBegin()));
-        end.setValue(new Integer(features[0].getEnd()));
-        colour.setBackground(
-                getColour(name.getSelectedItem().toString()));
-        name.addItemListener(new ItemListener()
+      description.setText(features[0].getDescription());
+      source.setSelectedItem(features[0].getFeatureGroup());
+      start.setValue(new Integer(features[0].getBegin()));
+      end.setValue(new Integer(features[0].getEnd()));
+      colour.setBackground(
+          getColour(name.getSelectedItem().toString()));
+      name.addItemListener(new ItemListener()
+      {
+        public void itemStateChanged(ItemEvent e)
         {
-          public void itemStateChanged(ItemEvent e)
+          int index = name.getSelectedIndex();
+          if (index != -1)
           {
-            int index = name.getSelectedIndex();
-            if(index!=-1)
-            {
-              featureIndex = index;
-              description.setText(features[index].getDescription());
-              source.setSelectedItem(features[index].getFeatureGroup());
-              start.setValue(new Integer(features[index].getBegin()));
-              end.setValue(new Integer(features[index].getEnd()));
-              colour.setBackground(
-                  getColour(name.getSelectedItem().toString()));
-
-              SearchResults highlight = new SearchResults();
-              highlight.addResult(sequences[0],
-                                  features[index].getBegin(),
-                                  features[index].getEnd());
+            featureIndex = index;
+            description.setText(features[index].getDescription());
+            source.setSelectedItem(features[index].getFeatureGroup());
+            start.setValue(new Integer(features[index].getBegin()));
+            end.setValue(new Integer(features[index].getEnd()));
+            colour.setBackground(
+                getColour(name.getSelectedItem().toString()));
 
-              ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
+            SearchResults highlight = new SearchResults();
+            highlight.addResult(sequences[0],
+                                features[index].getBegin(),
+                                features[index].getEnd());
 
-            }
-            Color col = getColour(name.getSelectedItem().toString());
-            if (col == null)
-              col = new
-                  jalview.schemes.UserColourScheme()
-                  .createColourFromName(name.getSelectedItem().toString());
+            ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
 
-            colour.setBackground(col);
           }
-        });
+          Color col = getColour(name.getSelectedItem().toString());
+          if (col == null)
+          {
+            col = new
+                jalview.schemes.UserColourScheme()
+                .createColourFromName(name.getSelectedItem().toString());
+          }
 
-      }
+          colour.setBackground(col);
+        }
+      });
 
+    }
 
-      Object [] options;
-      if(!newFeatures)
-        options = new Object[]{"Amend", "Delete", "Cancel"};
-      else
-        options = new Object[]{"OK", "Cancel"};
+    Object[] options;
+    if (!newFeatures)
+    {
+      options = new Object[]
+          {
+          "Amend", "Delete", "Cancel"};
+    }
+    else
+    {
+      options = new Object[]
+          {
+          "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");
+    int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop,
+        bigPanel,
+        title,
+        JOptionPane.YES_NO_CANCEL_OPTION,
+        JOptionPane.QUESTION_MESSAGE,
+        null,
+        options, "OK");
 
-      jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
+    jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
 
-      if (reply == JOptionPane.OK_OPTION
-          && name.getSelectedItem() != null
-          && source.getSelectedItem() != null)
+    if (reply == JOptionPane.OK_OPTION
+        && name.getSelectedItem() != null
+        && source.getSelectedItem() != null)
+    {
+      //This ensures that the last sequence
+      //is refreshed and new features are rendered
+      lastSeq = null;
+      lastFeatureAdded = name.getSelectedItem().toString();
+      lastFeatureGroupAdded = source.getSelectedItem().toString();
+      lastDescriptionAdded = description.getText().replaceAll("\n", " ");
+    }
+
+    if (!newFeatures)
+    {
+      SequenceFeature sf = features[featureIndex];
+
+      if (reply == JOptionPane.NO_OPTION)
       {
-        //This ensures that the last sequence
-        //is refreshed and new features are rendered
-        lastSeq=null;
-        lastFeatureAdded = name.getSelectedItem().toString();
-        lastFeatureGroupAdded = source.getSelectedItem().toString();
-        lastDescriptionAdded = description.getText().replaceAll("\n", " ");
+        sequences[0].getDatasetSequence().deleteFeature(sf);
       }
-
-      if(!newFeatures)
+      else if (reply == JOptionPane.YES_OPTION)
       {
-        SequenceFeature sf = features[featureIndex];
-
-        if(reply==JOptionPane.NO_OPTION)
-          sequences[0].getDatasetSequence().deleteFeature(sf);
-        else if(reply==JOptionPane.YES_OPTION)
+        sf.type = lastFeatureAdded;
+        sf.featureGroup = lastFeatureGroupAdded;
+        sf.description = lastDescriptionAdded;
+        setColour(sf.type, colour.getBackground());
+        try
         {
-          sf.type = lastFeatureAdded;
-          sf.featureGroup = lastFeatureGroupAdded;
-          sf.description = lastDescriptionAdded;
-          setColour(sf.type, colour.getBackground());
-          try{
-            sf.begin = ((Integer)start.getValue()).intValue();
-            sf.end = ((Integer)end.getValue()).intValue();
-          }catch(NumberFormatException ex)
-          {}
-
-          ffile.parseDescriptionHTML(sf, false);
+          sf.begin = ( (Integer) start.getValue()).intValue();
+          sf.end = ( (Integer) end.getValue()).intValue();
         }
+        catch (NumberFormatException ex)
+        {}
+
+        ffile.parseDescriptionHTML(sf, false);
       }
-      else
+    }
+    else
+    {
+      if (reply == JOptionPane.OK_OPTION
+          && name.getSelectedItem() != null
+          && source.getSelectedItem() != null)
       {
-        if (reply == JOptionPane.OK_OPTION
-            && name.getSelectedItem() != null
-            && source.getSelectedItem() != null)
+        for (int i = 0; i < sequences.length; i++)
         {
-          for (int i = 0; i < sequences.length; i++)
-          {
-            features[i].type = lastFeatureAdded;
-            features[i].featureGroup = lastFeatureGroupAdded;
-            features[i].description = lastDescriptionAdded;
-            sequences[i].addSequenceFeature(features[i]);
-            ffile.parseDescriptionHTML(features[i], false);
-          }
-
-          if (av.featuresDisplayed == null)
-            av.featuresDisplayed = new Hashtable();
+          features[i].type = lastFeatureAdded;
+          features[i].featureGroup = lastFeatureGroupAdded;
+          features[i].description = lastDescriptionAdded;
+          sequences[i].addSequenceFeature(features[i]);
+          ffile.parseDescriptionHTML(features[i], false);
+        }
 
-          if (featureGroups == null)
-            featureGroups = new Hashtable();
+        if (av.featuresDisplayed == null)
+        {
+          av.featuresDisplayed = new Hashtable();
+        }
 
-          featureGroups.put(lastFeatureGroupAdded, new Boolean(true));
+        if (featureGroups == null)
+        {
+          featureGroups = new Hashtable();
+        }
 
-          Color col = colour.getBackground();
-          setColour(lastFeatureAdded, colour.getBackground());
+        featureGroups.put(lastFeatureGroupAdded, new Boolean(true));
 
-          av.featuresDisplayed.put(lastFeatureGroupAdded,
-                                   new Integer(col.getRGB()));
+        Color col = colour.getBackground();
+        setColour(lastFeatureAdded, colour.getBackground());
 
-          findAllFeatures();
+        av.featuresDisplayed.put(lastFeatureGroupAdded,
+                                 new Integer(col.getRGB()));
 
-          return true;
-        }
-        else
-          return false;
-      }
-
-      if(name.getSelectedIndex()==-1)
         findAllFeatures();
 
-
-      return true;
+        return true;
+      }
+      else
+      {
+        return false;
+      }
     }
 
-    public void setColour(String featureType, Color col)
+    if (name.getSelectedIndex() == -1)
     {
-      featureColours.put(featureType, col);
+      findAllFeatures();
     }
 
-    public void setTransparency(float value)
+    return true;
+  }
+
+  public void setColour(String featureType, Color col)
+  {
+    featureColours.put(featureType, col);
+  }
+
+  public void setTransparency(float value)
+  {
+    transparency = value;
+  }
+
+  public float getTransparency()
+  {
+    return transparency;
+  }
+
+  public void setFeaturePriority(Object[][] data)
+  {
+    // The feature table will display high priority
+    // features at the top, but theses are the ones
+    // we need to render last, so invert the data
+    if (av.featuresDisplayed != null)
     {
-      transparency = value;
+      av.featuresDisplayed.clear();
     }
-
-    public float getTransparency()
+    else
     {
-      return transparency;
+      av.featuresDisplayed = new Hashtable();
     }
 
-    public void setFeaturePriority(Object [][] data)
-    {
-      // The feature table will display high priority
-      // features at the top, but theses are the ones
-      // we need to render last, so invert the data
-      if(av.featuresDisplayed!=null)
-        av.featuresDisplayed.clear();
-      else
-        av.featuresDisplayed = new Hashtable();
+    renderOrder = new String[data.length];
 
-      renderOrder = new String[data.length];
-
-      if (data.length > 0)
-        for (int i = 0; i < data.length; i++)
+    if (data.length > 0)
+    {
+      for (int i = 0; i < data.length; i++)
+      {
+        String type = data[i][0].toString();
+        setColour(type, (Color) data[i][1]);
+        if ( ( (Boolean) data[i][2]).booleanValue())
         {
-          String type = data[i][0].toString();
-          setColour(type, (Color) data[i][1]);
-          if ( ( (Boolean) data[i][2]).booleanValue())
-          {
-            av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB()));
-          }
-
-          renderOrder[data.length - i - 1] = type;
+          av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB()));
         }
 
+        renderOrder[data.length - i - 1] = type;
+      }
     }
 
-
-
+  }
 
 }
diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index a3a2396..955684c 100755
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,21 +18,20 @@
  */
 package jalview.gui;
 
-import jalview.datamodel.*;
-import javax.swing.*;
-import javax.swing.event.*;
-import java.awt.*;
+import java.io.*;
 import java.util.*;
-import javax.swing.BorderFactory;
+
+import java.awt.*;
 import java.awt.event.*;
+import javax.swing.*;
+import javax.swing.event.*;
 import javax.swing.table.*;
-import java.io.*;
-import jalview.io.JalviewFileChooser;
-import java.awt.BorderLayout;
-import java.awt.Font;
-import java.awt.Color;
 
-public class FeatureSettings extends JPanel
+import jalview.datamodel.*;
+import jalview.io.*;
+
+public class FeatureSettings
+    extends JPanel
 {
   DasSourceBrowser dassourceBrowser;
   jalview.io.DasSequenceFeatureFetcher dasFeatureFetcher;
@@ -41,7 +40,7 @@ public class FeatureSettings extends JPanel
 
   final FeatureRenderer fr;
   public final AlignFrame af;
-  Object [][] originalData;
+  Object[][] originalData;
   final JInternalFrame frame;
   JScrollPane scrollPane = new JScrollPane();
   JTable table;
@@ -55,72 +54,72 @@ public class FeatureSettings extends JPanel
     this.af = af;
     fr = af.getFeatureRenderer();
 
-    transparency.setMaximum( 100 - (int)(fr.transparency*100) ) ;
-
-   try
-   {
-     jbInit();
-   }
-   catch (Exception ex)
-   {
-     ex.printStackTrace();
-   }
-
-   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.setDefaultEditor(Color.class,
-                          new ColorEditor());
-
-   table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
-
-   table.addMouseListener(new MouseAdapter()
-   {
-     public void mousePressed(MouseEvent evt)
-     {
-       selectedRow = table.rowAtPoint(evt.getPoint());
-     }
-   });
-
-   table.addMouseMotionListener(new MouseMotionAdapter()
-   {
-     public void mouseDragged(MouseEvent evt)
-     {
-       int newRow = table.rowAtPoint(evt.getPoint());
-       if (newRow != selectedRow
-           && selectedRow != -1
-           && newRow != -1)
-       {
-         Object[] temp = new Object[3];
-         temp[0] = table.getValueAt(selectedRow, 0);
-         temp[1] = table.getValueAt(selectedRow, 1);
-         temp[2] = table.getValueAt(selectedRow, 2);
-
-         table.setValueAt(table.getValueAt(newRow, 0), selectedRow, 0);
-         table.setValueAt(table.getValueAt(newRow, 1), selectedRow, 1);
-         table.setValueAt(table.getValueAt(newRow, 2), selectedRow, 2);
-
-         table.setValueAt(temp[0], newRow, 0);
-         table.setValueAt(temp[1], newRow, 1);
-         table.setValueAt(temp[2], newRow, 2);
-
-         selectedRow = newRow;
-       }
-     }
-   });
-
-   scrollPane.setViewportView(table);
+    transparency.setMaximum(100 - (int) (fr.transparency * 100));
 
-    dassourceBrowser = new DasSourceBrowser();
-    dasSettingsPane.add(dassourceBrowser, BorderLayout.CENTER);
+    try
+    {
+      jbInit();
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
 
+    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.setDefaultEditor(Color.class,
+                           new ColorEditor());
 
-    if (af.getViewport().featuresDisplayed == null || fr.renderOrder==null)
-       fr.findAllFeatures();
+    table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+
+    table.addMouseListener(new MouseAdapter()
+    {
+      public void mousePressed(MouseEvent evt)
+      {
+        selectedRow = table.rowAtPoint(evt.getPoint());
+      }
+    });
+
+    table.addMouseMotionListener(new MouseMotionAdapter()
+    {
+      public void mouseDragged(MouseEvent evt)
+      {
+        int newRow = table.rowAtPoint(evt.getPoint());
+        if (newRow != selectedRow
+            && selectedRow != -1
+            && newRow != -1)
+        {
+          Object[] temp = new Object[3];
+          temp[0] = table.getValueAt(selectedRow, 0);
+          temp[1] = table.getValueAt(selectedRow, 1);
+          temp[2] = table.getValueAt(selectedRow, 2);
+
+          table.setValueAt(table.getValueAt(newRow, 0), selectedRow, 0);
+          table.setValueAt(table.getValueAt(newRow, 1), selectedRow, 1);
+          table.setValueAt(table.getValueAt(newRow, 2), selectedRow, 2);
+
+          table.setValueAt(temp[0], newRow, 0);
+          table.setValueAt(temp[1], newRow, 1);
+          table.setValueAt(temp[2], newRow, 2);
+
+          selectedRow = newRow;
+        }
+      }
+    });
+
+    scrollPane.setViewportView(table);
+
+    dassourceBrowser = new DasSourceBrowser();
+    dasSettingsPane.add(dassourceBrowser, BorderLayout.CENTER);
+
+    if (af.getViewport().featuresDisplayed == null || fr.renderOrder == null)
+    {
+      fr.findAllFeatures();
+    }
 
     setTableData();
 
@@ -133,7 +132,9 @@ public class FeatureSettings extends JPanel
   synchronized public void setTableData()
   {
     if (fr.featureGroups == null)
+    {
       fr.featureGroups = new Hashtable();
+    }
 
     Vector allFeatures = new Vector();
     Vector allGroups = new Vector();
@@ -142,151 +143,164 @@ public class FeatureSettings extends JPanel
 
     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)
       {
-        if(tmpfeatures[index].begin == 0 && tmpfeatures[index].end ==0)
+        if (tmpfeatures[index].begin == 0 && tmpfeatures[index].end == 0)
         {
           index++;
           continue;
         }
 
-        if(tmpfeatures[index].getFeatureGroup()!=null)
+        if (tmpfeatures[index].getFeatureGroup() != null)
         {
           group = tmpfeatures[index].featureGroup;
-          if(!allGroups.contains(group))
-           {
-             allGroups.addElement(group);
-
-             boolean visible = true;
-             if (fr.featureGroups.containsKey(group))
-             {
-               visible = ( (Boolean) fr.featureGroups.get(group)).booleanValue();
-             }
-
-               if (groupPanel == null)
-               {
-                 groupPanel = new JPanel();
-               }
-
-               boolean alreadyAdded = false;
-               for(int g=0; g<groupPanel.getComponentCount(); g++)
-               {
-                 if(((JCheckBox)groupPanel.getComponent(g))
-                    .getText().equals(group))
-                 {
-                   alreadyAdded = true;
-                   break;
-                 }
-               }
-
-               if(alreadyAdded)
-                 continue;
-
-               fr.featureGroups.put(group, new Boolean(visible));
-
-               final JCheckBox check = new JCheckBox(group, visible);
-               check.setFont(new Font("Serif", Font.BOLD, 12));
-               check.addItemListener(new ItemListener()
-               {
-                 public void itemStateChanged(ItemEvent evt)
-                 {
-                   fr.featureGroups.put(check.getText(),
-                                        new Boolean(check.isSelected()));
-                   af.alignPanel.seqPanel.seqCanvas.repaint();
-                   if (af.alignPanel.overviewPanel != null)
-                     af.alignPanel.overviewPanel.updateOverviewImage();
-
-                   resetTable(true);
-                 }
-               });
-               groupPanel.add(check);
-             }
-       }
-
-       if (!allFeatures.contains(tmpfeatures[index].getType()))
-       {
-           allFeatures.addElement(tmpfeatures[index].getType());
-       }
-       index ++;
+          if (!allGroups.contains(group))
+          {
+            allGroups.addElement(group);
+
+            boolean visible = true;
+            if (fr.featureGroups.containsKey(group))
+            {
+              visible = ( (Boolean) fr.featureGroups.get(group)).booleanValue();
+            }
+
+            if (groupPanel == null)
+            {
+              groupPanel = new JPanel();
+            }
+
+            boolean alreadyAdded = false;
+            for (int g = 0; g < groupPanel.getComponentCount(); g++)
+            {
+              if ( ( (JCheckBox) groupPanel.getComponent(g))
+                  .getText().equals(group))
+              {
+                alreadyAdded = true;
+                break;
+              }
+            }
+
+            if (alreadyAdded)
+            {
+              continue;
+            }
+
+            fr.featureGroups.put(group, new Boolean(visible));
+
+            final JCheckBox check = new JCheckBox(group, visible);
+            check.setFont(new Font("Serif", Font.BOLD, 12));
+            check.addItemListener(new ItemListener()
+            {
+              public void itemStateChanged(ItemEvent evt)
+              {
+                fr.featureGroups.put(check.getText(),
+                                     new Boolean(check.isSelected()));
+                af.alignPanel.seqPanel.seqCanvas.repaint();
+                if (af.alignPanel.overviewPanel != null)
+                {
+                  af.alignPanel.overviewPanel.updateOverviewImage();
+                }
+
+                resetTable(true);
+              }
+            });
+            groupPanel.add(check);
+          }
+        }
+
+        if (!allFeatures.contains(tmpfeatures[index].getType()))
+        {
+          allFeatures.addElement(tmpfeatures[index].getType());
+        }
+        index++;
+      }
     }
-  }
 
-     resetTable(false);
+    resetTable(false);
 
-     validate();
+    validate();
   }
 
-
   void resetTable(boolean groupsChanged)
   {
-   SequenceFeature [] tmpfeatures;
-   String group=null, type;
-   Vector visibleChecks = new Vector();
+    SequenceFeature[] tmpfeatures;
+    String group = null, type;
+    Vector visibleChecks = new Vector();
 
-   //Find out which features should be visible depending on which groups
-   //are selected / deselected
+    //Find out which features should be visible depending on which groups
+    //are selected / deselected
     for (int i = 0; i < af.getViewport().alignment.getHeight(); i++)
     {
 
-        tmpfeatures = af.getViewport().alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();
-        if (tmpfeatures == null)
-          continue;
+      tmpfeatures = af.getViewport().alignment.getSequenceAt(i).
+          getDatasetSequence().getSequenceFeatures();
+      if (tmpfeatures == null)
+      {
+        continue;
+      }
 
-        int index = 0;
-        while (index < tmpfeatures.length)
-        {
-          group = tmpfeatures[index].featureGroup;
+      int index = 0;
+      while (index < tmpfeatures.length)
+      {
+        group = tmpfeatures[index].featureGroup;
 
-          if(tmpfeatures[index].begin==0 && tmpfeatures[index].end==0)
-          {
-            index ++;
-            continue;
-          }
+        if (tmpfeatures[index].begin == 0 && tmpfeatures[index].end == 0)
+        {
+          index++;
+          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())
+        {
+          type = tmpfeatures[index].getType();
+          if (!visibleChecks.contains(type))
           {
-            type = tmpfeatures[index].getType();
-            if(!visibleChecks.contains(type) )
-            {
-              visibleChecks.addElement(type);
-            }
+            visibleChecks.addElement(type);
           }
-          index++;
         }
+        index++;
+      }
     }
 
     int fSize = visibleChecks.size();
-    Object [][] data = new Object[fSize][3];
+    Object[][] data = new Object[fSize][3];
     int dataIndex = 0;
 
-    if(fr.renderOrder!=null)
+    if (fr.renderOrder != null)
     {
       //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--)
+      for (int ro = fr.renderOrder.length - 1; ro > -1; ro--)
       {
-           type = fr.renderOrder[ro];
+        type = fr.renderOrder[ro];
 
-           if(!visibleChecks.contains(type))
-             continue;
+        if (!visibleChecks.contains(type))
+        {
+          continue;
+        }
 
-           data[dataIndex][0] = type;
-           data[dataIndex][1] = fr.getColour(type);
-           data[dataIndex][2] = new Boolean(af.getViewport().featuresDisplayed.containsKey(type));
-           dataIndex++;
-           visibleChecks.removeElement(type);
+        data[dataIndex][0] = type;
+        data[dataIndex][1] = fr.getColour(type);
+        data[dataIndex][2] = new Boolean(af.getViewport().featuresDisplayed.
+                                         containsKey(type));
+        dataIndex++;
+        visibleChecks.removeElement(type);
       }
     }
 
     fSize = visibleChecks.size();
-    for(int i=0; i<fSize; i++)
+    for (int i = 0; i < fSize; i++)
     {
       //These must be extra features belonging to the group
       //which was just selected
@@ -305,16 +319,15 @@ public class FeatureSettings extends JPanel
       dataIndex++;
     }
 
-    if(originalData==null)
+    if (originalData == null)
     {
       originalData = new Object[data.length][3];
-      System.arraycopy(data,0,originalData,0,data.length);
+      System.arraycopy(data, 0, originalData, 0, data.length);
     }
 
     table.setModel(new FeatureTableModel(data));
     table.getColumnModel().getColumn(0).setPreferredWidth(200);
 
-
     if (groupPanel != null)
     {
       groupPanel.setLayout(
@@ -330,50 +343,56 @@ public class FeatureSettings extends JPanel
 
   void load()
   {
-    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");
-
-     int value = chooser.showOpenDialog(this);
-
-     if (value == JalviewFileChooser.APPROVE_OPTION)
-     {
-       File file = chooser.getSelectedFile();
-
-       try
-       {
-         InputStreamReader in = new InputStreamReader(new FileInputStream(
-             file), "UTF-8");
-
-         jalview.binding.JalviewUserColours jucs = new jalview.binding.
-             JalviewUserColours();
-         jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in);
-
-
-         for (int i = 0; i < jucs.getColourCount(); i++)
-         {
-           fr.setColour( jucs.getColour(i).getName(),
-                          new Color(Integer.parseInt( jucs.getColour(i).getRGB(), 16)));
-         }
-
-         setTableData();
-         af.alignPanel.repaint();
-       }
-       catch (Exception ex)
-       {
-         System.out.println("Error loading User Colour File\n" + ex);
-       }
-     }
+    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");
+
+    int value = chooser.showOpenDialog(this);
+
+    if (value == JalviewFileChooser.APPROVE_OPTION)
+    {
+      File file = chooser.getSelectedFile();
+
+      try
+      {
+        InputStreamReader in = new InputStreamReader(new FileInputStream(
+            file), "UTF-8");
+
+        jalview.binding.JalviewUserColours jucs = new jalview.binding.
+            JalviewUserColours();
+        jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in);
+
+        for (int i = 0; i < jucs.getColourCount(); i++)
+        {
+          fr.setColour(jucs.getColour(i).getName(),
+                       new Color(Integer.parseInt(jucs.getColour(i).getRGB(),
+                                                  16)));
+        }
+
+        setTableData();
+        af.alignPanel.repaint();
+      }
+      catch (Exception ex)
+      {
+        System.out.println("Error loading User Colour File\n" + ex);
+      }
+    }
   }
 
   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");
@@ -382,43 +401,44 @@ public class FeatureSettings extends JPanel
 
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
-        String choice = chooser.getSelectedFile().getPath();
-        jalview.binding.JalviewUserColours ucs = new jalview.binding.JalviewUserColours();
-        ucs.setSchemeName("Sequence Features");
-        try
-        {
-            PrintWriter out = new PrintWriter(new OutputStreamWriter(
-                        new FileOutputStream(choice), "UTF-8"));
-
-            Enumeration e = fr.featureColours.keys();
-           while(e.hasMoreElements())
-           {
-                jalview.binding.Colour col = new jalview.binding.Colour();
-                col.setName(e.nextElement().toString());
-                col.setRGB(jalview.util.Format.getHexString(
-                        fr.getColour(col.getName())));
-                ucs.addColour(col);
-            }
+      String choice = chooser.getSelectedFile().getPath();
+      jalview.binding.JalviewUserColours ucs = new jalview.binding.
+          JalviewUserColours();
+      ucs.setSchemeName("Sequence Features");
+      try
+      {
+        PrintWriter out = new PrintWriter(new OutputStreamWriter(
+            new FileOutputStream(choice), "UTF-8"));
 
-            ucs.marshal(out);
-            out.close();
-        }
-        catch (Exception ex)
+        Enumeration e = fr.featureColours.keys();
+        while (e.hasMoreElements())
         {
-            ex.printStackTrace();
+          jalview.binding.Colour col = new jalview.binding.Colour();
+          col.setName(e.nextElement().toString());
+          col.setRGB(jalview.util.Format.getHexString(
+              fr.getColour(col.getName())));
+          ucs.addColour(col);
         }
+
+        ucs.marshal(out);
+        out.close();
+      }
+      catch (Exception ex)
+      {
+        ex.printStackTrace();
+      }
     }
   }
 
   public void invertSelection()
   {
-    for(int i=0; i<table.getRowCount(); i++)
+    for (int i = 0; i < table.getRowCount(); i++)
     {
-      Boolean value = (Boolean)table.getValueAt(i,2);
+      Boolean value = (Boolean) table.getValueAt(i, 2);
 
       table.setValueAt(
           new Boolean(!value.booleanValue()),
-                       i,2);
+          i, 2);
     }
   }
 
@@ -433,16 +453,18 @@ public class FeatureSettings extends JPanel
 
   }
 
-  public void updateFeatureRenderer(Object [][] data)
+  public void updateFeatureRenderer(Object[][] data)
   {
-    fr.setFeaturePriority( data );
+    fr.setFeaturePriority(data);
     af.alignPanel.repaint();
 
-    if(af.alignPanel.overviewPanel!=null)
+    if (af.alignPanel.overviewPanel != null)
+    {
       af.alignPanel.overviewPanel.updateOverviewImage();
+    }
   }
 
-  int selectedRow =-1;
+  int selectedRow = -1;
   JTabbedPane tabbedPane = new JTabbedPane();
   BorderLayout borderLayout1 = new BorderLayout();
   BorderLayout borderLayout2 = new BorderLayout();
@@ -481,8 +503,8 @@ public class FeatureSettings extends JPanel
     {
       public void actionPerformed(ActionEvent e)
       {
-          updateFeatureRenderer(originalData);
-          close();
+        updateFeatureRenderer(originalData);
+        close();
       }
     });
     ok.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
@@ -521,7 +543,6 @@ public class FeatureSettings extends JPanel
       }
     });
 
-
     transparency.setMaximum(70);
     fetchDAS.setText("Fetch DAS Features");
     fetchDAS.addActionListener(new ActionListener()
@@ -551,7 +572,7 @@ public class FeatureSettings extends JPanel
       }
     });
     this.add(tabbedPane, java.awt.BorderLayout.CENTER);
-    tabbedPane.addTab("Feature Settings", settingsPane );
+    tabbedPane.addTab("Feature Settings", settingsPane);
     tabbedPane.addTab("DAS Settings", dasSettingsPane);
     bigPanel.add(transPanel, java.awt.BorderLayout.SOUTH);
     transPanel.add(transparency);
@@ -575,11 +596,11 @@ public class FeatureSettings extends JPanel
     cancelDAS.setEnabled(true);
     Vector selectedSources = dassourceBrowser.getSelectedSources();
 
-    SequenceI [] dataset, seqs ;
+    SequenceI[] dataset, seqs;
     int iSize;
 
-    if(af.getViewport().getSelectionGroup()!=null
-      && af.getViewport().getSelectionGroup().getSize()>0)
+    if (af.getViewport().getSelectionGroup() != null
+        && af.getViewport().getSelectionGroup().getSize() > 0)
     {
       iSize = af.getViewport().getSelectionGroup().getSize();
       dataset = new SequenceI[iSize];
@@ -589,8 +610,8 @@ public class FeatureSettings extends JPanel
     }
     else
     {
-       iSize = af.getViewport().getAlignment().getHeight();
-       seqs = af.getViewport().getAlignment().getSequencesArray();
+      iSize = af.getViewport().getAlignment().getHeight();
+      seqs = af.getViewport().getAlignment().getSequencesArray();
     }
 
     dataset = new SequenceI[iSize];
@@ -601,9 +622,9 @@ public class FeatureSettings extends JPanel
 
     dasFeatureFetcher =
         new jalview.io.DasSequenceFeatureFetcher(
-        dataset,
-        this,
-        selectedSources);
+            dataset,
+            this,
+            selectedSources);
 
     af.getViewport().setShowSequenceFeatures(true);
     af.showSeqFeatures.setSelected(true);
@@ -638,153 +659,179 @@ public class FeatureSettings extends JPanel
       this.data = data;
     }
 
-    private String[] columnNames = {"Feature Type", "Colour","Display"};
-          private Object[][] data;
+    private String[] columnNames =
+        {
+        "Feature Type", "Colour", "Display"};
+    private Object[][] data;
 
-          public Object[][] getData()
-          {
-            return data;
-          }
+    public Object[][] getData()
+    {
+      return data;
+    }
 
-          public void setData(Object[][] data)
-          {
-            this.data = data;
-          }
+    public void setData(Object[][] data)
+    {
+      this.data = data;
+    }
 
-          public int getColumnCount() {
-              return columnNames.length;
-          }
+    public int getColumnCount()
+    {
+      return columnNames.length;
+    }
 
-          public Object[] getRow(int row)
-          {
-            return data[row];
-          }
+    public Object[] getRow(int row)
+    {
+      return data[row];
+    }
 
-          public int getRowCount() {
-              return data.length;
-          }
+    public int getRowCount()
+    {
+      return data.length;
+    }
 
-          public String getColumnName(int col) {
-              return columnNames[col];
-          }
+    public String getColumnName(int col)
+    {
+      return columnNames[col];
+    }
 
-          public Object getValueAt(int row, int col) {
-              return data[row][col];
-          }
+    public Object getValueAt(int row, int col)
+    {
+      return data[row][col];
+    }
 
-          public Class getColumnClass(int c) {
-              return getValueAt(0, c).getClass();
-          }
+    public Class getColumnClass(int c)
+    {
+      return getValueAt(0, c).getClass();
+    }
 
-          public boolean isCellEditable(int row, int col) {
-              return col==0 ? false:true;
-          }
+    public boolean isCellEditable(int row, int col)
+    {
+      return col == 0 ? false : true;
+    }
 
-          public void setValueAt(Object value, int row, int col) {
-              data[row][col] = value;
-              fireTableCellUpdated(row, col);
-              updateFeatureRenderer(data);
-          }
+    public void setValueAt(Object value, int row, int col)
+    {
+      data[row][col] = value;
+      fireTableCellUpdated(row, col);
+      updateFeatureRenderer(data);
+    }
+
+  }
 
+  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.
     }
-    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.
-       }
-
-       public Component getTableCellRendererComponent(
-                               JTable table, Object color,
-                               boolean isSelected, boolean hasFocus,
-                               int row, int column) {
-           Color newColor = (Color)color;
-           setBackground(newColor);
-               if (isSelected) {
-                   if (selectedBorder == null) {
-                       selectedBorder = BorderFactory.createMatteBorder(2,5,2,5,
-                                                 table.getSelectionBackground());
-                   }
-                   setBorder(selectedBorder);
-               } else {
-                   if (unselectedBorder == null) {
-                       unselectedBorder = BorderFactory.createMatteBorder(2,5,2,5,
-                                                 table.getBackground());
-                   }
-                   setBorder(unselectedBorder);
-               }
-
-           setToolTipText("RGB value: " + newColor.getRed() + ", "
-                                        + newColor.getGreen() + ", "
-                                        + newColor.getBlue());
-           return this;
-       }
-   }
+
+    public Component getTableCellRendererComponent(
+        JTable table, Object color,
+        boolean isSelected, boolean hasFocus,
+        int row, int column)
+    {
+      Color newColor = (Color) color;
+      setBackground(newColor);
+      if (isSelected)
+      {
+        if (selectedBorder == null)
+        {
+          selectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5,
+              table.getSelectionBackground());
+        }
+        setBorder(selectedBorder);
+      }
+      else
+      {
+        if (unselectedBorder == null)
+        {
+          unselectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5,
+              table.getBackground());
+        }
+        setBorder(unselectedBorder);
+      }
+
+      setToolTipText("RGB value: " + newColor.getRed() + ", "
+                     + newColor.getGreen() + ", "
+                     + newColor.getBlue());
+      return this;
+    }
+  }
 }
 
- 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.
-         button = new JButton();
-         button.setActionCommand(EDIT);
-         button.addActionListener(this);
-         button.setBorderPainted(false);
-         //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
-     }
-
-     /**
-      * 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.
-             button.setBackground(currentColor);
-             colorChooser.setColor(currentColor);
-             dialog.setVisible(true);
-
-             //Make the renderer reappear.
-             fireEditingStopped();
-
-         } else { //User pressed dialog's "OK" button.
-             currentColor = colorChooser.getColor();
-         }
-     }
-
-     //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) {
-         currentColor = (Color)value;
-         return button;
-     }
+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.
+    button = new JButton();
+    button.setActionCommand(EDIT);
+    button.addActionListener(this);
+    button.setBorderPainted(false);
+    //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
+  }
+
+  /**
+   * 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.
+      button.setBackground(currentColor);
+      colorChooser.setColor(currentColor);
+      dialog.setVisible(true);
+
+      //Make the renderer reappear.
+      fireEditingStopped();
+
+    }
+    else
+    { //User pressed dialog's "OK" button.
+      currentColor = colorChooser.getColor();
+    }
+  }
+
+  //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)
+  {
+    currentColor = (Color) value;
+    return button;
+  }
 }
diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index 0811f82..fcac4d2 100755
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,18 +18,14 @@
  */
 package jalview.gui;
 
-import jalview.datamodel.*;
-
-import jalview.jbgui.*;
+import java.util.*;
 
 import java.awt.*;
 import java.awt.event.*;
-
-import java.util.*;
-
 import javax.swing.*;
-import javax.swing.event.*;
 
+import jalview.datamodel.*;
+import jalview.jbgui.*;
 
 /**
  * DOCUMENT ME!
@@ -37,169 +33,175 @@ import javax.swing.event.*;
  * @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!
-     */
-    public Finder()
+  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!
+   */
+  public Finder()
+  {
+    frame = new JInternalFrame();
+    frame.setContentPane(this);
+    frame.setLayer(JLayeredPane.PALETTE_LAYER);
+    Desktop.addInternalFrame(frame, "Find", 340, 110);
+
+    textfield.requestFocus();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void findNext_actionPerformed(ActionEvent e)
+  {
+    if (getFocusedViewport())
     {
-      frame = new JInternalFrame();
-      frame.setContentPane(this);
-      frame.setLayer(JLayeredPane.PALETTE_LAYER);
-      Desktop.addInternalFrame(frame, "Find", 340, 110);
-
-      textfield.requestFocus();
+      doSearch(false);
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void findAll_actionPerformed(ActionEvent e)
+  {
+    if (getFocusedViewport())
+    {
+      resIndex = 0;
+      seqIndex = 0;
+      doSearch(true);
     }
+  }
 
+  boolean getFocusedViewport()
+  {
+    JInternalFrame frame = Desktop.desktop.getAllFrames()[1];
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void findNext_actionPerformed(ActionEvent e)
+    if (frame != null && frame instanceof AlignFrame)
     {
-      if (getFocusedViewport())
-        doSearch(false);
+      av = ( (AlignFrame) frame).viewport;
+      ap = ( (AlignFrame) frame).alignPanel;
+      return true;
+    }
+    return false;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void createNewGroup_actionPerformed(ActionEvent e)
+  {
+    JLabel label = new JLabel("Enter name of new sequence feature");
+    JTextField textinput = new JTextField(textfield.getText());
+    JPanel panel = new JPanel(new BorderLayout());
+    panel.add(label, BorderLayout.NORTH);
+    panel.add(textinput, BorderLayout.SOUTH);
+
+    SequenceI[] seqs = new SequenceI[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(textinput.getText(),
+                                        "Search Results", null,
+                                        searchResults.getResultStart(i),
+                                        searchResults.getResultEnd(i),
+                                        "Search Results");
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void findAll_actionPerformed(ActionEvent e)
+    if (ap.seqPanel.seqCanvas.getFeatureRenderer()
+        .createNewFeatures(seqs, features))
     {
-      if(getFocusedViewport())
-      {
-        resIndex = 0;
-        seqIndex = 0;
-        doSearch(true);
-      }
+      ap.alignFrame.showSeqFeatures.setSelected(true);
+      av.setShowSequenceFeatures(true);
+      ap.highlightSearchResults(null);
     }
+  }
 
-    boolean getFocusedViewport()
+  /**
+   * DOCUMENT ME!
+   *
+   * @param findAll DOCUMENT ME!
+   */
+  void doSearch(boolean findAll)
+  {
+    createNewGroup.setEnabled(false);
+
+    String searchString = textfield.getText().trim();
+
+    if (searchString.length() < 1)
+    {
+      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);
+    finder.setCaseSensitive(caseSensitive.isSelected());
+    finder.setFindAll(findAll);
+
+    finder.find(searchString); // returns true if anything was actually found
+
+    seqIndex = finder.getSeqIndex();
+    resIndex = finder.getResIndex();
+
+    searchResults = finder.getSearchResults(); // find(regex, caseSensitive.isSelected(), )
+    Vector idMatch = finder.getIdMatch();
+    // set or reset the GUI
+    if ( (searchResults.getSize() == 0) && (idMatch.size() > 0))
     {
-      JInternalFrame frame = Desktop.desktop.getAllFrames()[1];
-
-      if(frame!=null && frame instanceof AlignFrame)
-      {
-        av = ((AlignFrame)frame).viewport;
-        ap = ((AlignFrame)frame).alignPanel;
-        return true;
-      }
-      return false;
+      ap.idPanel.highlightSearchResults(idMatch);
     }
 
+    int resultSize = searchResults.getSize();
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void createNewGroup_actionPerformed(ActionEvent e)
+    if (searchResults.getSize() > 0)
+    {
+      createNewGroup.setEnabled(true);
+    }
+    else
     {
-        JLabel label = new JLabel("Enter name of new sequence feature");
-        JTextField textinput = new JTextField(textfield.getText());
-        JPanel panel = new JPanel(new BorderLayout());
-        panel.add(label, BorderLayout.NORTH);
-        panel.add(textinput, BorderLayout.SOUTH);
-
-
-        SequenceI [] seqs = new SequenceI[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(textinput.getText(),
-                "Search Results", null,
-                searchResults.getResultStart(i),
-                searchResults.getResultEnd(i),
-               "Search Results");
-        }
-
-        if( ap.seqPanel.seqCanvas.getFeatureRenderer()
-            .createNewFeatures(seqs, features))
-        {
-          ap.alignFrame.showSeqFeatures.setSelected(true);
-          av.setShowSequenceFeatures(true);
-          ap.highlightSearchResults(null);
-        }
+      searchResults = null;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param findAll DOCUMENT ME!
-     */
-    void doSearch(boolean findAll)
+    // if allResults is null, this effectively switches displaySearch flag in seqCanvas
+    ap.highlightSearchResults(searchResults);
+    // TODO: add enablers for 'SelectSequences' or 'SelectColumns' or 'SelectRegion' selection
+    if (!findAll && resultSize == 0)
     {
-        createNewGroup.setEnabled(false);
-
-        String searchString = textfield.getText().trim();
-        
-        if(searchString.length()<1)
-          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);
-        finder.setCaseSensitive(caseSensitive.isSelected());
-        finder.setFindAll(findAll);
-        
-        finder.find(searchString); // returns true if anything was actually found
-
-        seqIndex=finder.getSeqIndex();
-        resIndex=finder.getResIndex();
-
-        searchResults = finder.getSearchResults(); // find(regex, caseSensitive.isSelected(), )
-        Vector idMatch = finder.getIdMatch();
-        // set or reset the GUI
-        if ((searchResults.getSize() == 0) && (idMatch.size() > 0))
-        {
-            ap.idPanel.highlightSearchResults(idMatch);
-        }
-
-
-        int resultSize = searchResults.getSize();
-
-        if (searchResults.getSize() > 0)
-          createNewGroup.setEnabled(true);
-        else
-          searchResults = null;
-
-        // if allResults is null, this effectively switches displaySearch flag in seqCanvas
-        ap.highlightSearchResults(searchResults);
-        // TODO: add enablers for 'SelectSequences' or 'SelectColumns' or 'SelectRegion' selection
-        if(!findAll && resultSize==0)
-        {
-            JOptionPane.showInternalMessageDialog(this, "Finished searching",
-                null, JOptionPane.INFORMATION_MESSAGE);
-            resIndex = 0;
-            seqIndex = 0;
-        }
-
-        if (findAll)
-        {
-          String message = resultSize + " matches found.";
-          JOptionPane.showInternalMessageDialog(this, message, null,
-                                                JOptionPane.INFORMATION_MESSAGE);
-        }
+      JOptionPane.showInternalMessageDialog(this, "Finished searching",
+                                            null,
+                                            JOptionPane.INFORMATION_MESSAGE);
+      resIndex = 0;
+      seqIndex = 0;
+    }
 
+    if (findAll)
+    {
+      String message = resultSize + " matches found.";
+      JOptionPane.showInternalMessageDialog(this, message, null,
+                                            JOptionPane.INFORMATION_MESSAGE);
     }
+
+  }
 }
diff --git a/src/jalview/gui/FontChooser.java b/src/jalview/gui/FontChooser.java
index 9803822..0263836 100755
--- a/src/jalview/gui/FontChooser.java
+++ b/src/jalview/gui/FontChooser.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,15 +18,12 @@
  */
 package jalview.gui;
 
-import jalview.bin.*;
-
-import jalview.jbgui.*;
-
 import java.awt.*;
 import java.awt.event.*;
-
 import javax.swing.*;
 
+import jalview.bin.*;
+import jalview.jbgui.*;
 
 /**
  * DOCUMENT ME!
@@ -34,226 +31,229 @@ import javax.swing.*;
  * @author $author$
  * @version $Revision$
  */
-public class FontChooser extends GFontChooser
+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)
+  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)
     {
-      this.tp = tp;
-      ap = tp.treeCanvas.ap;
-      oldFont = tp.getTreeFont();
-      defaultButton.setVisible(false);
-      smoothFont.setEnabled(false);
-      init();
+      Desktop.addInternalFrame(frame, "Change Font (Tree Panel)", 340, 170, false);
     }
-    /**
-     * Creates a new FontChooser object.
-     *
-     * @param ap DOCUMENT ME!
-     */
-    public FontChooser(AlignmentPanel ap)
+    else
     {
-      oldFont = ap.av.getFont();
-      this.ap = ap;
-      init();
+      Desktop.addInternalFrame(frame, "Change Font", 340, 170, false);
     }
 
-    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);
+    frame.setLayer(JLayeredPane.PALETTE_LAYER);
 
-        String[] fonts = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment()
-                                                     .getAvailableFontFamilyNames();
+    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;
+    for (int i = 0; i < fonts.length; i++)
+    {
+      fontName.addItem(fonts[i]);
     }
 
-    public void smoothFont_actionPerformed(ActionEvent e)
+    for (int i = 1; i < 51; i++)
     {
-      ap.av.antiAlias = smoothFont.isSelected();
-      ap.annotationPanel.image = null;
-      ap.repaint();
+      fontSize.addItem(i + "");
     }
 
-
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void ok_actionPerformed(ActionEvent e)
+    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.repaint();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void ok_actionPerformed(ActionEvent e)
+  {
+    try
     {
-        try
-        {
-            frame.setClosed(true);
-        }
-        catch (Exception ex)
-        {
-        }
-
-        if(ap!=null)
-        {
-          if (ap.getOverviewPanel() != null)
-          {
-            ap.getOverviewPanel().updateOverviewImage();
-          }
-        }
+      frame.setClosed(true);
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void cancel_actionPerformed(ActionEvent e)
+    catch (Exception ex)
     {
-        if(ap!=null)
-        {
-          ap.av.setFont(oldFont);
-          ap.repaint();
-        }
-        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()
+    if (ap != null)
     {
-      Font newFont = new Font(fontName.getSelectedItem().toString(),
-                              fontStyle.getSelectedIndex(),
-                              Integer.parseInt(fontSize.getSelectedItem().toString()));
-      if(tp != null)
+      if (ap.getOverviewPanel() != null)
       {
-        tp.setTreeFont(newFont);
-      }
-      else if(ap != null)
-      {
-        ap.av.setFont(newFont);
-        ap.fontChanged();
+        ap.getOverviewPanel().updateOverviewImage();
       }
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void cancel_actionPerformed(ActionEvent e)
+  {
+    if (ap != null)
+    {
+      ap.av.setFont(oldFont);
+      ap.repaint();
+    }
+    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);
+    FontMetrics fm = getGraphics().getFontMetrics(newFont);
 
-      monospaced.setSelected( fm.getStringBounds("M",getGraphics()).getWidth()
-                                ==fm.getStringBounds("|",getGraphics()).getWidth());
+    monospaced.setSelected(fm.getStringBounds("M", getGraphics()).getWidth()
+                           == fm.getStringBounds("|", getGraphics()).getWidth());
 
-    }
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void fontName_actionPerformed(ActionEvent e)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void fontName_actionPerformed(ActionEvent e)
+  {
+    if (init)
     {
-        if (init)
-        {
-            return;
-        }
-
-        changeFont();
+      return;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void fontSize_actionPerformed(ActionEvent e)
+    changeFont();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void fontSize_actionPerformed(ActionEvent e)
+  {
+    if (init)
     {
-        if (init)
-        {
-            return;
-        }
-
-        changeFont();
+      return;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void fontStyle_actionPerformed(ActionEvent e)
+    changeFont();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void fontStyle_actionPerformed(ActionEvent e)
+  {
+    if (init)
     {
-        if (init)
-        {
-            return;
-        }
-
-        changeFont();
+      return;
     }
 
-    /**
-     * 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()));
-    }
+    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/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index 71cc483..97b8669 100755
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,13 +18,11 @@
  */
 package jalview.gui;
 
-import jalview.datamodel.*;
-
 import java.awt.*;
 import java.awt.image.*;
-
 import javax.swing.*;
 
+import jalview.datamodel.*;
 
 /**
  * DOCUMENT ME!
@@ -32,418 +30,448 @@ import javax.swing.*;
  * @author $author$
  * @version $Revision$
  */
-public class IdCanvas extends JPanel
+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)
+  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
     {
-        setLayout(new BorderLayout());
-        this.av = av;
-        PaintRefresher.Register(this, av.getSequenceSetId());
+      gg.setColor(av.getSequenceColour(s));
+      gg.fillRect(0, ( (i - starty) * charHeight) + ypos, getWidth(),
+                  charHeight);
+      gg.setColor(Color.black);
     }
 
-    /**
-     * 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)
+    if (av.rightAlignIds)
     {
-        int xPos = 0;
-        int panelWidth = getWidth();
-        int charHeight = av.charHeight;
+      xPos = panelWidth - fm.stringWidth(
+          s.getDisplayId(av.getShowJVSuffix())
+          ) - 4;
+    }
 
-        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);
-        }
+    gg.drawString(s.getDisplayId(av.getShowJVSuffix()),
+                  xPos,
+                  ( ( (i - starty + 1) * charHeight) + ypos) - (charHeight / 5));
 
-        if (av.rightAlignIds)
-        {
-          xPos = panelWidth - fm.stringWidth(
-              s.getDisplayId(av.getShowJVSuffix())
-              ) - 4;
-        }
+    if (av.hasHiddenRows && av.showHiddenMarkers)
+    {
+      drawMarker(i, starty, ypos);
+    }
 
-        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;
+      }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param vertical DOCUMENT ME!
-     */
-    public void fastPaint(int vertical)
+    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)
     {
-        if (gg == null)
-        {
-            repaint();
+      fastPaint = false;
+      g.drawImage(image, 0, 0, this);
 
-            return;
-        }
+      return;
+    }
 
-        gg.copyArea(0, 0, getWidth(), imgHeight, 0, -vertical * av.charHeight);
+    int oldHeight = imgHeight;
 
-        int ss = av.startSeq;
-        int es = av.endSeq;
-        int transY = 0;
+    imgHeight = getHeight();
+    imgHeight -= (imgHeight % av.charHeight);
 
-        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 (imgHeight < 1)
+    {
+      return;
+    }
 
-            if (es > av.endSeq)
-            {
-                es = av.endSeq;
-            }
-        }
+    if (oldHeight != imgHeight || image.getWidth(this) != getWidth())
+    {
+      image = new BufferedImage(getWidth(), imgHeight,
+                                BufferedImage.TYPE_INT_RGB);
+    }
 
-        gg.translate(0, transY);
+    gg = (Graphics2D) image.getGraphics();
 
-        drawIds(ss, es);
+    //Fill in the background
+    gg.setColor(Color.white);
+    gg.fillRect(0, 0, getWidth(), imgHeight);
 
-        gg.translate(0, -transY);
+    drawIds(av.getStartSeq(), av.endSeq);
 
-        fastPaint = true;
-        repaint();
+    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();
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param g DOCUMENT ME!
-     */
-    public void paintComponent(Graphics g)
+    gg.setFont(idfont);
+    fm = gg.getFontMetrics();
+
+    if (av.antiAlias)
     {
-        g.setColor(Color.white);
-        g.fillRect(0, 0, getWidth(), getHeight());
+      gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+                          RenderingHints.VALUE_ANTIALIAS_ON);
+    }
 
-        if (fastPaint)
-        {
-            fastPaint = false;
-            g.drawImage(image, 0, 0, this);
+    Color currentColor = Color.white;
+    Color currentTextColor = Color.black;
 
-            return;
-        }
+    if (av.getWrapAlignment())
+    {
+      int maxwidth = av.alignment.getWidth();
+      int alheight = av.alignment.getHeight();
 
-        int oldHeight = imgHeight;
+      if (av.hasHiddenColumns)
+      {
+        maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+      }
 
-        imgHeight = getHeight();
-        imgHeight -= (imgHeight % av.charHeight);
+      int annotationHeight = 0;
 
-        if (imgHeight < 1)
+      if (av.showAnnotation)
+      {
+        if (ap == null)
         {
-            return;
+          ap = new AnnotationPanel(av);
         }
 
-        if(oldHeight!=imgHeight || image.getWidth(this)!=getWidth())
+        annotationHeight = ap.adjustPanelHeight();
+        if (labels == null)
         {
-          image = new BufferedImage(getWidth(), imgHeight,
-                                    BufferedImage.TYPE_INT_RGB);
+          labels = new AnnotationLabels(av);
         }
+      }
 
-        gg = (Graphics2D) image.getGraphics();
+      int hgap = av.charHeight;
+      if (av.scaleAboveWrapped)
+      {
+        hgap += av.charHeight;
+      }
 
-        //Fill in the background
-        gg.setColor(Color.white);
-        gg.fillRect(0, 0, getWidth(), imgHeight);
+      int cHeight = alheight * av.charHeight
+          + hgap
+          + annotationHeight;
 
-        drawIds(av.getStartSeq(), av.endSeq);
+      int rowSize = av.getEndRes() - av.getStartRes();
 
-        g.drawImage(image, 0, 0, this);
-    }
+      // 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);
+          }
 
-    /**
-     * 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());
+          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
-      idfont = av.getFont();
+    {
+      //No need to hang on to labels if we're not wrapped
+      labels = null;
 
-      gg.setFont(idfont);
-      fm = gg.getFontMetrics();
+      //Now draw the id strings
+      int panelWidth = getWidth();
+      int xPos = 0;
 
-      if (av.antiAlias)
-        gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
-                            RenderingHints.VALUE_ANTIALIAS_ON);
+      SequenceI sequence;
+      //Now draw the id strings
+      for (int i = starty; i < endy; i++)
+      {
+        sequence = av.alignment.getSequenceAt(i);
 
-        Color currentColor = Color.white;
-        Color currentTextColor = Color.black;
+        if (sequence == null)
+        {
+          continue;
+        }
 
-        if (av.getWrapAlignment())
+        if (av.hasHiddenRows)
         {
-          int maxwidth = av.alignment.getWidth();
-          int alheight = av.alignment.getHeight();
+          setHiddenFont(sequence);
+        }
 
-          if (av.hasHiddenColumns)
-            maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+        // 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;
+        }
 
-          int annotationHeight = 0;
+        gg.setColor(currentColor);
 
+        gg.fillRect(0, (i - starty) * av.charHeight, getWidth(),
+                    av.charHeight);
 
-          if(av.showAnnotation)
-          {
-            if (ap == null)
-              ap = new AnnotationPanel(av);
+        gg.setColor(currentTextColor);
 
-            annotationHeight = ap.adjustPanelHeight();
-            if (labels == null)
-              labels = new AnnotationLabels(av);
-          }
+        String string = sequence.getDisplayId(av.getShowJVSuffix());
 
-          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
+        if (av.rightAlignIds)
         {
-          //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);
-
-            }
+          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)
-    {
+  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;
+    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;
+    int hiddenIndex = i;
+    int lastIndex = i - 1;
+    int nextIndex = i + 1;
 
-      for(int j=0; j<hSize; j++)
+    for (int j = 0; j < hSize; j++)
+    {
+      if (hseqs[j] != null)
       {
-        if (hseqs[j] != null)
+        if (j - 1 < hiddenIndex)
         {
-          if(j-1<hiddenIndex)
-            hiddenIndex++;
-          if(j-1<lastIndex)
-            lastIndex++;
-          if(j-1<nextIndex)
-            nextIndex++;
+          hiddenIndex++;
         }
-      }
-
-      boolean below = (hiddenIndex > lastIndex + 1);
-      boolean above = (nextIndex > hiddenIndex+1);
-
-
-        gg.setColor(Color.blue);
-        if(below)
+        if (j - 1 < lastIndex)
         {
-          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);
+          lastIndex++;
         }
-        if(above)
+        if (j - 1 < nextIndex)
         {
-          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);
-
+          nextIndex++;
         }
+      }
     }
 
-    void setHiddenFont(SequenceI seq)
-    {
-      Font bold = new Font(av.getFont().getName(), Font.BOLD,
-                           av.getFont().getSize());
+    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);
 
-      if (av.hiddenRepSequences!=null &&
-          av.hiddenRepSequences.containsKey(seq))
-        gg.setFont(bold);
-      else
-        gg.setFont(idfont);
     }
+  }
+
+  void setHiddenFont(SequenceI seq)
+  {
+    Font bold = new Font(av.getFont().getName(), Font.BOLD,
+                         av.getFont().getSize());
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param found DOCUMENT ME!
-     */
-    public void setHighlighted(java.util.Vector found)
+    if (av.hiddenRepSequences != null &&
+        av.hiddenRepSequences.containsKey(seq))
     {
-        searchResults = found;
-        repaint();
+      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 04c1efe..e3a81dc 100755
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,13 +18,11 @@
  */
 package jalview.gui;
 
-import jalview.datamodel.*;
-
 import java.awt.*;
 import java.awt.event.*;
-
 import javax.swing.*;
 
+import jalview.datamodel.*;
 
 /**
  * DOCUMENT ME!
@@ -32,386 +30,393 @@ import javax.swing.*;
  * @author $author$
  * @version $Revision$
  */
-public class IdPanel extends JPanel implements MouseListener,
+public class IdPanel
+    extends JPanel 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;
-
-    /**
-     * Creates a new IdPanel object.
-     *
-     * @param av DOCUMENT ME!
-     * @param parent DOCUMENT ME!
-     */
-    public IdPanel(AlignViewport av, AlignmentPanel parent)
+  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!
+   */
+  public IdPanel(AlignViewport av, AlignmentPanel parent)
+  {
+    this.av = av;
+    alignPanel = parent;
+    idCanvas = new IdCanvas(av);
+    setLayout(new BorderLayout());
+    add(idCanvas, BorderLayout.CENTER);
+    addMouseListener(this);
+    addMouseMotionListener(this);
+    ToolTipManager.sharedInstance().registerComponent(this);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void mouseMoved(MouseEvent e)
+  {
+    int seq = Math.max(0, alignPanel.seqPanel.findSeq(e));
+    if (seq > -1 && seq < av.alignment.getHeight())
     {
-        this.av = av;
-        alignPanel = parent;
-        idCanvas = new IdCanvas(av);
-        setLayout(new BorderLayout());
-        add(idCanvas, BorderLayout.CENTER);
-        addMouseListener(this);
-        addMouseMotionListener(this);
-        ToolTipManager.sharedInstance().registerComponent(this);
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void mouseMoved(MouseEvent e)
-    {
-      int seq = Math.max(0, alignPanel.seqPanel.findSeq(e));
-      if(seq>-1 && seq<av.alignment.getHeight())
+      SequenceI sequence = av.alignment.getSequenceAt(seq);
+      StringBuffer tip = new StringBuffer("<html>");
+      tip.append(sequence.getDisplayId(true));
+      if (sequence.getDescription() != null)
       {
-        SequenceI sequence = av.alignment.getSequenceAt(seq);
-        StringBuffer tip = new StringBuffer("<html>");
-        tip.append(sequence.getDisplayId(true));
-        if (sequence.getDescription() != null)
-        {
-          tip.append("<table width=250 border=0><tr><td><i>");
-          tip.append(sequence.getDescription());
+        tip.append("<table width=250 border=0><tr><td><i>");
+        tip.append(sequence.getDescription());
 
-          //ADD NON POSITIONAL SEQUENCE INFO
-          SequenceFeature [] features = sequence.getDatasetSequence().getSequenceFeatures();
-          if(features!=null)
+        //ADD NON POSITIONAL SEQUENCE INFO
+        SequenceFeature[] features = sequence.getDatasetSequence().
+            getSequenceFeatures();
+        if (features != null)
+        {
+          for (int i = 0; i < features.length; i++)
           {
-            for(int i=0; i<features.length; i++)
+            if (features[i].begin == 0 && features[i].end == 0)
             {
-              if(features[i].begin == 0 && features[i].end ==0)
-              {
-                tip.append("<br>"+features[i].featureGroup
-                          +" "+ features[i].getType()+" "+features[i].description);
-              }
+              tip.append("<br>" + features[i].featureGroup
+                         + " " + features[i].getType() + " " +
+                         features[i].description);
             }
           }
-          tip.append("</i></td></tr></table>");
         }
+        tip.append("</i></td></tr></table>");
+      }
 
-        DBRefEntry[] dbrefs = sequence.getDatasetSequence().getDBRef();
-        if (dbrefs != null)
+      DBRefEntry[] dbrefs = sequence.getDatasetSequence().getDBRef();
+      if (dbrefs != null)
+      {
+        tip.append("<i>");
+        for (int i = 0; i < dbrefs.length; i++)
         {
-          tip.append("<i>");
-          for (int i = 0; i < dbrefs.length; i++)
-          {
-            tip.append("<br>");
-            tip.append(dbrefs[i].getSource() + " "
-                       + dbrefs[i].getAccessionId());
-          }
-          tip.append("</i>");
+          tip.append("<br>");
+          tip.append(dbrefs[i].getSource() + " "
+                     + dbrefs[i].getAccessionId());
         }
-
-        tip.append("</html>");
-        setToolTipText(tip.toString());
+        tip.append("</i>");
       }
-    }
-
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void mouseDragged(MouseEvent e)
-    {
-        mouseDragging = true;
+      tip.append("</html>");
+      setToolTipText(tip.toString());
+    }
+  }
 
-        int seq = Math.max(0, alignPanel.seqPanel.findSeq(e));
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void mouseDragged(MouseEvent e)
+  {
+    mouseDragging = true;
 
-        if (seq < lastid)
-        {
-            selectSeqs(lastid - 1, seq);
-        }
-        else if (seq > lastid)
-        {
-            selectSeqs(lastid + 1, seq);
-        }
+    int seq = Math.max(0, alignPanel.seqPanel.findSeq(e));
 
-        lastid = seq;
-        alignPanel.repaint();
+    if (seq < lastid)
+    {
+      selectSeqs(lastid - 1, seq);
     }
-
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void mouseClicked(MouseEvent e)
+    else if (seq > lastid)
     {
-      if (e.getClickCount() < 2)
-        return;
+      selectSeqs(lastid + 1, seq);
+    }
 
-      java.util.Vector links = Preferences.sequenceURLLinks;
-      if (links == null || links.size() < 1)
-        return;
+    lastid = seq;
+    alignPanel.repaint();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void mouseClicked(MouseEvent e)
+  {
+    if (e.getClickCount() < 2)
+    {
+      return;
+    }
 
-      int seq = alignPanel.seqPanel.findSeq(e);
+    java.util.Vector links = Preferences.sequenceURLLinks;
+    if (links == null || links.size() < 1)
+    {
+      return;
+    }
 
-      //DEFAULT LINK IS FIRST IN THE LINK LIST
+    int seq = alignPanel.seqPanel.findSeq(e);
 
-      String id = av.getAlignment().getSequenceAt(seq).getName();
-      if (id.indexOf("|") > -1)
-        id = id.substring(id.lastIndexOf("|") + 1);
+    //DEFAULT LINK IS FIRST IN THE LINK LIST
 
+    String id = av.getAlignment().getSequenceAt(seq).getName();
+    if (id.indexOf("|") > -1)
+    {
+      id = id.substring(id.lastIndexOf("|") + 1);
+    }
 
-      String url = links.elementAt(0).toString();
-      url = url.substring(url.indexOf("|")+1);
+    String url = links.elementAt(0).toString();
+    url = url.substring(url.indexOf("|") + 1);
 
-      int index = url.indexOf("$SEQUENCE_ID$");
-      url = url.substring(0, index)+ id + url.substring(index+13);
+    int index = url.indexOf("$SEQUENCE_ID$");
+    url = url.substring(0, index) + id + url.substring(index + 13);
 
-      try
-      {
-        jalview.util.BrowserLauncher.openURL(url);
-      }
-      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 );
-        ex.printStackTrace();
-      }
+    try
+    {
+      jalview.util.BrowserLauncher.openURL(url);
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void mouseEntered(MouseEvent e)
+    catch (Exception ex)
     {
-        if (scrollThread != null)
-        {
-            scrollThread.running = false;
-        }
+      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!
-     */
-    public void mouseExited(MouseEvent e)
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void mouseEntered(MouseEvent e)
+  {
+    if (scrollThread != null)
     {
-        if (av.getWrapAlignment())
-        {
-            return;
-        }
-
-        if (mouseDragging && (e.getY() < 0) && (av.getStartSeq() > 0))
-        {
-            scrollThread = new ScrollThread(true);
-        }
-
-        if (mouseDragging && (e.getY() >= getHeight()) &&
-                (av.alignment.getHeight() > av.getEndSeq()))
-        {
-            scrollThread = new ScrollThread(false);
-        }
+      scrollThread.running = false;
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void mouseExited(MouseEvent e)
+  {
+    if (av.getWrapAlignment())
+    {
+      return;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void mousePressed(MouseEvent e)
+    if (mouseDragging && (e.getY() < 0) && (av.getStartSeq() > 0))
     {
-        if (e.getClickCount() == 2)
-        {
-            return;
-        }
+      scrollThread = new ScrollThread(true);
+    }
 
-        int seq = alignPanel.seqPanel.findSeq(e);
+    if (mouseDragging && (e.getY() >= getHeight()) &&
+        (av.alignment.getHeight() > av.getEndSeq()))
+    {
+      scrollThread = new ScrollThread(false);
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void mousePressed(MouseEvent e)
+  {
+    if (e.getClickCount() == 2)
+    {
+      return;
+    }
 
+    int seq = alignPanel.seqPanel.findSeq(e);
 
-        if (javax.swing.SwingUtilities.isRightMouseButton(e))
-        {
-            jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(alignPanel,
-                    (Sequence) av.getAlignment().getSequenceAt(seq),
-                    Preferences.sequenceURLLinks);
-            pop.show(this, e.getX(), e.getY());
+    if (javax.swing.SwingUtilities.isRightMouseButton(e))
+    {
+      jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(alignPanel,
+          (Sequence) av.getAlignment().getSequenceAt(seq),
+          Preferences.sequenceURLLinks);
+      pop.show(this, e.getX(), e.getY());
 
-            return;
-        }
+      return;
+    }
 
+    if ( (av.getSelectionGroup() == null) ||
+        ( (!e.isControlDown() && !e.isShiftDown()) && av.getSelectionGroup() != null))
+    {
+      av.setSelectionGroup(new SequenceGroup());
+      av.getSelectionGroup().setStartRes(0);
+      av.getSelectionGroup().setEndRes(av.alignment.getWidth() - 1);
+    }
 
+    if (e.isShiftDown() && (lastid != -1))
+    {
+      selectSeqs(lastid, seq);
+    }
+    else
+    {
+      selectSeq(seq);
+    }
 
-        if ((av.getSelectionGroup() == null) ||
-                ((!e.isControlDown() && !e.isShiftDown()) && av.getSelectionGroup() != null))
-        {
-          av.setSelectionGroup(new SequenceGroup());
-          av.getSelectionGroup().setStartRes(0);
-          av.getSelectionGroup().setEndRes(av.alignment.getWidth() - 1);
-        }
+    alignPanel.repaint();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param seq DOCUMENT ME!
+   */
+  void selectSeq(int seq)
+  {
+    lastid = seq;
+
+    SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);
+    av.getSelectionGroup().addOrRemove(pickedSeq, true);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param start DOCUMENT ME!
+   * @param end DOCUMENT ME!
+   */
+  void selectSeqs(int start, int end)
+  {
+    if (av.getSelectionGroup() == null)
+    {
+      return;
+    }
 
+    if (end >= av.getAlignment().getHeight())
+    {
+      end = av.getAlignment().getHeight() - 1;
+    }
 
-        if (e.isShiftDown() && (lastid != -1))
-        {
-            selectSeqs(lastid, seq);
-        }
-        else
-        {
-            selectSeq(seq);
-        }
+    lastid = start;
 
-        alignPanel.repaint();
+    if (end < start)
+    {
+      int tmp = start;
+      start = end;
+      end = tmp;
+      lastid = end;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param seq DOCUMENT ME!
-     */
-    void selectSeq(int seq)
+    for (int i = start; i <= end; i++)
     {
-        lastid = seq;
-
-        SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);
-        av.getSelectionGroup().addOrRemove(pickedSeq, true);
+      av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i),
+                                         true);
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param start DOCUMENT ME!
-     * @param end DOCUMENT ME!
-     */
-    void selectSeqs(int start, int end)
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void mouseReleased(MouseEvent e)
+  {
+    if (scrollThread != null)
     {
-        if(av.getSelectionGroup()==null)
-            return;
+      scrollThread.running = false;
+    }
 
-          if (end >= av.getAlignment().getHeight())
-          {
-            end = av.getAlignment().getHeight() - 1;
-          }
+    mouseDragging = false;
+    PaintRefresher.Refresh(this, av.getSequenceSetId());
+  }
 
-        lastid = start;
+  /**
+   * DOCUMENT ME!
+   *
+   * @param found DOCUMENT ME!
+   */
+  public void highlightSearchResults(java.util.Vector found)
+  {
+    idCanvas.setHighlighted(found);
 
-        if (end < start)
-        {
-            int tmp = start;
-            start = end;
-            end = tmp;
-            lastid = end;
-        }
+    if (found == null)
+    {
+      return;
+    }
 
-        for (int i = start; i <= end; i++)
-        {
-          av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i),
-                true);
-        }
+    int index = av.alignment.findIndex( (SequenceI) found.get(0));
+
+    // do we need to scroll the panel?
+    if ( (av.getStartSeq() > index) || (av.getEndSeq() < index))
+    {
+      alignPanel.setScrollValues(av.getStartRes(), index);
     }
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void mouseReleased(MouseEvent e)
+  // this class allows scrolling off the bottom of the visible alignment
+  class ScrollThread
+      extends Thread
+  {
+    boolean running = false;
+    boolean up = true;
+
+    public ScrollThread(boolean up)
     {
-        if (scrollThread != null)
-        {
-            scrollThread.running = false;
-        }
+      this.up = up;
+      start();
+    }
 
-        mouseDragging = false;
-        PaintRefresher.Refresh(this, av.getSequenceSetId());
+    public void stopScrolling()
+    {
+      running = false;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param found DOCUMENT ME!
-     */
-    public void highlightSearchResults(java.util.Vector found)
+    public void run()
     {
-        idCanvas.setHighlighted(found);
+      running = true;
 
-        if (found == null)
+      while (running)
+      {
+        if (alignPanel.scrollUp(up))
         {
-            return;
-        }
-
-        int index = av.alignment.findIndex((SequenceI) found.get(0));
+          // scroll was ok, so add new sequence to selection
+          int seq = av.getStartSeq();
 
-        // do we need to scroll the panel?
-        if ((av.getStartSeq() > index) || (av.getEndSeq() < index))
-        {
-            alignPanel.setScrollValues(av.getStartRes(), index);
-        }
-    }
+          if (!up)
+          {
+            seq = av.getEndSeq();
+          }
 
-    // this class allows scrolling off the bottom of the visible alignment
-    class ScrollThread extends Thread
-    {
-        boolean running = false;
-        boolean up = true;
+          if (seq < lastid)
+          {
+            selectSeqs(lastid - 1, seq);
+          }
+          else if (seq > lastid)
+          {
+            selectSeqs(lastid + 1, seq);
+          }
 
-        public ScrollThread(boolean up)
+          lastid = seq;
+        }
+        else
         {
-            this.up = up;
-            start();
+          running = false;
         }
 
-        public void stopScrolling()
+        alignPanel.repaint();
+
+        try
         {
-            running = false;
+          Thread.sleep(100);
         }
-
-        public void run()
+        catch (Exception ex)
         {
-            running = true;
-
-            while (running)
-            {
-                if (alignPanel.scrollUp(up))
-                {
-                    // scroll was ok, so add new sequence to selection
-                    int seq = av.getStartSeq();
-
-                    if (!up)
-                    {
-                        seq = av.getEndSeq();
-                    }
-
-                    if (seq < lastid)
-                    {
-                        selectSeqs(lastid - 1, seq);
-                    }
-                    else if (seq > lastid)
-                    {
-                        selectSeqs(lastid + 1, seq);
-                    }
-
-                    lastid = seq;
-                }
-                else
-                {
-                    running = false;
-                }
-
-                alignPanel.repaint();
-
-                try
-                {
-                    Thread.sleep(100);
-                }
-                catch (Exception ex)
-                {
-                }
-            }
         }
+      }
     }
+  }
 }
diff --git a/src/jalview/gui/IdwidthAdjuster.java b/src/jalview/gui/IdwidthAdjuster.java
index 1b7b26b..fc732ad 100755
--- a/src/jalview/gui/IdwidthAdjuster.java
+++ b/src/jalview/gui/IdwidthAdjuster.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -20,143 +20,142 @@ 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,
+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.repaint();
-        }
-
-        oldX = evt.getX();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mouseMoved(MouseEvent evt)
+  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);
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mouseClicked(MouseEvent evt)
+    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.repaint();
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param g DOCUMENT ME!
-     */
-    public void paintComponent(Graphics g)
+    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)
     {
-        g.setColor(Color.white);
-        g.fillRect(0, 0, getWidth(), getHeight());
-
-        if (active)
-        {
-            if (image != null)
-            {
-                g.drawImage(image, getWidth() - 20, 2, this);
-            }
-        }
+      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 7d6d519..2894dec 100755
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,25 +18,16 @@
  */
 package jalview.gui;
 
-
-import jalview.schemes.*;
-
 import java.io.*;
-
 import java.net.*;
-
 import java.util.*;
-
 import java.util.jar.*;
 
 import javax.swing.*;
 
 import org.exolab.castor.xml.*;
-
 import jalview.schemabinding.version2.*;
-
-
-
+import jalview.schemes.*;
 
 /**
  * DOCUMENT ME!
@@ -60,1663 +51,1714 @@ public class Jalview2XML
 
   String uniqueSetSuffix = "";
 
+  // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE
+  public void SaveState(File statefile)
+  {
+    JInternalFrame[] frames = Desktop.desktop.getAllFrames();
 
-    // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE
-    public void SaveState(File statefile)
+    if (frames == null)
     {
-        JInternalFrame[] frames = Desktop.desktop.getAllFrames();
-
-        if (frames == null)
-        {
-            return;
-        }
-
-        try
-        {
-            FileOutputStream fos = new FileOutputStream(statefile);
-            JarOutputStream jout = new JarOutputStream(fos);
-
-            //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
-            ////////////////////////////////////////////////////
-            PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
-                        "UTF-8"));
+      return;
+    }
 
-            Vector shortNames = new Vector();
+    try
+    {
+      FileOutputStream fos = new FileOutputStream(statefile);
+      JarOutputStream jout = new JarOutputStream(fos);
 
-            //REVERSE ORDER
-            for (int i = frames.length - 1; i > -1; i--)
-            {
-                if (frames[i] instanceof AlignFrame)
-                {
-                    AlignFrame af = (AlignFrame) frames[i];
+      //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
+      ////////////////////////////////////////////////////
+      PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
+          "UTF-8"));
 
-                    String shortName = af.getTitle();
+      Vector shortNames = new Vector();
 
-                    if (shortName.indexOf(File.separatorChar) > -1)
-                    {
-                        shortName = shortName.substring(shortName.lastIndexOf(
-                                    File.separatorChar) + 1);
-                    }
+      //REVERSE ORDER
+      for (int i = frames.length - 1; i > -1; i--)
+      {
+        if (frames[i] instanceof AlignFrame)
+        {
+          AlignFrame af = (AlignFrame) frames[i];
 
-                    int count = 1;
+          String shortName = af.getTitle();
 
-                    while (shortNames.contains(shortName))
-                    {
-                        if (shortName.endsWith("_" + (count - 1)))
-                        {
-                            shortName = shortName.substring(0,
-                                    shortName.lastIndexOf("_"));
-                        }
-
-                        shortName = shortName.concat("_" + count);
-                        count++;
-                    }
+          if (shortName.indexOf(File.separatorChar) > -1)
+          {
+            shortName = shortName.substring(shortName.lastIndexOf(
+                File.separatorChar) + 1);
+          }
 
-                    shortNames.addElement(shortName);
+          int count = 1;
 
-                    if (!shortName.endsWith(".xml"))
-                    {
-                        shortName = shortName + ".xml";
-                    }
+          while (shortNames.contains(shortName))
+          {
+            if (shortName.endsWith("_" + (count - 1)))
+            {
+              shortName = shortName.substring(0,
+                                              shortName.lastIndexOf("_"));
+            }
 
-                    int ap, apSize= af.alignPanels.size();
-                    for (ap = 0; ap < apSize; ap++)
-                    {
-                      AlignmentPanel apanel = (AlignmentPanel) af.alignPanels.
-                          elementAt(ap);
+            shortName = shortName.concat("_" + count);
+            count++;
+          }
 
-                      SaveState(apanel,
-                                apSize == 1 ? shortName : ap+shortName,
-                                jout, out);
-                    }
-                }
-            }
+          shortNames.addElement(shortName);
 
-            out.close();
-            jout.close();
-        }
-        catch (Exception ex)
-        {
-            ex.printStackTrace();
-        }
-    }
+          if (!shortName.endsWith(".xml"))
+          {
+            shortName = shortName + ".xml";
+          }
 
-    // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
-    public boolean SaveAlignment(AlignFrame af, String jarFile,
-        String fileName)
-    {
-        try
-        {
-          int ap, apSize= af.alignPanels.size();
-          FileOutputStream fos = new FileOutputStream(jarFile);
-          JarOutputStream jout = new JarOutputStream(fos);
-          PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
-                "UTF-8"));
-          for( ap=0; ap<apSize; ap++)
+          int ap, apSize = af.alignPanels.size();
+          for (ap = 0; ap < apSize; ap++)
           {
-            AlignmentPanel apanel = (AlignmentPanel)af.alignPanels.elementAt(ap);
+            AlignmentPanel apanel = (AlignmentPanel) af.alignPanels.
+                elementAt(ap);
 
             SaveState(apanel,
-                      apSize==1?fileName:fileName+ap,
+                      apSize == 1 ? shortName : ap + shortName,
                       jout, out);
           }
-
-          out.close();
-          jout.close();
-          return true;
-        }
-        catch (Exception ex)
-        {
-          ex.printStackTrace();
-          return false;
         }
+      }
+
+      out.close();
+      jout.close();
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
     }
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param af DOCUMENT ME!
-     * @param timeStamp DOCUMENT ME!
-     * @param fileName DOCUMENT ME!
-     * @param jout DOCUMENT ME!
-     * @param out DOCUMENT ME!
-     */
-    public JalviewModel SaveState(AlignmentPanel ap,
-                          String fileName,
-                          JarOutputStream jout,
-                          PrintWriter out)
+  // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
+  public boolean SaveAlignment(AlignFrame af, String jarFile,
+                               String fileName)
+  {
+    try
     {
-      if (seqRefIds == null)
-        seqRefIds = new Hashtable();
+      int ap, apSize = af.alignPanels.size();
+      FileOutputStream fos = new FileOutputStream(jarFile);
+      JarOutputStream jout = new JarOutputStream(fos);
+      PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
+          "UTF-8"));
+      for (ap = 0; ap < apSize; ap++)
+      {
+        AlignmentPanel apanel = (AlignmentPanel) af.alignPanels.elementAt(ap);
 
-        Vector userColours = new Vector();
+        SaveState(apanel,
+                  apSize == 1 ? fileName : fileName + ap,
+                  jout, out);
+      }
+
+      out.close();
+      jout.close();
+      return true;
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+      return false;
+    }
+  }
 
-        AlignViewport av = ap.av;
+  /**
+   * DOCUMENT ME!
+   *
+   * @param af DOCUMENT ME!
+   * @param timeStamp DOCUMENT ME!
+   * @param fileName DOCUMENT ME!
+   * @param jout DOCUMENT ME!
+   * @param out DOCUMENT ME!
+   */
+  public JalviewModel SaveState(AlignmentPanel ap,
+                                String fileName,
+                                JarOutputStream jout,
+                                PrintWriter out)
+  {
+    if (seqRefIds == null)
+    {
+      seqRefIds = new Hashtable();
+    }
 
-        JalviewModel object = new JalviewModel();
-        object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
+    Vector userColours = new Vector();
 
-        object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
-        object.setVersion(jalview.bin.Cache.getProperty("VERSION"));
+    AlignViewport av = ap.av;
 
-        jalview.datamodel.AlignmentI jal = av.alignment;
+    JalviewModel object = new JalviewModel();
+    object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
 
-        if(av.hasHiddenRows)
-        {
-          jal = jal.getHiddenSequences().getFullAlignment();
-        }
+    object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
+    object.setVersion(jalview.bin.Cache.getProperty("VERSION"));
 
-        SequenceSet vamsasSet = new SequenceSet();
-        Sequence vamsasSeq;
-        JalviewModelSequence jms = new JalviewModelSequence();
+    jalview.datamodel.AlignmentI jal = av.alignment;
 
-        vamsasSet.setGapChar(jal.getGapCharacter() + "");
+    if (av.hasHiddenRows)
+    {
+      jal = jal.getHiddenSequences().getFullAlignment();
+    }
 
-        JSeq jseq;
-        Vector pdbfiles = null;
+    SequenceSet vamsasSet = new SequenceSet();
+    Sequence vamsasSeq;
+    JalviewModelSequence jms = new JalviewModelSequence();
 
-        //SAVE SEQUENCES
-        int id = 0;
-        jalview.datamodel.SequenceI jds;
-        for (int i = 0; i < jal.getHeight(); i++)
-        {
-            jds = jal.getSequenceAt(i);
-            id = jds.hashCode();
+    vamsasSet.setGapChar(jal.getGapCharacter() + "");
 
-            if(seqRefIds.get(id+"")!=null)
-            {
+    JSeq jseq;
+    Vector pdbfiles = null;
 
-            }
-            else
-            {
-              vamsasSeq = new Sequence();
-              vamsasSeq.setId(id + "");
-              vamsasSeq.setName(jds.getName());
-              vamsasSeq.setSequence(jds.getSequenceAsString());
-              vamsasSeq.setDescription(jds.getDescription());
+    //SAVE SEQUENCES
+    int id = 0;
+    jalview.datamodel.SequenceI jds;
+    for (int i = 0; i < jal.getHeight(); i++)
+    {
+      jds = jal.getSequenceAt(i);
+      id = jds.hashCode();
 
-              if (jds.getDatasetSequence().getDBRef() != null)
-              {
-                jalview.datamodel.DBRefEntry[] dbrefs =
-                    jds.getDatasetSequence().getDBRef();
+      if (seqRefIds.get(id + "") != null)
+      {
 
-                for (int d = 0; d < dbrefs.length; d++)
-                {
-                  DBRef dbref = new DBRef();
-                  dbref.setSource(dbrefs[d].getSource());
-                  dbref.setVersion(dbrefs[d].getVersion());
-                  dbref.setAccessionId(dbrefs[d].getAccessionId());
-                  vamsasSeq.addDBRef(dbref);
-                }
-              }
+      }
+      else
+      {
+        vamsasSeq = new Sequence();
+        vamsasSeq.setId(id + "");
+        vamsasSeq.setName(jds.getName());
+        vamsasSeq.setSequence(jds.getSequenceAsString());
+        vamsasSeq.setDescription(jds.getDescription());
 
-              vamsasSet.addSequence(vamsasSeq);
-              seqRefIds.put(id+"", jal.getSequenceAt(i));
-            }
+        if (jds.getDatasetSequence().getDBRef() != null)
+        {
+          jalview.datamodel.DBRefEntry[] dbrefs =
+              jds.getDatasetSequence().getDBRef();
 
-            jseq = new JSeq();
-            jseq.setStart(jds.getStart());
-            jseq.setEnd(jds.getEnd());
-            jseq.setColour( av.getSequenceColour(jds).getRGB());
+          for (int d = 0; d < dbrefs.length; d++)
+          {
+            DBRef dbref = new DBRef();
+            dbref.setSource(dbrefs[d].getSource());
+            dbref.setVersion(dbrefs[d].getVersion());
+            dbref.setAccessionId(dbrefs[d].getAccessionId());
+            vamsasSeq.addDBRef(dbref);
+          }
+        }
 
-            jseq.setId(id);
+        vamsasSet.addSequence(vamsasSeq);
+        seqRefIds.put(id + "", jal.getSequenceAt(i));
+      }
 
-            if (av.hasHiddenRows)
-            {
-              jseq.setHidden(av.alignment.getHiddenSequences().isHidden(jds));
+      jseq = new JSeq();
+      jseq.setStart(jds.getStart());
+      jseq.setEnd(jds.getEnd());
+      jseq.setColour(av.getSequenceColour(jds).getRGB());
 
-              if(av.hiddenRepSequences!=null
-              && av.hiddenRepSequences.containsKey(jal.getSequenceAt(i)))
-              {
-                jalview.datamodel.SequenceI[] reps =
-                    ( (jalview.datamodel.SequenceGroup)
-                     av.hiddenRepSequences.get(
-                         jal.getSequenceAt(i))).getSequencesInOrder(jal);
+      jseq.setId(id);
 
-                for(int h=0; h<reps.length; h++)
-                {
-                  if (reps[h] != jal.getSequenceAt(i))
-                    jseq.addHiddenSequences(
-                        jal.findIndex(reps[h])
-                        );
-                }
-              }
-            }
+      if (av.hasHiddenRows)
+      {
+        jseq.setHidden(av.alignment.getHiddenSequences().isHidden(jds));
 
+        if (av.hiddenRepSequences != null
+            && av.hiddenRepSequences.containsKey(jal.getSequenceAt(i)))
+        {
+          jalview.datamodel.SequenceI[] reps =
+              ( (jalview.datamodel.SequenceGroup)
+               av.hiddenRepSequences.get(
+                   jal.getSequenceAt(i))).getSequencesInOrder(jal);
 
-            if(jds.getDatasetSequence().getSequenceFeatures()!=null)
+          for (int h = 0; h < reps.length; h++)
+          {
+            if (reps[h] != jal.getSequenceAt(i))
             {
-              jalview.datamodel.SequenceFeature[] sf
-                  = jds.getDatasetSequence().getSequenceFeatures();
-              int index = 0;
-              while(index < sf.length)
-              {
-                Features features = new Features();
-
-                features.setBegin(sf[index].getBegin());
-                features.setEnd(sf[index].getEnd());
-                features.setDescription(sf[index].getDescription());
-                features.setType(sf[index].getType());
-                features.setFeatureGroup(sf[index].getFeatureGroup());
-                features.setScore(sf[index].getScore());
-                if(sf[index].links!=null)
-                {
-                  for(int l=0; l<sf[index].links.size(); l++)
-                  {
-                    OtherData keyValue = new OtherData();
-                    keyValue.setKey("LINK_"+l);
-                    keyValue.setValue(sf[index].links.elementAt(l).toString());
-                    features.addOtherData(keyValue);
-                  }
-                }
-                if(sf[index].otherDetails!=null)
-                {
-                  String key;
-                  Enumeration keys = sf[index].otherDetails.keys();
-                  while(keys.hasMoreElements())
-                  {
-                    key = keys.nextElement().toString();
-                    OtherData keyValue = new OtherData();
-                    keyValue.setKey( key );
-                    keyValue.setValue(
-                        sf[index].otherDetails.get(key).toString());
-                    features.addOtherData(keyValue);
-                  }
-                }
-
-                jseq.addFeatures(features);
-                index ++;
-              }
+              jseq.addHiddenSequences(
+                  jal.findIndex(reps[h])
+                  );
             }
+          }
+        }
+      }
 
-            if(jds.getDatasetSequence().getPDBId()!=null)
+      if (jds.getDatasetSequence().getSequenceFeatures() != null)
+      {
+        jalview.datamodel.SequenceFeature[] sf
+            = jds.getDatasetSequence().getSequenceFeatures();
+        int index = 0;
+        while (index < sf.length)
+        {
+          Features features = new Features();
+
+          features.setBegin(sf[index].getBegin());
+          features.setEnd(sf[index].getEnd());
+          features.setDescription(sf[index].getDescription());
+          features.setType(sf[index].getType());
+          features.setFeatureGroup(sf[index].getFeatureGroup());
+          features.setScore(sf[index].getScore());
+          if (sf[index].links != null)
+          {
+            for (int l = 0; l < sf[index].links.size(); l++)
             {
-              Enumeration en = jds.getDatasetSequence().getPDBId().elements();
-              while(en.hasMoreElements())
-              {
-                Pdbids pdb = new Pdbids();
-                jalview.datamodel.PDBEntry entry
-                   = (jalview.datamodel.PDBEntry)en.nextElement();
-
-                pdb.setId(entry.getId());
-                pdb.setType(entry.getType());
-
-
-                if(entry.getFile()!=null)
-                {
-                  pdb.setFile(entry.getFile());
-                  if(pdbfiles==null)
-                    pdbfiles = new Vector();
-
-                  if(!pdbfiles.contains(entry.getId()))
-                  {
-                    pdbfiles.addElement(entry.getId());
-                    try
-                    {
-                      File file = new File(entry.getFile());
-                      if(file.exists() && jout!=null)
-                      {
-                        byte[] data = new byte[ (int) file.length()];
-                        jout.putNextEntry(new JarEntry(entry.getId()));
-                        DataInputStream dis = new DataInputStream(new
-                            FileInputStream(file));
-                        dis.readFully(data);
-
-                        DataOutputStream dout = new DataOutputStream(jout);
-                        dout.write(data, 0, data.length);
-                        jout.closeEntry();
-                      }
-                    }
-                    catch (Exception ex)
-                    {
-                      ex.printStackTrace();
-                    }
-                  }
-                }
-
-
-                if(entry.getProperty()!=null)
-                {
-                  PdbentryItem item = new PdbentryItem();
-                  Hashtable properties = entry.getProperty();
-                  Enumeration en2 = properties.keys();
-                  while(en2.hasMoreElements())
-                  {
-                    Property prop = new Property();
-                    String key = en2.nextElement().toString();
-                    prop.setName(key);
-                    prop.setValue( properties.get(key).toString() );
-                    item.addProperty(prop);
-                  }
-                  pdb.addPdbentryItem(item);
-                }
-
-                jseq.addPdbids(pdb);
-              }
+              OtherData keyValue = new OtherData();
+              keyValue.setKey("LINK_" + l);
+              keyValue.setValue(sf[index].links.elementAt(l).toString());
+              features.addOtherData(keyValue);
             }
+          }
+          if (sf[index].otherDetails != null)
+          {
+            String key;
+            Enumeration keys = sf[index].otherDetails.keys();
+            while (keys.hasMoreElements())
+            {
+              key = keys.nextElement().toString();
+              OtherData keyValue = new OtherData();
+              keyValue.setKey(key);
+              keyValue.setValue(
+                  sf[index].otherDetails.get(key).toString());
+              features.addOtherData(keyValue);
+            }
+          }
 
-            jms.addJSeq(jseq);
+          jseq.addFeatures(features);
+          index++;
         }
+      }
 
-        if(av.hasHiddenRows)
-          jal = av.alignment;
+      if (jds.getDatasetSequence().getPDBId() != null)
+      {
+        Enumeration en = jds.getDatasetSequence().getPDBId().elements();
+        while (en.hasMoreElements())
+        {
+          Pdbids pdb = new Pdbids();
+          jalview.datamodel.PDBEntry entry
+              = (jalview.datamodel.PDBEntry) en.nextElement();
 
+          pdb.setId(entry.getId());
+          pdb.setType(entry.getType());
 
-        //SAVE TREES
-        ///////////////////////////////////
-        if (av.currentTree != null)
-        {
-          // FIND ANY ASSOCIATED TREES
-          // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
-          if (Desktop.desktop != null)
+          if (entry.getFile() != null)
           {
-            JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+            pdb.setFile(entry.getFile());
+            if (pdbfiles == null)
+            {
+              pdbfiles = new Vector();
+            }
 
-            for (int t = 0; t < frames.length; t++)
+            if (!pdbfiles.contains(entry.getId()))
             {
-              if (frames[t] instanceof TreePanel)
+              pdbfiles.addElement(entry.getId());
+              try
               {
-                TreePanel tp = (TreePanel) frames[t];
-
-                if (tp.treeCanvas.av.alignment == jal)
+                File file = new File(entry.getFile());
+                if (file.exists() && jout != null)
                 {
-                  Tree tree = new Tree();
-                  tree.setTitle(tp.getTitle());
-                  tree.setCurrentTree( (av.currentTree == tp.getTree()));
-                  tree.setNewick(tp.getTree().toString());
-                  tree.setThreshold(tp.treeCanvas.threshold);
-
-                  tree.setFitToWindow(tp.fitToWindow.getState());
-                  tree.setFontName(tp.getTreeFont().getName());
-                  tree.setFontSize(tp.getTreeFont().getSize());
-                  tree.setFontStyle(tp.getTreeFont().getStyle());
-                  tree.setMarkUnlinked(tp.placeholdersMenu.getState());
-
-                  tree.setShowBootstrap(tp.bootstrapMenu.getState());
-                  tree.setShowDistances(tp.distanceMenu.getState());
-
-                  tree.setHeight(tp.getHeight());
-                  tree.setWidth(tp.getWidth());
-                  tree.setXpos(tp.getX());
-                  tree.setYpos(tp.getY());
-
-                  jms.addTree(tree);
+                  byte[] data = new byte[ (int) file.length()];
+                  jout.putNextEntry(new JarEntry(entry.getId()));
+                  DataInputStream dis = new DataInputStream(new
+                      FileInputStream(file));
+                  dis.readFully(data);
+
+                  DataOutputStream dout = new DataOutputStream(jout);
+                  dout.write(data, 0, data.length);
+                  jout.closeEntry();
                 }
               }
+              catch (Exception ex)
+              {
+                ex.printStackTrace();
+              }
             }
           }
-        }
 
-        //SAVE ANNOTATIONS
-        if (jal.getAlignmentAnnotation() != null)
-        {
-            jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
-
-            for (int i = 0; i < aa.length; i++)
+          if (entry.getProperty() != null)
+          {
+            PdbentryItem item = new PdbentryItem();
+            Hashtable properties = entry.getProperty();
+            Enumeration en2 = properties.keys();
+            while (en2.hasMoreElements())
             {
-                Annotation an = new Annotation();
-
-                if(aa[i].annotationId!=null)
-                {
-                  annotationIds.put(aa[i].annotationId, aa[i]);
-                }
-
-                an.setId(aa[i].annotationId);
-
-                if (aa[i]==av.quality ||
-                        aa[i]==av.conservation ||
-                        aa[i]==av.consensus)
-                {
-                    an.setLabel(aa[i].label);
-                    an.setGraph(true);
-                    vamsasSet.addAnnotation(an);
-                    continue;
-                }
-
-
-                an.setDescription(aa[i].description);
-
-                if(aa[i].sequenceRef!=null)
-                 {
-                   an.setSequenceRef(aa[i].sequenceRef.getName());
-                 }
-
-                if(aa[i].graph>0)
-                {
-                  an.setGraph(true);
-                  an.setGraphType(aa[i].graph);
-                  an.setGraphGroup(aa[i].graphGroup);
-                  if(aa[i].getThreshold()!=null)
-                  {
-                    ThresholdLine line = new ThresholdLine();
-                    line.setLabel(aa[i].getThreshold().label);
-                    line.setValue(aa[i].getThreshold().value);
-                    line.setColour(aa[i].getThreshold().colour.getRGB());
-                    an.setThresholdLine(line);
-                  }
-                }
-                else
-                  an.setGraph(false);
-
-                an.setLabel(aa[i].label);
-
-                AnnotationElement ae;
-
-                for (int a = 0; a < aa[i].annotations.length; a++)
-                {
-                    if ((aa[i] == null) || (aa[i].annotations[a] == null))
-                    {
-                        continue;
-                    }
+              Property prop = new Property();
+              String key = en2.nextElement().toString();
+              prop.setName(key);
+              prop.setValue(properties.get(key).toString());
+              item.addProperty(prop);
+            }
+            pdb.addPdbentryItem(item);
+          }
 
-                    ae = new AnnotationElement();
-                    ae.setDescription(aa[i].annotations[a].description);
-                    ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
-                    ae.setValue(aa[i].annotations[a].value);
-                    ae.setPosition(a);
-                    ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +
-                        "");
+          jseq.addPdbids(pdb);
+        }
+      }
 
-                    if(aa[i].annotations[a].colour!=java.awt.Color.black)
-                      ae.setColour(aa[i].annotations[a].colour.getRGB());
+      jms.addJSeq(jseq);
+    }
 
-                    an.addAnnotationElement(ae);
-                }
+    if (av.hasHiddenRows)
+    {
+      jal = av.alignment;
+    }
 
-                vamsasSet.addAnnotation(an);
-            }
-        }
+    //SAVE TREES
+    ///////////////////////////////////
+    if (av.currentTree != null)
+    {
+      // FIND ANY ASSOCIATED TREES
+      // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
+      if (Desktop.desktop != null)
+      {
+        JInternalFrame[] frames = Desktop.desktop.getAllFrames();
 
-        //SAVE GROUPS
-        if (jal.getGroups() != null)
+        for (int t = 0; t < frames.length; t++)
         {
-            JGroup[] groups = new JGroup[jal.getGroups().size()];
+          if (frames[t] instanceof TreePanel)
+          {
+            TreePanel tp = (TreePanel) frames[t];
 
-            for (int i = 0; i < groups.length; i++)
+            if (tp.treeCanvas.av.alignment == jal)
             {
-                groups[i] = new JGroup();
-
-                jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal.getGroups()
-                                                                                          .elementAt(i);
-                groups[i].setStart(sg.getStartRes());
-                groups[i].setEnd(sg.getEndRes());
-                groups[i].setName(sg.getName());
-                if(sg.cs!=null)
-                {
-                  if (sg.cs.conservationApplied())
-                  {
-                    groups[i].setConsThreshold(sg.cs.getConservationInc());
-
-                    if (sg.cs instanceof jalview.schemes.UserColourScheme)
-                    {
-                      groups[i].setColour(SetUserColourScheme(sg.cs,
-                          userColours,
-                          jms));
-                    }
-                    else
-                    {
-                      groups[i].setColour(ColourSchemeProperty.getColourName(sg.
-                          cs));
-                    }
-                  }
-                  else if(sg.cs instanceof jalview.schemes.AnnotationColourGradient)
-                  {
-                    groups[i].setColour(
-                        ColourSchemeProperty.getColourName(
-                      ( (jalview.schemes.AnnotationColourGradient) sg.cs).getBaseColour()));
-                  }
-                  else if (sg.cs instanceof jalview.schemes.UserColourScheme)
-                  {
-                    groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
-                        jms));
-                  }
-                  else
-                  {
-                    groups[i].setColour(ColourSchemeProperty.getColourName(
-                        sg.cs));
-                  }
-
-                  groups[i].setPidThreshold(sg.cs.getThreshold());
-                }
-
-                groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
-                groups[i].setDisplayBoxes(sg.getDisplayBoxes());
-                groups[i].setDisplayText(sg.getDisplayText());
-                groups[i].setColourText(sg.getColourText());
-                groups[i].setTextCol1(sg.textColour.getRGB());
-                groups[i].setTextCol2(sg.textColour2.getRGB());
-                groups[i].setTextColThreshold(sg.thresholdTextColour);
-
-                for (int s = 0; s < sg.getSize(); s++)
-                {
-                    jalview.datamodel.Sequence seq =
-                        (jalview.datamodel.Sequence) sg.getSequenceAt(s);
-                    groups[i].addSeq(seq.hashCode());
-                }
+              Tree tree = new Tree();
+              tree.setTitle(tp.getTitle());
+              tree.setCurrentTree( (av.currentTree == tp.getTree()));
+              tree.setNewick(tp.getTree().toString());
+              tree.setThreshold(tp.treeCanvas.threshold);
+
+              tree.setFitToWindow(tp.fitToWindow.getState());
+              tree.setFontName(tp.getTreeFont().getName());
+              tree.setFontSize(tp.getTreeFont().getSize());
+              tree.setFontStyle(tp.getTreeFont().getStyle());
+              tree.setMarkUnlinked(tp.placeholdersMenu.getState());
+
+              tree.setShowBootstrap(tp.bootstrapMenu.getState());
+              tree.setShowDistances(tp.distanceMenu.getState());
+
+              tree.setHeight(tp.getHeight());
+              tree.setWidth(tp.getWidth());
+              tree.setXpos(tp.getX());
+              tree.setYpos(tp.getY());
+
+              jms.addTree(tree);
             }
-
-            jms.setJGroup(groups);
+          }
         }
+      }
+    }
 
+    //SAVE ANNOTATIONS
+    if (jal.getAlignmentAnnotation() != null)
+    {
+      jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
 
-        ///////////SAVE VIEWPORT
-        Viewport view = new Viewport();
-        view.setTitle(ap.alignFrame.getTitle());
-        view.setSequenceSetId(av.getSequenceSetId());
-        view.setViewName(av.viewName);
-        view.setGatheredViews(av.gatherViewsHere);
-
+      for (int i = 0; i < aa.length; i++)
+      {
+        Annotation an = new Annotation();
 
-        if (ap.av.explodedPosition != null)
-        {
-          view.setXpos(av.explodedPosition.x);
-          view.setYpos(av.explodedPosition.y);
-          view.setWidth(av.explodedPosition.width);
-          view.setHeight(av.explodedPosition.height);
-        }
-        else
+        if (aa[i].annotationId != null)
         {
-          view.setXpos(ap.alignFrame.getBounds().x);
-          view.setYpos(ap.alignFrame.getBounds().y);
-          view.setWidth(ap.alignFrame.getBounds().width);
-          view.setHeight(ap.alignFrame.getBounds().height);
+          annotationIds.put(aa[i].annotationId, aa[i]);
         }
 
-        view.setStartRes(av.startRes);
-        view.setStartSeq(av.startSeq);
+        an.setId(aa[i].annotationId);
 
-        if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
+        if (aa[i] == av.quality ||
+            aa[i] == av.conservation ||
+            aa[i] == av.consensus)
         {
-            view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
-                    userColours, jms));
+          an.setLabel(aa[i].label);
+          an.setGraph(true);
+          vamsasSet.addAnnotation(an);
+          continue;
         }
-        else if(av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
-        {
-           jalview.schemes.AnnotationColourGradient acg
-              = (jalview.schemes.AnnotationColourGradient)av.getGlobalColourScheme();
-
-            AnnotationColours ac = new AnnotationColours();
-            ac.setAboveThreshold(acg.getAboveThreshold());
-            ac.setThreshold(acg.getAnnotationThreshold());
-            ac.setAnnotation(acg.getAnnotation());
-            if(acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
-              ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),
-                    userColours, jms));
-            else
-              ac.setColourScheme(ColourSchemeProperty.getColourName(acg.getBaseColour()));
 
-            ac.setMaxColour(acg.getMaxColour().getRGB());
-            ac.setMinColour(acg.getMinColour().getRGB());
-            view.setAnnotationColours(ac);
-            view.setBgColour("AnnotationColourGradient");
-        }
-        else
+        an.setDescription(aa[i].description);
+
+        if (aa[i].sequenceRef != null)
         {
-            view.setBgColour(ColourSchemeProperty.getColourName(
-                    av.getGlobalColourScheme()));
+          an.setSequenceRef(aa[i].sequenceRef.getName());
         }
 
-        ColourSchemeI cs = av.getGlobalColourScheme();
-
-        if(cs!=null)
+        if (aa[i].graph > 0)
         {
-          if (cs.conservationApplied())
-          {
-            view.setConsThreshold(cs.getConservationInc());
-            if (cs instanceof jalview.schemes.UserColourScheme)
-              view.setBgColour(SetUserColourScheme(cs, userColours, jms));
-          }
-
-          if (cs instanceof ResidueColourScheme)
+          an.setGraph(true);
+          an.setGraphType(aa[i].graph);
+          an.setGraphGroup(aa[i].graphGroup);
+          if (aa[i].getThreshold() != null)
           {
-            view.setPidThreshold(cs.getThreshold());
+            ThresholdLine line = new ThresholdLine();
+            line.setLabel(aa[i].getThreshold().label);
+            line.setValue(aa[i].getThreshold().value);
+            line.setColour(aa[i].getThreshold().colour.getRGB());
+            an.setThresholdLine(line);
           }
         }
-
-        view.setConservationSelected(av.getConservationSelected());
-        view.setPidSelected(av.getAbovePIDThreshold());
-        view.setFontName(av.font.getName());
-        view.setFontSize(av.font.getSize());
-        view.setFontStyle(av.font.getStyle());
-        view.setRenderGaps(av.renderGaps);
-        view.setShowAnnotation(av.getShowAnnotation());
-        view.setShowBoxes(av.getShowBoxes());
-        view.setShowColourText(av.getColourText());
-        view.setShowFullId(av.getShowJVSuffix());
-        view.setRightAlignIds(av.rightAlignIds);
-        view.setShowSequenceFeatures(av.showSequenceFeatures);
-        view.setShowText(av.getShowText());
-        view.setWrapAlignment(av.getWrapAlignment());
-        view.setTextCol1(av.textColour.getRGB());
-        view.setTextCol2(av.textColour2.getRGB());
-        view.setTextColThreshold(av.thresholdTextColour);
-
-
-        if(av.featuresDisplayed!=null)
+        else
         {
-          jalview.schemabinding.version2.FeatureSettings fs
-              = new jalview.schemabinding.version2.FeatureSettings();
-
-          String [] renderOrder =
-              ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
-
-          Vector settingsAdded = new Vector();
-          for(int ro=0; ro<renderOrder.length; ro++)
-          {
-            Setting setting = new Setting();
-            setting.setType(renderOrder[ro]);
-            setting.setColour(
-                ap.seqPanel.seqCanvas.getFeatureRenderer().getColour(renderOrder[ro]).getRGB()
-                );
+          an.setGraph(false);
+        }
 
-            setting.setDisplay(
-                av.featuresDisplayed.containsKey(renderOrder[ro])
-                );
+        an.setLabel(aa[i].label);
 
-            fs.addSetting(setting);
-            settingsAdded.addElement(renderOrder[ro]);
-          }
+        AnnotationElement ae;
 
-          //Make sure we save none displayed feature settings
-          Enumeration en =
-              ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours.keys();
-          while(en.hasMoreElements())
+        for (int a = 0; a < aa[i].annotations.length; a++)
+        {
+          if ( (aa[i] == null) || (aa[i].annotations[a] == null))
           {
-            String key = en.nextElement().toString();
-            if(settingsAdded.contains(key))
-              continue;
-
-            Setting setting = new Setting();
-            setting.setType(key);
-            setting.setColour(
-                ap.seqPanel.seqCanvas.getFeatureRenderer().getColour(key).getRGB()
-                );
-
-            setting.setDisplay(false);
-
-            fs.addSetting(setting);
-            settingsAdded.addElement(key);
+            continue;
           }
 
-          jms.setFeatureSettings(fs);
-
-        }
+          ae = new AnnotationElement();
+          ae.setDescription(aa[i].annotations[a].description);
+          ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
+          ae.setValue(aa[i].annotations[a].value);
+          ae.setPosition(a);
+          ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +
+                                   "");
 
-        if(av.hasHiddenColumns)
-        {
-          for(int c=0; c<av.getColumnSelection().getHiddenColumns().size(); c++)
+          if (aa[i].annotations[a].colour != java.awt.Color.black)
           {
-            int [] region = (int[]) av.getColumnSelection().getHiddenColumns().elementAt(c);
-            HiddenColumns hc = new HiddenColumns();
-            hc.setStart(region[0]);
-            hc.setEnd(region[1]);
-            view.addHiddenColumns(hc);
+            ae.setColour(aa[i].annotations[a].colour.getRGB());
           }
-        }
 
-        jms.addViewport(view);
+          an.addAnnotationElement(ae);
+        }
 
+        vamsasSet.addAnnotation(an);
+      }
+    }
 
-        object.setJalviewModelSequence(jms);
-        object.getVamsasModel().addSequenceSet(vamsasSet);
+    //SAVE GROUPS
+    if (jal.getGroups() != null)
+    {
+      JGroup[] groups = new JGroup[jal.getGroups().size()];
 
-        if(out!=null)
+      for (int i = 0; i < groups.length; i++)
+      {
+        groups[i] = new JGroup();
+
+        jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup)
+            jal.getGroups()
+            .elementAt(i);
+        groups[i].setStart(sg.getStartRes());
+        groups[i].setEnd(sg.getEndRes());
+        groups[i].setName(sg.getName());
+        if (sg.cs != null)
         {
-          //We may not want to right the object to disk,
-          //eg we can copy the alignViewport to a new view object
-          //using save and then load
-          try
+          if (sg.cs.conservationApplied())
           {
-            if (!fileName.endsWith(".xml"))
+            groups[i].setConsThreshold(sg.cs.getConservationInc());
+
+            if (sg.cs instanceof jalview.schemes.UserColourScheme)
             {
-              fileName = fileName + ".xml";
+              groups[i].setColour(SetUserColourScheme(sg.cs,
+                  userColours,
+                  jms));
             }
-
-            JarEntry entry = new JarEntry(fileName);
-            jout.putNextEntry(entry);
-
-            object.marshal(out);
+            else
+            {
+              groups[i].setColour(ColourSchemeProperty.getColourName(sg.
+                  cs));
+            }
+          }
+          else if (sg.cs instanceof jalview.schemes.AnnotationColourGradient)
+          {
+            groups[i].setColour(
+                ColourSchemeProperty.getColourName(
+                    ( (jalview.schemes.AnnotationColourGradient) sg.cs).
+                    getBaseColour()));
           }
-          catch (Exception ex)
+          else if (sg.cs instanceof jalview.schemes.UserColourScheme)
           {
-            ex.printStackTrace();
+            groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
+                jms));
           }
+          else
+          {
+            groups[i].setColour(ColourSchemeProperty.getColourName(
+                sg.cs));
+          }
+
+          groups[i].setPidThreshold(sg.cs.getThreshold());
         }
-        return object;
-    }
 
-    String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
-        Vector userColours, JalviewModelSequence jms)
-    {
-        String id = null;
-        jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
+        groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
+        groups[i].setDisplayBoxes(sg.getDisplayBoxes());
+        groups[i].setDisplayText(sg.getDisplayText());
+        groups[i].setColourText(sg.getColourText());
+        groups[i].setTextCol1(sg.textColour.getRGB());
+        groups[i].setTextCol2(sg.textColour2.getRGB());
+        groups[i].setTextColThreshold(sg.thresholdTextColour);
 
-        if (!userColours.contains(ucs))
+        for (int s = 0; s < sg.getSize(); s++)
         {
-            userColours.add(ucs);
-
-            java.awt.Color[] colours = ucs.getColours();
-            jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();
-            jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();
-
-            for (int i = 0; i < colours.length; i++)
-            {
-                jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
-                col.setName(ResidueProperties.aa[i]);
-                col.setRGB(jalview.util.Format.getHexString(colours[i]));
-                jbucs.addColour(col);
-            }
-            if(ucs.getLowerCaseColours()!=null)
-            {
-              colours = ucs.getLowerCaseColours();
-              for (int i = 0; i < colours.length; i++)
-             {
-                 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
-                 col.setName(ResidueProperties.aa[i].toLowerCase());
-                 col.setRGB(jalview.util.Format.getHexString(colours[i]));
-                 jbucs.addColour(col);
-             }
-            }
-
-            id = "ucs" + userColours.indexOf(ucs);
-            uc.setId(id);
-            uc.setUserColourScheme(jbucs);
-            jms.addUserColours(uc);
+          jalview.datamodel.Sequence seq =
+              (jalview.datamodel.Sequence) sg.getSequenceAt(s);
+          groups[i].addSeq(seq.hashCode());
         }
+      }
 
-        return id;
+      jms.setJGroup(groups);
     }
 
-   jalview.schemes.UserColourScheme GetUserColourScheme(
-        JalviewModelSequence jms, String id)
-    {
-        UserColours[] uc = jms.getUserColours();
-        UserColours colours = null;
+    ///////////SAVE VIEWPORT
+    Viewport view = new Viewport();
+    view.setTitle(ap.alignFrame.getTitle());
+    view.setSequenceSetId(av.getSequenceSetId());
+    view.setViewName(av.viewName);
+    view.setGatheredViews(av.gatherViewsHere);
 
-        for (int i = 0; i < uc.length; i++)
-        {
-            if (uc[i].getId().equals(id))
-            {
-                colours = uc[i];
+    if (ap.av.explodedPosition != null)
+    {
+      view.setXpos(av.explodedPosition.x);
+      view.setYpos(av.explodedPosition.y);
+      view.setWidth(av.explodedPosition.width);
+      view.setHeight(av.explodedPosition.height);
+    }
+    else
+    {
+      view.setXpos(ap.alignFrame.getBounds().x);
+      view.setYpos(ap.alignFrame.getBounds().y);
+      view.setWidth(ap.alignFrame.getBounds().width);
+      view.setHeight(ap.alignFrame.getBounds().height);
+    }
 
-                break;
-            }
-        }
+    view.setStartRes(av.startRes);
+    view.setStartSeq(av.startSeq);
 
-        java.awt.Color[] newColours = new java.awt.Color[24];
+    if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
+    {
+      view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
+                                           userColours, jms));
+    }
+    else if (av.getGlobalColourScheme() instanceof jalview.schemes.
+             AnnotationColourGradient)
+    {
+      jalview.schemes.AnnotationColourGradient acg
+          = (jalview.schemes.AnnotationColourGradient) av.getGlobalColourScheme();
+
+      AnnotationColours ac = new AnnotationColours();
+      ac.setAboveThreshold(acg.getAboveThreshold());
+      ac.setThreshold(acg.getAnnotationThreshold());
+      ac.setAnnotation(acg.getAnnotation());
+      if (acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
+      {
+        ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),
+                                               userColours, jms));
+      }
+      else
+      {
+        ac.setColourScheme(ColourSchemeProperty.getColourName(acg.getBaseColour()));
+      }
 
-        for (int i = 0; i < 24; i++)
-        {
-            newColours[i] = new java.awt.Color(Integer.parseInt(
-                        colours.getUserColourScheme().getColour(i).getRGB(), 16));
-        }
+      ac.setMaxColour(acg.getMaxColour().getRGB());
+      ac.setMinColour(acg.getMinColour().getRGB());
+      view.setAnnotationColours(ac);
+      view.setBgColour("AnnotationColourGradient");
+    }
+    else
+    {
+      view.setBgColour(ColourSchemeProperty.getColourName(
+          av.getGlobalColourScheme()));
+    }
 
-        jalview.schemes.UserColourScheme ucs =
-            new jalview.schemes.UserColourScheme(newColours);
+    ColourSchemeI cs = av.getGlobalColourScheme();
 
-        if (colours.getUserColourScheme().getColourCount() > 24)
+    if (cs != null)
+    {
+      if (cs.conservationApplied())
+      {
+        view.setConsThreshold(cs.getConservationInc());
+        if (cs instanceof jalview.schemes.UserColourScheme)
         {
-          newColours = new java.awt.Color[23];
-          for (int i = 0; i < 23; i++)
-          {
-            newColours[i] = new java.awt.Color(Integer.parseInt(
-                colours.getUserColourScheme().getColour(i+24).getRGB(), 16));
-          }
-          ucs.setLowerCaseColours(newColours);
+          view.setBgColour(SetUserColourScheme(cs, userColours, jms));
         }
+      }
 
-        return ucs;
+      if (cs instanceof ResidueColourScheme)
+      {
+        view.setPidThreshold(cs.getThreshold());
+      }
     }
 
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param file DOCUMENT ME!
-     */
-    public AlignFrame LoadJalviewAlign(final String file)
+    view.setConservationSelected(av.getConservationSelected());
+    view.setPidSelected(av.getAbovePIDThreshold());
+    view.setFontName(av.font.getName());
+    view.setFontSize(av.font.getSize());
+    view.setFontStyle(av.font.getStyle());
+    view.setRenderGaps(av.renderGaps);
+    view.setShowAnnotation(av.getShowAnnotation());
+    view.setShowBoxes(av.getShowBoxes());
+    view.setShowColourText(av.getColourText());
+    view.setShowFullId(av.getShowJVSuffix());
+    view.setRightAlignIds(av.rightAlignIds);
+    view.setShowSequenceFeatures(av.showSequenceFeatures);
+    view.setShowText(av.getShowText());
+    view.setWrapAlignment(av.getWrapAlignment());
+    view.setTextCol1(av.textColour.getRGB());
+    view.setTextCol2(av.textColour2.getRGB());
+    view.setTextColThreshold(av.thresholdTextColour);
+
+    if (av.featuresDisplayed != null)
     {
-        uniqueSetSuffix = System.currentTimeMillis()%100000 +"";
-
-        jalview.gui.AlignFrame af = null;
+      jalview.schemabinding.version2.FeatureSettings fs
+          = new jalview.schemabinding.version2.FeatureSettings();
 
-        seqRefIds = new Hashtable();
-        viewportsAdded = new Hashtable();
+      String[] renderOrder =
+          ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
 
-        Vector gatherToThisFrame= new Vector();
+      Vector settingsAdded = new Vector();
+      for (int ro = 0; ro < renderOrder.length; ro++)
+      {
+        Setting setting = new Setting();
+        setting.setType(renderOrder[ro]);
+        setting.setColour(
+            ap.seqPanel.seqCanvas.getFeatureRenderer().getColour(renderOrder[ro]).
+            getRGB()
+            );
+
+        setting.setDisplay(
+            av.featuresDisplayed.containsKey(renderOrder[ro])
+            );
+
+        fs.addSetting(setting);
+        settingsAdded.addElement(renderOrder[ro]);
+      }
 
-        try
+      //Make sure we save none displayed feature settings
+      Enumeration en =
+          ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours.keys();
+      while (en.hasMoreElements())
+      {
+        String key = en.nextElement().toString();
+        if (settingsAdded.contains(key))
         {
-            //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
-            URL url = null;
+          continue;
+        }
 
-            if (file.startsWith("http://"))
-            {
-                url = new URL(file);
-            }
+        Setting setting = new Setting();
+        setting.setType(key);
+        setting.setColour(
+            ap.seqPanel.seqCanvas.getFeatureRenderer().getColour(key).getRGB()
+            );
 
-            JarInputStream jin = null;
-            JarEntry jarentry = null;
-            int entryCount = 1;
+        setting.setDisplay(false);
 
-            do
-            {
-                if (url != null)
-                {
-                    jin = new JarInputStream(url.openStream());
-                }
-                else
-                {
-                    jin = new JarInputStream(new FileInputStream(file));
-                }
+        fs.addSetting(setting);
+        settingsAdded.addElement(key);
+      }
 
-                for (int i = 0; i < entryCount; i++)
-                {
-                    jarentry = jin.getNextJarEntry();
-                }
+      jms.setFeatureSettings(fs);
 
-                if (jarentry != null && jarentry.getName().endsWith(".xml"))
-                {
-                    InputStreamReader in = new InputStreamReader(jin, "UTF-8");
-                    JalviewModel object = new JalviewModel();
+    }
 
-                    Unmarshaller unmar = new Unmarshaller(object);
-                    unmar.setValidation(false);
-                    object = (JalviewModel) unmar.unmarshal( in );
+    if (av.hasHiddenColumns)
+    {
+      for (int c = 0; c < av.getColumnSelection().getHiddenColumns().size(); c++)
+      {
+        int[] region = (int[]) av.getColumnSelection().getHiddenColumns().
+            elementAt(c);
+        HiddenColumns hc = new HiddenColumns();
+        hc.setStart(region[0]);
+        hc.setEnd(region[1]);
+        view.addHiddenColumns(hc);
+      }
+    }
 
-                    af = LoadFromObject(object, file, true);
-                    if(af.viewport.gatherViewsHere)
-                    {
-                      gatherToThisFrame.add(af);
-                    }
-                    entryCount++;
-                }
-                else if (jarentry != null)
-                {
-                  //Some other file here.
-                  entryCount++;
-                }
-            }
-            while (jarentry != null);
-        }
-        catch(java.net.UnknownHostException ex)
-        {
-          ex.printStackTrace();
-          System.err.println("Couldn't locate Jalview XML file : " +
-              ex + "\n");
+    jms.addViewport(view);
 
-          javax.swing.SwingUtilities.invokeLater(new Runnable()
-          {
-            public void run()
-            {
-              JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                  "Couldn't locate " + file,
-                  "URL not found",
-                  JOptionPane.WARNING_MESSAGE);
-            }
-          });
-        }
-        catch (Exception ex)
+    object.setJalviewModelSequence(jms);
+    object.getVamsasModel().addSequenceSet(vamsasSet);
+
+    if (out != null)
+    {
+      //We may not want to right the object to disk,
+      //eg we can copy the alignViewport to a new view object
+      //using save and then load
+      try
+      {
+        if (!fileName.endsWith(".xml"))
         {
-          //Is Version 1 Jar file?
-          af =  new Jalview2XML_V1().LoadJalviewAlign(file);
+          fileName = fileName + ".xml";
+        }
 
-          if(af!=null)
-          {
-            System.out.println("Successfully loaded archive file");
-            return af;
-          }
-          ex.printStackTrace();
+        JarEntry entry = new JarEntry(fileName);
+        jout.putNextEntry(entry);
 
-            System.err.println("Exception whilst loading jalview XML file : " +
-                ex + "\n");
-            javax.swing.SwingUtilities.invokeLater(new Runnable()
-            {
-              public void run()
-              {
+        object.marshal(out);
+      }
+      catch (Exception ex)
+      {
+        ex.printStackTrace();
+      }
+    }
+    return object;
+  }
 
-                JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                    "Error loading  " + file,
-                    "Error loading Jalview file",
-                    JOptionPane.WARNING_MESSAGE);
-              }});
-        }
+  String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
+                             Vector userColours, JalviewModelSequence jms)
+  {
+    String id = null;
+    jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme)
+        cs;
+
+    if (!userColours.contains(ucs))
+    {
+      userColours.add(ucs);
 
-        if (Desktop.instance != null)
-          Desktop.instance.stopLoading();
+      java.awt.Color[] colours = ucs.getColours();
+      jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.
+          version2.UserColours();
+      jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.
+          schemabinding.version2.UserColourScheme();
 
-        for (int i = 0; i < gatherToThisFrame.size(); i++)
+      for (int i = 0; i < colours.length; i++)
+      {
+        jalview.schemabinding.version2.Colour col = new jalview.schemabinding.
+            version2.Colour();
+        col.setName(ResidueProperties.aa[i]);
+        col.setRGB(jalview.util.Format.getHexString(colours[i]));
+        jbucs.addColour(col);
+      }
+      if (ucs.getLowerCaseColours() != null)
+      {
+        colours = ucs.getLowerCaseColours();
+        for (int i = 0; i < colours.length; i++)
         {
-          Desktop.instance.gatherViews(
-              (AlignFrame) gatherToThisFrame.elementAt(i));
+          jalview.schemabinding.version2.Colour col = new jalview.schemabinding.
+              version2.Colour();
+          col.setName(ResidueProperties.aa[i].toLowerCase());
+          col.setRGB(jalview.util.Format.getHexString(colours[i]));
+          jbucs.addColour(col);
         }
+      }
 
-        return af;
+      id = "ucs" + userColours.indexOf(ucs);
+      uc.setId(id);
+      uc.setUserColourScheme(jbucs);
+      jms.addUserColours(uc);
     }
 
-    String loadPDBFile(String file, String pdbId)
+    return id;
+  }
+
+  jalview.schemes.UserColourScheme GetUserColourScheme(
+      JalviewModelSequence jms, String id)
+  {
+    UserColours[] uc = jms.getUserColours();
+    UserColours colours = null;
+
+    for (int i = 0; i < uc.length; i++)
     {
-      System.out.println(file +" "+pdbId);
-      try
+      if (uc[i].getId().equals(id))
+      {
+        colours = uc[i];
+
+        break;
+      }
+    }
+
+    java.awt.Color[] newColours = new java.awt.Color[24];
+
+    for (int i = 0; i < 24; i++)
+    {
+      newColours[i] = new java.awt.Color(Integer.parseInt(
+          colours.getUserColourScheme().getColour(i).getRGB(), 16));
+    }
+
+    jalview.schemes.UserColourScheme ucs =
+        new jalview.schemes.UserColourScheme(newColours);
+
+    if (colours.getUserColourScheme().getColourCount() > 24)
+    {
+      newColours = new java.awt.Color[23];
+      for (int i = 0; i < 23; i++)
       {
-        JarInputStream jin = null;
+        newColours[i] = new java.awt.Color(Integer.parseInt(
+            colours.getUserColourScheme().getColour(i + 24).getRGB(), 16));
+      }
+      ucs.setLowerCaseColours(newColours);
+    }
+
+    return ucs;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param file DOCUMENT ME!
+   */
+  public AlignFrame LoadJalviewAlign(final String file)
+  {
+    uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
+
+    jalview.gui.AlignFrame af = null;
+
+    seqRefIds = new Hashtable();
+    viewportsAdded = new Hashtable();
+
+    Vector gatherToThisFrame = new Vector();
 
-        if (file.startsWith("http://"))
+    try
+    {
+      //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
+      URL url = null;
+
+      if (file.startsWith("http://"))
+      {
+        url = new URL(file);
+      }
+
+      JarInputStream jin = null;
+      JarEntry jarentry = null;
+      int entryCount = 1;
+
+      do
+      {
+        if (url != null)
         {
-          jin = new JarInputStream(new URL(file).openStream());
+          jin = new JarInputStream(url.openStream());
         }
         else
         {
           jin = new JarInputStream(new FileInputStream(file));
         }
 
-        JarEntry entry = null;
-        do
+        for (int i = 0; i < entryCount; i++)
         {
-          entry = jin.getNextJarEntry();
+          jarentry = jin.getNextJarEntry();
         }
-        while (!entry.getName().equals(pdbId));
 
-        BufferedReader in = new BufferedReader(new InputStreamReader(jin));
-        File outFile = File.createTempFile("jalview_pdb", ".txt");
-        outFile.deleteOnExit();
-        PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
-        String data;
+        if (jarentry != null && jarentry.getName().endsWith(".xml"))
+        {
+          InputStreamReader in = new InputStreamReader(jin, "UTF-8");
+          JalviewModel object = new JalviewModel();
+
+          Unmarshaller unmar = new Unmarshaller(object);
+          unmar.setValidation(false);
+          object = (JalviewModel) unmar.unmarshal(in);
 
-        while ( (data = in.readLine()) != null)
+          af = LoadFromObject(object, file, true);
+          if (af.viewport.gatherViewsHere)
+          {
+            gatherToThisFrame.add(af);
+          }
+          entryCount++;
+        }
+        else if (jarentry != null)
         {
-          out.println(data);
+          //Some other file here.
+          entryCount++;
         }
-        out.close();
-        return outFile.getAbsolutePath();
-
       }
-      catch (Exception ex)
+      while (jarentry != null);
+    }
+    catch (java.net.UnknownHostException ex)
+    {
+      ex.printStackTrace();
+      System.err.println("Couldn't locate Jalview XML file : " +
+                         ex + "\n");
+
+      javax.swing.SwingUtilities.invokeLater(new Runnable()
       {
-        ex.printStackTrace();
+        public void run()
+        {
+          JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                                                "Couldn't locate " + file,
+                                                "URL not found",
+                                                JOptionPane.WARNING_MESSAGE);
+        }
+      });
+    }
+    catch (Exception ex)
+    {
+      //Is Version 1 Jar file?
+      af = new Jalview2XML_V1().LoadJalviewAlign(file);
+
+      if (af != null)
+      {
+        System.out.println("Successfully loaded archive file");
+        return af;
       }
+      ex.printStackTrace();
 
-      return null;
+      System.err.println("Exception whilst loading jalview XML file : " +
+                         ex + "\n");
+      javax.swing.SwingUtilities.invokeLater(new Runnable()
+      {
+        public void run()
+        {
+
+          JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                                                "Error loading  " + file,
+                                                "Error loading Jalview file",
+                                                JOptionPane.WARNING_MESSAGE);
+        }
+      });
     }
 
+    if (Desktop.instance != null)
+    {
+      Desktop.instance.stopLoading();
+    }
 
-    AlignFrame LoadFromObject(JalviewModel object,
-                              String file,
-                              boolean loadTrees )
+    for (int i = 0; i < gatherToThisFrame.size(); i++)
     {
-        SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
-        Sequence[] vamsasSeq = vamsasSet.getSequence();
+      Desktop.instance.gatherViews(
+          (AlignFrame) gatherToThisFrame.elementAt(i));
+    }
 
-        JalviewModelSequence jms = object.getJalviewModelSequence();
+    return af;
+  }
 
-        Viewport view = jms.getViewport(0);
+  String loadPDBFile(String file, String pdbId)
+  {
+    System.out.println(file + " " + pdbId);
+    try
+    {
+      JarInputStream jin = null;
 
-        //////////////////////////////////
-        //LOAD SEQUENCES
+      if (file.startsWith("http://"))
+      {
+        jin = new JarInputStream(new URL(file).openStream());
+      }
+      else
+      {
+        jin = new JarInputStream(new FileInputStream(file));
+      }
 
-        Vector hiddenSeqs = null;
-        jalview.datamodel.Sequence jseq;
+      JarEntry entry = null;
+      do
+      {
+        entry = jin.getNextJarEntry();
+      }
+      while (!entry.getName().equals(pdbId));
 
-        ArrayList tmpseqs = new ArrayList();
+      BufferedReader in = new BufferedReader(new InputStreamReader(jin));
+      File outFile = File.createTempFile("jalview_pdb", ".txt");
+      outFile.deleteOnExit();
+      PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
+      String data;
 
-        boolean multipleView = false;
+      while ( (data = in.readLine()) != null)
+      {
+        out.println(data);
+      }
+      out.close();
+      return outFile.getAbsolutePath();
 
-        JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
-        for (int i = 0; i < JSEQ.length; i++)
-        {
-          String seqId = JSEQ[i].getId() + "";
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
 
-          if (seqRefIds.get(seqId) != null)
-          {
-            tmpseqs.add( (jalview.datamodel.Sequence) seqRefIds.get(seqId));
-            multipleView = true;
-          }
-          else
-          {
-            jseq = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
-                vamsasSeq[i].getSequence());
-            jseq.setDescription(vamsasSeq[i].getDescription());
-            jseq.setStart(JSEQ[i].getStart());
-            jseq.setEnd(JSEQ[i].getEnd());
-            seqRefIds.put(vamsasSeq[i].getId(), jseq);
-            tmpseqs.add( jseq );
-          }
+    return null;
+  }
 
+  AlignFrame LoadFromObject(JalviewModel object,
+                            String file,
+                            boolean loadTrees)
+  {
+    SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
+    Sequence[] vamsasSeq = vamsasSet.getSequence();
 
+    JalviewModelSequence jms = object.getJalviewModelSequence();
 
-          if (JSEQ[i].getHidden())
-          {
-            if (hiddenSeqs == null)
-              hiddenSeqs = new Vector();
+    Viewport view = jms.getViewport(0);
 
+    //////////////////////////////////
+    //LOAD SEQUENCES
 
-            hiddenSeqs.addElement(
-                (jalview.datamodel.Sequence) seqRefIds.get(seqId));
-          }
+    Vector hiddenSeqs = null;
+    jalview.datamodel.Sequence jseq;
 
+    ArrayList tmpseqs = new ArrayList();
+
+    boolean multipleView = false;
+
+    JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
+    for (int i = 0; i < JSEQ.length; i++)
+    {
+      String seqId = JSEQ[i].getId() + "";
+
+      if (seqRefIds.get(seqId) != null)
+      {
+        tmpseqs.add( (jalview.datamodel.Sequence) seqRefIds.get(seqId));
+        multipleView = true;
+      }
+      else
+      {
+        jseq = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
+                                              vamsasSeq[i].getSequence());
+        jseq.setDescription(vamsasSeq[i].getDescription());
+        jseq.setStart(JSEQ[i].getStart());
+        jseq.setEnd(JSEQ[i].getEnd());
+        seqRefIds.put(vamsasSeq[i].getId(), jseq);
+        tmpseqs.add(jseq);
+      }
+
+      if (JSEQ[i].getHidden())
+      {
+        if (hiddenSeqs == null)
+        {
+          hiddenSeqs = new Vector();
         }
 
-        ///SequenceFeatures are added to the DatasetSequence,
-        // so we must create the dataset before loading features
-        /////////////////////////////////
+        hiddenSeqs.addElement(
+            (jalview.datamodel.Sequence) seqRefIds.get(seqId));
+      }
 
+    }
 
-      jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[
-          tmpseqs.size()];
+    ///SequenceFeatures are added to the DatasetSequence,
+    // so we must create the dataset before loading features
+    /////////////////////////////////
 
-       tmpseqs.toArray(orderedSeqs) ;
 
+    jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[
+        tmpseqs.size()];
 
-        jalview.datamodel.Alignment al =
-            new jalview.datamodel.Alignment(orderedSeqs);
+    tmpseqs.toArray(orderedSeqs);
 
-        al.setDataset(null);
-        /////////////////////////////////
+    jalview.datamodel.Alignment al =
+        new jalview.datamodel.Alignment(orderedSeqs);
 
+    al.setDataset(null);
+    /////////////////////////////////
 
-        Hashtable pdbloaded = new Hashtable();
-        if(!multipleView)
+
+    Hashtable pdbloaded = new Hashtable();
+    if (!multipleView)
+    {
+      for (int i = 0; i < vamsasSeq.length; i++)
+      {
+        if (JSEQ[i].getFeaturesCount() > 0)
         {
-          for (int i = 0; i < vamsasSeq.length; i++)
+          Features[] features = JSEQ[i].getFeatures();
+          for (int f = 0; f < features.length; f++)
           {
-            if (JSEQ[i].getFeaturesCount() > 0)
+            jalview.datamodel.SequenceFeature sf
+                = new jalview.datamodel.SequenceFeature(features[f].getType(),
+                features[f].getDescription(), features[f].getStatus(),
+                features[f].getBegin(), features[f].getEnd(),
+                features[f].getFeatureGroup());
+
+            sf.setScore(features[f].getScore());
+            for (int od = 0; od < features[f].getOtherDataCount(); od++)
             {
-              Features[] features = JSEQ[i].getFeatures();
-              for (int f = 0; f < features.length; f++)
+              OtherData keyValue = features[f].getOtherData(od);
+              if (keyValue.getKey().startsWith("LINK"))
               {
-                jalview.datamodel.SequenceFeature sf
-                    = new jalview.datamodel.SequenceFeature(features[f].getType(),
-                    features[f].getDescription(), features[f].getStatus(),
-                    features[f].getBegin(), features[f].getEnd(),
-                    features[f].getFeatureGroup());
-
-                sf.setScore(features[f].getScore());
-                for (int od = 0; od < features[f].getOtherDataCount(); od++)
-                {
-                  OtherData keyValue = features[f].getOtherData(od);
-                  if (keyValue.getKey().startsWith("LINK"))
-                    sf.addLink(keyValue.getValue());
-                  else
-                    sf.setValue(keyValue.getKey(), keyValue.getValue());
-
-                }
-
-                al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
+                sf.addLink(keyValue.getValue());
               }
-            }
-            if (JSEQ[i].getPdbidsCount() > 0)
-            {
-              Pdbids[] ids = JSEQ[i].getPdbids();
-              for (int p = 0; p < ids.length; p++)
+              else
               {
-                jalview.datamodel.PDBEntry entry = new jalview.datamodel.
-                    PDBEntry();
-                entry.setId(ids[p].getId());
-                entry.setType(ids[p].getType());
-                if (ids[p].getFile() != null)
-                {
-                  if (!pdbloaded.containsKey(ids[p].getFile()))
-                  {
-                    String tmppdb = loadPDBFile(file, ids[p].getId());
-                    entry.setFile(tmppdb);
-                    pdbloaded.put(ids[p].getId(), tmppdb);
-                  }
-                  else
-                    entry.setFile(pdbloaded.get(ids[p].getId()).toString());
-                }
-
-                al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
+                sf.setValue(keyValue.getKey(), keyValue.getValue());
               }
+
             }
-            if (vamsasSeq[i].getDBRefCount() > 0)
+
+            al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
+          }
+        }
+        if (JSEQ[i].getPdbidsCount() > 0)
+        {
+          Pdbids[] ids = JSEQ[i].getPdbids();
+          for (int p = 0; p < ids.length; p++)
+          {
+            jalview.datamodel.PDBEntry entry = new jalview.datamodel.
+                PDBEntry();
+            entry.setId(ids[p].getId());
+            entry.setType(ids[p].getType());
+            if (ids[p].getFile() != null)
             {
-              for (int d = 0; d < vamsasSeq[i].getDBRefCount(); d++)
+              if (!pdbloaded.containsKey(ids[p].getFile()))
               {
-                jalview.datamodel.DBRefEntry entry =
-                    new jalview.datamodel.DBRefEntry(
-                        vamsasSeq[i].getDBRef(d).getSource(),
-                        vamsasSeq[i].getDBRef(d).getVersion(),
-                        vamsasSeq[i].getDBRef(d).getAccessionId()
-                    );
-                al.getSequenceAt(i).getDatasetSequence().addDBRef(entry);
+                String tmppdb = loadPDBFile(file, ids[p].getId());
+                entry.setFile(tmppdb);
+                pdbloaded.put(ids[p].getId(), tmppdb);
+              }
+              else
+              {
+                entry.setFile(pdbloaded.get(ids[p].getId()).toString());
               }
-
             }
+
+            al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
           }
         }
+        if (vamsasSeq[i].getDBRefCount() > 0)
+        {
+          for (int d = 0; d < vamsasSeq[i].getDBRefCount(); d++)
+          {
+            jalview.datamodel.DBRefEntry entry =
+                new jalview.datamodel.DBRefEntry(
+                    vamsasSeq[i].getDBRef(d).getSource(),
+                    vamsasSeq[i].getDBRef(d).getVersion(),
+                    vamsasSeq[i].getDBRef(d).getAccessionId()
+                );
+            al.getSequenceAt(i).getDatasetSequence().addDBRef(entry);
+          }
 
+        }
+      }
+    }
 
-         /////////////////////////////////
-        //////////////////////////////////
-        //LOAD ANNOTATIONS
-        boolean hideQuality = true,
-            hideConservation = true,
-            hideConsensus = true;
-
-        if (vamsasSet.getAnnotationCount()>0)
-        {
-            Annotation[] an = vamsasSet.getAnnotation();
+    /////////////////////////////////
+    //////////////////////////////////
+    //LOAD ANNOTATIONS
+    boolean hideQuality = true,
+        hideConservation = true,
+        hideConsensus = true;
 
-            for (int i = 0; i < an.length; i++)
-            {
-               if (an[i].getLabel().equals("Quality"))
-                {
-                 hideQuality = false;
-                 continue;
-                }
-               else if(an[i].getLabel().equals("Conservation"))
-               {
-                 hideConservation = false;
-                 continue;
-               }
-               else if(an[i].getLabel().equals("Consensus"))
-               {
-                 hideConsensus = false;
-                 continue;
-               }
-
-               if (an[i].getId() != null
-                   && annotationIds.containsKey(an[i].getId()))
-               {
-                 al.addAnnotation(
-                     (jalview.datamodel.AlignmentAnnotation)annotationIds.get(an[i].getId())
-                     );
-
-                 continue;
-              }
+    if (vamsasSet.getAnnotationCount() > 0)
+    {
+      Annotation[] an = vamsasSet.getAnnotation();
 
-                AnnotationElement[] ae = an[i].getAnnotationElement();
-                jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al.getWidth()];
+      for (int i = 0; i < an.length; i++)
+      {
+        if (an[i].getLabel().equals("Quality"))
+        {
+          hideQuality = false;
+          continue;
+        }
+        else if (an[i].getLabel().equals("Conservation"))
+        {
+          hideConservation = false;
+          continue;
+        }
+        else if (an[i].getLabel().equals("Consensus"))
+        {
+          hideConsensus = false;
+          continue;
+        }
 
-                for (int aa = 0; aa < ae.length && aa<anot.length; aa++)
-                {
-                    anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].getDisplayCharacter(),
-                            ae[aa].getDescription(),
-                            ae[aa].getSecondaryStructure().length()==0?' ':ae[aa].getSecondaryStructure().charAt(0),
-                            ae[aa].getValue());
-                    anot[ae[aa].getPosition()].colour = new java.awt.Color( ae[aa].getColour() );
-                }
+        if (an[i].getId() != null
+            && annotationIds.containsKey(an[i].getId()))
+        {
+          al.addAnnotation(
+              (jalview.datamodel.AlignmentAnnotation) annotationIds.get(an[i].
+              getId())
+              );
 
-                jalview.datamodel.AlignmentAnnotation jaa = null;
+          continue;
+        }
 
-                if (an[i].getGraph())
-                {
-                  jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
-                      an[i].getDescription(), anot, 0, 0,
-                      an[i].getGraphType());
+        AnnotationElement[] ae = an[i].getAnnotationElement();
+        jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[
+            al.getWidth()];
 
-                  jaa.graphGroup = an[i].getGraphGroup();
+        for (int aa = 0; aa < ae.length && aa < anot.length; aa++)
+        {
+          anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].
+              getDisplayCharacter(),
+              ae[aa].getDescription(),
+              ae[aa].getSecondaryStructure().length() == 0 ? ' ' :
+              ae[aa].getSecondaryStructure().charAt(0),
+                   ae[aa].getValue());
+          anot[ae[aa].getPosition()].colour = new java.awt.Color(ae[aa].
+              getColour());
+        }
 
-                  if (an[i].getThresholdLine() != null)
-                  {
-                    jaa.setThreshold(new jalview.datamodel.GraphLine(
-                                  an[i].getThresholdLine().getValue(),
-                                  an[i].getThresholdLine().getLabel(),
-                                new java.awt.Color(an[i].getThresholdLine().getColour()))
-                             );
+        jalview.datamodel.AlignmentAnnotation jaa = null;
 
-                  }
+        if (an[i].getGraph())
+        {
+          jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
+              an[i].getDescription(), anot, 0, 0,
+              an[i].getGraphType());
 
-                }
-                else
-                {
-                    jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
-                            an[i].getDescription(), anot);
-                }
+          jaa.graphGroup = an[i].getGraphGroup();
 
-                if(an[i].getId()!=null)
-                {
-                  annotationIds.put(an[i].getId(), jaa);
-                  jaa.annotationId = an[i].getId();
-                }
+          if (an[i].getThresholdLine() != null)
+          {
+            jaa.setThreshold(new jalview.datamodel.GraphLine(
+                an[i].getThresholdLine().getValue(),
+                an[i].getThresholdLine().getLabel(),
+                new java.awt.Color(an[i].getThresholdLine().getColour()))
+                );
 
-                if(an[i].getSequenceRef()!=null)
-                {
-                  jaa.createSequenceMapping(
-                      al.findName(an[i].getSequenceRef()), 1, true
-                      );
-                  al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
-                }
+          }
 
-                al.addAnnotation(jaa);
-            }
         }
-
-        /////////////////////////
-        //LOAD GROUPS
-        if (jms.getJGroupCount() > 0)
+        else
         {
-            JGroup[] groups = jms.getJGroup();
-
-            for (int i = 0; i < groups.length; i++)
-            {
-                ColourSchemeI cs = null;
-
-                if (groups[i].getColour() != null)
-                {
-                    if (groups[i].getColour().startsWith("ucs"))
-                    {
-                        cs = GetUserColourScheme(jms, groups[i].getColour());
-                    }
-                    else
-                    {
-                        cs = ColourSchemeProperty.getColour(al,
-                                groups[i].getColour());
-                    }
+          jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
+              an[i].getDescription(), anot);
+        }
 
-                    if(cs!=null)
-                      cs.setThreshold(groups[i].getPidThreshold(), true);
-                }
+        if (an[i].getId() != null)
+        {
+          annotationIds.put(an[i].getId(), jaa);
+          jaa.annotationId = an[i].getId();
+        }
 
-                Vector seqs = new Vector();
+        if (an[i].getSequenceRef() != null)
+        {
+          jaa.createSequenceMapping(
+              al.findName(an[i].getSequenceRef()), 1, true
+              );
+          al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
+        }
 
-                for (int s = 0; s < groups[i].getSeqCount(); s++)
-                {
-                    String seqId = groups[i].getSeq(s)+"";
-                    jalview.datamodel.SequenceI ts = (jalview.datamodel.SequenceI)
-                        seqRefIds.get(seqId);
+        al.addAnnotation(jaa);
+      }
+    }
 
-                    if (ts != null)
-                      seqs.addElement(ts);
-                }
+    /////////////////////////
+    //LOAD GROUPS
+    if (jms.getJGroupCount() > 0)
+    {
+      JGroup[] groups = jms.getJGroup();
 
-                if(seqs.size()<1)
-                  continue;
+      for (int i = 0; i < groups.length; i++)
+      {
+        ColourSchemeI cs = null;
 
-                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());
+        if (groups[i].getColour() != null)
+        {
+          if (groups[i].getColour().startsWith("ucs"))
+          {
+            cs = GetUserColourScheme(jms, groups[i].getColour());
+          }
+          else
+          {
+            cs = ColourSchemeProperty.getColour(al,
+                                                groups[i].getColour());
+          }
 
-                sg.setOutlineColour(new java.awt.Color(
-                        groups[i].getOutlineColour()));
+          if (cs != null)
+          {
+            cs.setThreshold(groups[i].getPidThreshold(), true);
+          }
+        }
 
-                sg.textColour = new java.awt.Color(groups[i].getTextCol1());
-                sg.textColour2 = new java.awt.Color(groups[i].getTextCol2());
-                sg.thresholdTextColour = groups[i].getTextColThreshold();
+        Vector seqs = new Vector();
 
-                if (groups[i].getConsThreshold() != 0)
-                {
-                    jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",
-                            ResidueProperties.propHash, 3, sg.getSequences(null), 0,
-                            sg.getWidth() - 1);
-                    c.calculate();
-                    c.verdict(false, 25);
-                    sg.cs.setConservation(c);
-                }
+        for (int s = 0; s < groups[i].getSeqCount(); s++)
+        {
+          String seqId = groups[i].getSeq(s) + "";
+          jalview.datamodel.SequenceI ts = (jalview.datamodel.SequenceI)
+              seqRefIds.get(seqId);
 
-                al.addGroup(sg);
-            }
+          if (ts != null)
+          {
+            seqs.addElement(ts);
+          }
         }
 
+        if (seqs.size() < 1)
+        {
+          continue;
+        }
 
-        /////////////////////////////////
-        // LOAD VIEWPORT
+        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());
 
-        AlignFrame af = new AlignFrame(al,
-                                       view.getWidth(),
-                                       view.getHeight() );
+        sg.setOutlineColour(new java.awt.Color(
+            groups[i].getOutlineColour()));
 
-        af.setFileName(file, "Jalview");
+        sg.textColour = new java.awt.Color(groups[i].getTextCol1());
+        sg.textColour2 = new java.awt.Color(groups[i].getTextCol2());
+        sg.thresholdTextColour = groups[i].getTextColThreshold();
 
-        for (int i = 0; i < JSEQ.length; i++)
+        if (groups[i].getConsThreshold() != 0)
         {
-          af.viewport.setSequenceColour(
-              af.viewport.alignment.getSequenceAt(i),
-              new java.awt.Color(
-                  JSEQ[i].getColour()));
+          jalview.analysis.Conservation c = new jalview.analysis.Conservation(
+              "All",
+              ResidueProperties.propHash, 3, sg.getSequences(null), 0,
+              sg.getWidth() - 1);
+          c.calculate();
+          c.verdict(false, 25);
+          sg.cs.setConservation(c);
         }
 
-        //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;
+        al.addGroup(sg);
+      }
+    }
 
-        af.viewport.gatherViewsHere = view.getGatheredViews();
+    /////////////////////////////////
+    // LOAD VIEWPORT
 
-        if (view.getSequenceSetId() != null)
-        {
-          jalview.gui.AlignViewport av =
-              (jalview.gui.AlignViewport)
-              viewportsAdded.get(uniqueSeqSetId);
+    AlignFrame af = new AlignFrame(al,
+                                   view.getWidth(),
+                                   view.getHeight());
 
-          af.viewport.sequenceSetID = uniqueSeqSetId;
-          if(av!=null)
-          {
+    af.setFileName(file, "Jalview");
 
-            af.viewport.historyList = av.historyList;
-            af.viewport.redoList = av.redoList;
-          }
-          else
-          {
-            viewportsAdded.put(uniqueSeqSetId, af.viewport);
-          }
+    for (int i = 0; i < JSEQ.length; i++)
+    {
+      af.viewport.setSequenceColour(
+          af.viewport.alignment.getSequenceAt(i),
+          new java.awt.Color(
+              JSEQ[i].getColour()));
+    }
 
-          PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
-        }
-        if(hiddenSeqs!=null)
-        {
-          for(int s=0; s<JSEQ.length; s++)
-          {
-            jalview.datamodel.SequenceGroup hidden =
-                new jalview.datamodel.SequenceGroup();
+    //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;
 
-            for(int r=0; r<JSEQ[s].getHiddenSequencesCount(); r++)
-            {
-              hidden.addSequence(
-                  al.getSequenceAt(JSEQ[s].getHiddenSequences(r))
-                  , false
-                  );
-            }
-            af.viewport.hideRepSequences(al.getSequenceAt(s), hidden);
-          }
+    af.viewport.gatherViewsHere = view.getGatheredViews();
 
-          jalview.datamodel.SequenceI [] hseqs = new
-              jalview.datamodel.SequenceI[hiddenSeqs.size()];
-
-          for(int s=0; s<hiddenSeqs.size(); s++)
-            hseqs[s] = (jalview.datamodel.SequenceI)hiddenSeqs.elementAt(s);
+    if (view.getSequenceSetId() != null)
+    {
+      jalview.gui.AlignViewport av =
+          (jalview.gui.AlignViewport)
+          viewportsAdded.get(uniqueSeqSetId);
 
-          af.viewport.hideSequence( hseqs );
+      af.viewport.sequenceSetID = uniqueSeqSetId;
+      if (av != null)
+      {
 
-        }
+        af.viewport.historyList = av.historyList;
+        af.viewport.redoList = av.redoList;
+      }
+      else
+      {
+        viewportsAdded.put(uniqueSeqSetId, af.viewport);
+      }
 
+      PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
+    }
+    if (hiddenSeqs != null)
+    {
+      for (int s = 0; s < JSEQ.length; s++)
+      {
+        jalview.datamodel.SequenceGroup hidden =
+            new jalview.datamodel.SequenceGroup();
 
-        if((hideConsensus || hideQuality || hideConservation)
-            && al.getAlignmentAnnotation()!=null)
+        for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++)
         {
-          int hSize = al.getAlignmentAnnotation().length;
-          for (int h = 0; h < hSize; h++)
-          {
-            if (
-                (hideConsensus &&
-                 al.getAlignmentAnnotation()[h].label.equals("Consensus"))
-                ||
-                (hideQuality &&
-                 al.getAlignmentAnnotation()[h].label.equals("Quality"))
-                ||
-                (hideConservation &&
-                 al.getAlignmentAnnotation()[h].label.equals("Conservation")))
-            {
-              al.deleteAnnotation(al.getAlignmentAnnotation()[h]);
-              hSize--;
-              h--;
-            }
-          }
-          af.alignPanel.adjustAnnotationHeight();
+          hidden.addSequence(
+              al.getSequenceAt(JSEQ[s].getHiddenSequences(r))
+              , false
+              );
         }
+        af.viewport.hideRepSequences(al.getSequenceAt(s), hidden);
+      }
+
+      jalview.datamodel.SequenceI[] hseqs = new
+          jalview.datamodel.SequenceI[hiddenSeqs.size()];
 
-        if(view.getViewName()!=null)
+      for (int s = 0; s < hiddenSeqs.size(); s++)
+      {
+        hseqs[s] = (jalview.datamodel.SequenceI) hiddenSeqs.elementAt(s);
+      }
+
+      af.viewport.hideSequence(hseqs);
+
+    }
+
+    if ( (hideConsensus || hideQuality || hideConservation)
+        && al.getAlignmentAnnotation() != null)
+    {
+      int hSize = al.getAlignmentAnnotation().length;
+      for (int h = 0; h < hSize; h++)
+      {
+        if (
+            (hideConsensus &&
+             al.getAlignmentAnnotation()[h].label.equals("Consensus"))
+            ||
+            (hideQuality &&
+             al.getAlignmentAnnotation()[h].label.equals("Quality"))
+            ||
+            (hideConservation &&
+             al.getAlignmentAnnotation()[h].label.equals("Conservation")))
         {
-          af.viewport.viewName = view.getViewName();
-          af.setInitialTabVisible();
+          al.deleteAnnotation(al.getAlignmentAnnotation()[h]);
+          hSize--;
+          h--;
         }
-        af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
-            view.getHeight());
+      }
+      af.alignPanel.adjustAnnotationHeight();
+    }
 
-        af.viewport.setShowAnnotation(view.getShowAnnotation());
-        af.viewport.setAbovePIDThreshold(view.getPidSelected());
+    if (view.getViewName() != null)
+    {
+      af.viewport.viewName = view.getViewName();
+      af.setInitialTabVisible();
+    }
+    af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
+                 view.getHeight());
 
-        af.viewport.setColourText(view.getShowColourText());
+    af.viewport.setShowAnnotation(view.getShowAnnotation());
+    af.viewport.setAbovePIDThreshold(view.getPidSelected());
 
-        af.viewport.setConservationSelected(view.getConservationSelected());
-        af.viewport.setShowJVSuffix(view.getShowFullId());
-        af.viewport.rightAlignIds=view.getRightAlignIds();
-        af.viewport.setFont(new java.awt.Font(view.getFontName(),
-                view.getFontStyle(), view.getFontSize()));
-        af.alignPanel.fontChanged();
-        af.viewport.setRenderGaps(view.getRenderGaps());
-        af.viewport.setWrapAlignment(view.getWrapAlignment());
-        af.alignPanel.setWrapAlignment(view.getWrapAlignment());
-        af.viewport.setShowAnnotation(view.getShowAnnotation());
-        af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
+    af.viewport.setColourText(view.getShowColourText());
 
-        af.viewport.setShowBoxes(view.getShowBoxes());
+    af.viewport.setConservationSelected(view.getConservationSelected());
+    af.viewport.setShowJVSuffix(view.getShowFullId());
+    af.viewport.rightAlignIds = view.getRightAlignIds();
+    af.viewport.setFont(new java.awt.Font(view.getFontName(),
+                                          view.getFontStyle(), view.getFontSize()));
+    af.alignPanel.fontChanged();
+    af.viewport.setRenderGaps(view.getRenderGaps());
+    af.viewport.setWrapAlignment(view.getWrapAlignment());
+    af.alignPanel.setWrapAlignment(view.getWrapAlignment());
+    af.viewport.setShowAnnotation(view.getShowAnnotation());
+    af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
 
-        af.viewport.setShowText(view.getShowText());
+    af.viewport.setShowBoxes(view.getShowBoxes());
 
-        af.viewport.textColour = new java.awt.Color(view.getTextCol1());
-        af.viewport.textColour2 = new java.awt.Color(view.getTextCol2());
-        af.viewport.thresholdTextColour = view.getTextColThreshold();
+    af.viewport.setShowText(view.getShowText());
 
-        af.viewport.setStartRes(view.getStartRes());
-        af.viewport.setStartSeq(view.getStartSeq());
+    af.viewport.textColour = new java.awt.Color(view.getTextCol1());
+    af.viewport.textColour2 = new java.awt.Color(view.getTextCol2());
+    af.viewport.thresholdTextColour = view.getTextColThreshold();
 
-        ColourSchemeI cs = null;
+    af.viewport.setStartRes(view.getStartRes());
+    af.viewport.setStartSeq(view.getStartSeq());
+
+    ColourSchemeI cs = null;
 
-        if (view.getBgColour() != null)
+    if (view.getBgColour() != null)
+    {
+      if (view.getBgColour().startsWith("ucs"))
+      {
+        cs = GetUserColourScheme(jms, view.getBgColour());
+      }
+      else if (view.getBgColour().startsWith("Annotation"))
+      {
+        //int find annotation
+        for (int i = 0;
+             i < af.viewport.alignment.getAlignmentAnnotation().length; i++)
         {
-            if (view.getBgColour().startsWith("ucs"))
+          if (af.viewport.alignment.getAlignmentAnnotation()[i].label.
+              equals(view.getAnnotationColours().getAnnotation()))
+          {
+            if (af.viewport.alignment.getAlignmentAnnotation()[i].
+                getThreshold() == null)
             {
-                cs = GetUserColourScheme(jms, view.getBgColour());
+              af.viewport.alignment.getAlignmentAnnotation()[i].
+                  setThreshold(
+                      new jalview.datamodel.GraphLine(
+                          view.getAnnotationColours().getThreshold(),
+                          "Threshold", java.awt.Color.black)
+
+                  );
             }
-            else if(view.getBgColour().startsWith("Annotation"))
+
+            if (view.getAnnotationColours().getColourScheme().equals(
+                "None"))
+            {
+              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().
+                     startsWith("ucs"))
+            {
+              cs = new AnnotationColourGradient(
+                  af.viewport.alignment.getAlignmentAnnotation()[i],
+                  GetUserColourScheme(jms, view.getAnnotationColours().
+                                      getColourScheme()),
+                  view.getAnnotationColours().getAboveThreshold()
+                  );
+            }
+            else
             {
-              //int find annotation
-              for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++)
+              cs = new AnnotationColourGradient(
+                  af.viewport.alignment.getAlignmentAnnotation()[i],
+                  ColourSchemeProperty.getColour(al,
+                                                 view.getAnnotationColours().
+                                                 getColourScheme()),
+                  view.getAnnotationColours().getAboveThreshold()
+                  );
+            }
+
+            // Also use these settings for all the groups
+            if (al.getGroups() != null)
+            {
+              for (int g = 0; g < al.getGroups().size(); g++)
               {
-                if (af.viewport.alignment.getAlignmentAnnotation()[i].label.
-                    equals(view.getAnnotationColours().getAnnotation()))
+                jalview.datamodel.SequenceGroup sg
+                    = (jalview.datamodel.SequenceGroup) al.getGroups().
+                    elementAt(g);
+
+                if (sg.cs == null)
                 {
-                  if (af.viewport.alignment.getAlignmentAnnotation()[i].
-                      getThreshold() == null)
-                  {
-                    af.viewport.alignment.getAlignmentAnnotation()[i].
-                        setThreshold(
-                            new jalview.datamodel.GraphLine(
-                                view.getAnnotationColours().getThreshold(),
-                                "Threshold", java.awt.Color.black)
-
-                        );
-                  }
-
-
-                  if (view.getAnnotationColours().getColourScheme().equals(
-                      "None"))
-                  {
-                    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().
-                           startsWith("ucs"))
-                  {
-                     cs = new AnnotationColourGradient(
-                         af.viewport.alignment.getAlignmentAnnotation()[i],
-                         GetUserColourScheme(jms, view.getAnnotationColours().
-                                                        getColourScheme()),
-                         view.getAnnotationColours().getAboveThreshold()
-                         );
-                   }
-                   else
-                   {
-                     cs = new AnnotationColourGradient(
-                         af.viewport.alignment.getAlignmentAnnotation()[i],
-                         ColourSchemeProperty.getColour(al,
-                         view.getAnnotationColours().getColourScheme()),
-                         view.getAnnotationColours().getAboveThreshold()
-                         );
-                   }
-
-                  // Also use these settings for all the groups
-                  if (al.getGroups() != null)
-                    for (int g = 0; g < al.getGroups().size(); g++)
-                    {
-                      jalview.datamodel.SequenceGroup sg
-                          = (jalview.datamodel.SequenceGroup)al.getGroups().elementAt(g);
-
-                      if(sg.cs == null)
-                        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*/
-                      {
-                        sg.cs = new AnnotationColourGradient(
-                            af.viewport.alignment.getAlignmentAnnotation()[i],
-                            sg.cs,
-                            view.getAnnotationColours().getAboveThreshold()
-                            );
-                      }
+                  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());
                     }
-
-
-                  break;
+                    else*/
+                {
+                  sg.cs = new AnnotationColourGradient(
+                      af.viewport.alignment.getAlignmentAnnotation()[i],
+                      sg.cs,
+                      view.getAnnotationColours().getAboveThreshold()
+                      );
                 }
 
               }
             }
-            else
-            {
-                cs = ColourSchemeProperty.getColour(al, view.getBgColour());
-            }
 
-            if(cs!=null)
-            {
-              cs.setThreshold(view.getPidThreshold(), true);
-              cs.setConsensus(af.viewport.hconsensus);
-            }
+            break;
+          }
+
         }
+      }
+      else
+      {
+        cs = ColourSchemeProperty.getColour(al, view.getBgColour());
+      }
 
+      if (cs != null)
+      {
+        cs.setThreshold(view.getPidThreshold(), true);
+        cs.setConsensus(af.viewport.hconsensus);
+      }
+    }
 
-        af.viewport.setGlobalColourScheme(cs);
-        af.viewport.setColourAppliesToAllGroups(false);
+    af.viewport.setGlobalColourScheme(cs);
+    af.viewport.setColourAppliesToAllGroups(false);
 
-        if (view.getConservationSelected() && cs!=null)
-        {
-          cs.setConservationInc(view.getConsThreshold());
-        }
+    if (view.getConservationSelected() && cs != null)
+    {
+      cs.setConservationInc(view.getConsThreshold());
+    }
 
-        af.changeColour(cs);
+    af.changeColour(cs);
 
-        af.viewport.setColourAppliesToAllGroups(true);
+    af.viewport.setColourAppliesToAllGroups(true);
 
+    if (view.getShowSequenceFeatures())
+    {
+      af.viewport.showSequenceFeatures = true;
+    }
 
+    if (jms.getFeatureSettings() != null)
+    {
+      af.viewport.featuresDisplayed = new Hashtable();
+      String[] renderOrder = new String[jms.getFeatureSettings().
+          getSettingCount()];
+      for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
+      {
+        Setting setting = jms.getFeatureSettings().getSetting(fs);
 
-        if (view.getShowSequenceFeatures())
-        {
-           af.viewport.showSequenceFeatures = true;
-        }
+        af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.
+            getType(),
+            new java.awt.Color(setting.getColour()));
 
-        if(jms.getFeatureSettings()!=null)
-        {
-          af.viewport.featuresDisplayed = new Hashtable();
-          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()));
-
-           renderOrder[fs] = setting.getType();
-
-           if(setting.getDisplay())
-             af.viewport.featuresDisplayed.put(
-                 setting.getType(), new Integer(setting.getColour()));
-         }
-         af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
-        }
+        renderOrder[fs] = setting.getType();
 
-        if (view.getHiddenColumnsCount() > 0)
+        if (setting.getDisplay())
         {
-          for (int c = 0; c < view.getHiddenColumnsCount(); c++)
-          {
-              af.viewport.hideColumns(
-                view.getHiddenColumns(c).getStart(),
-                view.getHiddenColumns(c).getEnd() //+1
-                );
-          }
+          af.viewport.featuresDisplayed.put(
+              setting.getType(), new Integer(setting.getColour()));
         }
+      }
+      af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder =
+          renderOrder;
+    }
 
-        af.setMenusFromViewport(af.viewport);
+    if (view.getHiddenColumnsCount() > 0)
+    {
+      for (int c = 0; c < view.getHiddenColumnsCount(); c++)
+      {
+        af.viewport.hideColumns(
+            view.getHiddenColumns(c).getStart(),
+            view.getHiddenColumns(c).getEnd() //+1
+            );
+      }
+    }
 
+    af.setMenusFromViewport(af.viewport);
 
-        Desktop.addInternalFrame(af, view.getTitle(),
-             view.getWidth(), view.getHeight());
+    Desktop.addInternalFrame(af, view.getTitle(),
+                             view.getWidth(), view.getHeight());
 
-        //LOAD TREES
-        ///////////////////////////////////////
-        if (loadTrees && jms.getTreeCount() > 0)
+    //LOAD TREES
+    ///////////////////////////////////////
+    if (loadTrees && jms.getTreeCount() > 0)
+    {
+      try
+      {
+        for (int t = 0; t < jms.getTreeCount(); t++)
         {
-            try
-            {
-                for (int t = 0; t < jms.getTreeCount(); t++)
-                {
 
-                    Tree tree = jms.getTree(t);
+          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);
+          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()));
-                    else
-                      tp.setTreeFont(new java.awt.Font(view.getFontName(),
-                                            view.getFontStyle(),
-                                            tree.getFontSize()));
-
-                    tp.showPlaceholders(tree.getMarkUnlinked());
-                    tp.showBootstrap(tree.getShowBootstrap());
-                    tp.showDistances(tree.getShowDistances());
-
-                    tp.treeCanvas.threshold = tree.getThreshold();
+          if (tree.getFontName() != null)
+          {
+            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()));
+          }
 
-                    if (tree.getCurrentTree())
-                      af.viewport.setCurrentTree(tp.getTree());
-                }
+          tp.showPlaceholders(tree.getMarkUnlinked());
+          tp.showBootstrap(tree.getShowBootstrap());
+          tp.showDistances(tree.getShowDistances());
 
-            }
-            catch (Exception ex)
-            {
-                ex.printStackTrace();
-            }
+          tp.treeCanvas.threshold = tree.getThreshold();
 
+          if (tree.getCurrentTree())
+          {
+            af.viewport.setCurrentTree(tp.getTree());
+          }
         }
 
-        return af;
+      }
+      catch (Exception ex)
+      {
+        ex.printStackTrace();
+      }
+
     }
 
-    public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap, boolean keepSeqRefs )
-    {
-      jalview.schemabinding.version2.JalviewModel jm
-          = SaveState(ap, null, null, null);
+    return af;
+  }
 
-      if (!keepSeqRefs)
-      {
-        seqRefIds.clear();
-        jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null);
-      }
-      else
-        uniqueSetSuffix = "";
+  public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap,
+      boolean keepSeqRefs)
+  {
+    jalview.schemabinding.version2.JalviewModel jm
+        = SaveState(ap, null, null, null);
 
-      viewportsAdded = new Hashtable();
+    if (!keepSeqRefs)
+    {
+      seqRefIds.clear();
+      jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null);
+    }
+    else
+    {
+      uniqueSetSuffix = "";
+    }
 
-      AlignFrame af = LoadFromObject(jm, null, false);
-      af.alignPanels.clear();
-      af.closeMenuItem_actionPerformed(true);
+    viewportsAdded = new Hashtable();
+
+    AlignFrame af = LoadFromObject(jm, null, false);
+    af.alignPanels.clear();
+    af.closeMenuItem_actionPerformed(true);
 
     /*  if(ap.av.alignment.getAlignmentAnnotation()!=null)
       {
@@ -1730,7 +1772,6 @@ public class Jalview2XML
         }
       }   */
 
-      return af.alignPanel;
-    }
+    return af.alignPanel;
+  }
 }
-
diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java
index 393b192..d8e79ce 100755
--- a/src/jalview/gui/Jalview2XML_V1.java
+++ b/src/jalview/gui/Jalview2XML_V1.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,24 +18,16 @@
  */
 package jalview.gui;
 
-import jalview.schemes.*;
-
 import java.io.*;
-
 import java.net.*;
-
 import java.util.*;
-
 import java.util.jar.*;
 
 import javax.swing.*;
 
 import org.exolab.castor.xml.*;
-
 import jalview.binding.*;
-
-
-
+import jalview.schemes.*;
 
 /**
  * DOCUMENT ME!
@@ -45,437 +37,448 @@ import jalview.binding.*;
  */
 public class Jalview2XML_V1
 {
-   jalview.schemes.UserColourScheme GetUserColourScheme(
-        JalviewModelSequence jms, String id)
+  jalview.schemes.UserColourScheme GetUserColourScheme(
+      JalviewModelSequence jms, String id)
+  {
+    UserColours[] uc = jms.getUserColours();
+    UserColours colours = null;
+
+    for (int i = 0; i < uc.length; i++)
+    {
+      if (uc[i].getId().equals(id))
+      {
+        colours = uc[i];
+
+        break;
+      }
+    }
+
+    int csize = colours.getUserColourScheme().getColourCount();
+    java.awt.Color[] newColours = new java.awt.Color[csize];
+
+    for (int i = 0; i < csize; i++)
     {
-        UserColours[] uc = jms.getUserColours();
-        UserColours colours = null;
+      newColours[i] = new java.awt.Color(Integer.parseInt(
+          colours.getUserColourScheme().getColour(i).getRGB(), 16));
+    }
+
+    return new jalview.schemes.UserColourScheme(newColours);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param file DOCUMENT ME!
+   */
+  public AlignFrame LoadJalviewAlign(final String file)
+  {
+
+    jalview.gui.AlignFrame af = null;
+
+    try
+    {
+      //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
+      URL url = null;
+
+      if (file.startsWith("http://"))
+      {
+        url = new URL(file);
+      }
+
+      JarInputStream jin = null;
+      JarEntry jarentry = null;
+      int entryCount = 1;
+
+      do
+      {
+        if (url != null)
+        {
+          jin = new JarInputStream(url.openStream());
+        }
+        else
+        {
+          jin = new JarInputStream(new FileInputStream(file));
+        }
 
-        for (int i = 0; i < uc.length; i++)
+        for (int i = 0; i < entryCount; i++)
         {
-            if (uc[i].getId().equals(id))
-            {
-                colours = uc[i];
+          jarentry = jin.getNextJarEntry();
+        }
 
-                break;
-            }
+        class NoDescIDResolver
+            implements IDResolver
+        {
+          public Object resolve(String idref)
+          {
+            System.out.println(idref + " used");
+            return null;
+          }
         }
 
-        int csize = colours.getUserColourScheme().getColourCount();
-        java.awt.Color[] newColours = new java.awt.Color[csize];
+        if (jarentry != null)
+        {
+          InputStreamReader in = new InputStreamReader(jin, "UTF-8");
+          JalviewModel object = new JalviewModel();
+
+          object = (JalviewModel) object.unmarshal(in);
 
-        for (int i = 0; i < csize; i++)
+          af = LoadFromObject(object, file);
+          entryCount++;
+        }
+      }
+      while (jarentry != null);
+    }
+    catch (final java.net.UnknownHostException ex)
+    {
+      ex.printStackTrace();
+      javax.swing.SwingUtilities.invokeLater(new Runnable()
+      {
+        public void run()
         {
-            newColours[i] = new java.awt.Color(Integer.parseInt(
-                        colours.getUserColourScheme().getColour(i).getRGB(), 16));
+
+          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)
+    {
+      ex.printStackTrace();
+      System.err.println("Exception whilst loading jalview XML file : " +
+                         ex + "\n");
+      javax.swing.SwingUtilities.invokeLater(new Runnable()
+      {
+        public void run()
+        {
 
-        return new jalview.schemes.UserColourScheme(newColours);
+          JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                                                "Error loading  " + file,
+                                                "Error loading Jalview file",
+                                                JOptionPane.WARNING_MESSAGE);
+        }
+      });
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param file DOCUMENT ME!
-     */
-    public AlignFrame LoadJalviewAlign(final String file)
+    return af;
+  }
+
+  AlignFrame LoadFromObject(JalviewModel object, String file)
+  {
+    Vector seqids = new Vector();
+    SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
+    Sequence[] vamsasSeq = vamsasSet.getSequence();
+
+    JalviewModelSequence jms = object.getJalviewModelSequence();
+
+    //////////////////////////////////
+    //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());
+      jseqs[i].setStart(JSEQ[i].getStart());
+      jseqs[i].setEnd(JSEQ[i].getEnd());
+      seqids.add(jseqs[i]);
+    }
 
-        jalview.gui.AlignFrame af = null;
+    ///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);
+    /////////////////////////////////
 
-        try
-        {
-            //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
-            URL url = null;
-
-            if (file.startsWith("http://"))
-            {
-                url = new URL(file);
-            }
-
-            JarInputStream jin = null;
-            JarEntry jarentry = null;
-            int entryCount = 1;
-
-            do
-            {
-                if (url != null)
-                {
-                    jin = new JarInputStream(url.openStream());
-                }
-                else
-                {
-                    jin = new JarInputStream(new FileInputStream(file));
-                }
-
-                for (int i = 0; i < entryCount; i++)
-                {
-                    jarentry = jin.getNextJarEntry();
-                  }
-
-                  class NoDescIDResolver implements IDResolver
-                  {
-                    public Object resolve(String idref)
-                    {
-                      System.out.println(idref+" used");
-                      return null;
-                    }
-                  }
-
-
-                if (jarentry != null)
-                {
-                    InputStreamReader in = new InputStreamReader(jin, "UTF-8");
-                    JalviewModel object = new JalviewModel();
-
-                    object = (JalviewModel) object.unmarshal(in);
-
-                    af = LoadFromObject(object, file);
-                    entryCount++;
-                }
-            }
-            while (jarentry != null);
-        }
-        catch (final java.net.UnknownHostException ex)
+    for (int i = 0; i < vamsasSeq.length; i++)
+    {
+      if (JSEQ[i].getFeaturesCount() > 0)
+      {
+        Features[] features = JSEQ[i].getFeatures();
+        for (int f = 0; f < features.length; f++)
         {
-          ex.printStackTrace();
-          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);
-            }
-          });
+          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);
         }
-        catch (Exception ex)
+      }
+      if (JSEQ[i].getPdbidsCount() > 0)
+      {
+        Pdbids[] ids = JSEQ[i].getPdbids();
+        for (int p = 0; p < ids.length; p++)
         {
-          ex.printStackTrace();
-          System.err.println("Exception whilst loading jalview XML file : " +
-                             ex + "\n");
-          javax.swing.SwingUtilities.invokeLater(new Runnable()
-          {
-            public void run()
-            {
-
-              JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                  "Error loading  " + file,
-                  "Error loading Jalview file",
-                  JOptionPane.WARNING_MESSAGE);
-            }
-          });
+          jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
+          entry.setId(ids[p].getId());
+          entry.setType(ids[p].getType());
+          al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
         }
 
-        return af;
+      }
     }
 
-    AlignFrame LoadFromObject(JalviewModel object, String file)
+    /////////////////////////////////
+    //////////////////////////////////
+    //LOAD ANNOTATIONS
+    if (vamsasSet.getAnnotation() != null)
     {
-        Vector seqids = new Vector();
-        SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
-        Sequence[] vamsasSeq = vamsasSet.getSequence();
+      Annotation[] an = vamsasSet.getAnnotation();
+
+      for (int i = 0; i < an.length; i++)
+      {
+        AnnotationElement[] ae = an[i].getAnnotationElement();
+        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());
+        }
 
-        JalviewModelSequence jms = object.getJalviewModelSequence();
+        jalview.datamodel.AlignmentAnnotation jaa = null;
 
-        //////////////////////////////////
-        //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++)
+        if (an[i].getGraph())
         {
-            jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
-                    vamsasSeq[i].getSequence());
-            jseqs[i].setStart(JSEQ[i].getStart());
-            jseqs[i].setEnd(JSEQ[i].getEnd());
-            seqids.add(jseqs[i]);
+          jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
+              an[i].getDescription(), anot, 0, 0,
+              jalview.datamodel.AlignmentAnnotation.BAR_GRAPH);
         }
+        else
+        {
+          jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
+              an[i].getDescription(), anot);
+        }
+
+        al.addAnnotation(jaa);
+      }
+    }
+
+    /////////////////////////////////
+    // LOAD VIEWPORT
+    Viewport[] views = jms.getViewport();
+    Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
+
+    AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight());
 
-        ///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);
-        /////////////////////////////////
+    af.setFileName(file, "Jalview");
 
-        for (int i = 0; i < vamsasSeq.length; i++)
+    for (int i = 0; i < JSEQ.length; i++)
+    {
+      af.viewport.setSequenceColour(
+          af.viewport.alignment.getSequenceAt(i),
+          new java.awt.Color(
+              JSEQ[i].getColour()));
+    }
+
+    //  af.changeColour() );
+    /////////////////////////
+    //LOAD GROUPS
+    if (jms.getJGroupCount() > 0)
+    {
+      JGroup[] groups = jms.getJGroup();
+
+      for (int i = 0; i < groups.length; i++)
+      {
+        ColourSchemeI cs = null;
+
+        if (groups[i].getColour() != null)
         {
-          if (JSEQ[i].getFeaturesCount() > 0)
+          if (groups[i].getColour().startsWith("ucs"))
           {
-            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);
-
-              al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
-            }
+            cs = GetUserColourScheme(jms, groups[i].getColour());
           }
-          if (JSEQ[i].getPdbidsCount() > 0)
+          else
           {
-            Pdbids[] ids = JSEQ[i].getPdbids();
-            for (int p = 0; p < ids.length; p++)
-            {
-              jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
-              entry.setId(ids[p].getId());
-              entry.setType(ids[p].getType());
-              al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
-            }
+            cs = ColourSchemeProperty.getColour(al,
+                                                groups[i].getColour());
+          }
 
+          if (cs != null)
+          {
+            cs.setThreshold(groups[i].getPidThreshold(), true);
           }
-        }
 
-         /////////////////////////////////
-        //////////////////////////////////
-        //LOAD ANNOTATIONS
-        if (vamsasSet.getAnnotation() != null)
-        {
-            Annotation[] an = vamsasSet.getAnnotation();
-
-            for (int i = 0; i < an.length; i++)
-            {
-                AnnotationElement[] ae = an[i].getAnnotationElement();
-                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());
-                }
-
-                jalview.datamodel.AlignmentAnnotation jaa = null;
-
-                if (an[i].getGraph())
-                {
-                    jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
-                            an[i].getDescription(), anot, 0, 0,
-                            jalview.datamodel.AlignmentAnnotation.BAR_GRAPH);
-                }
-                else
-                {
-                    jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
-                            an[i].getDescription(), anot);
-                }
-
-                al.addAnnotation(jaa);
-            }
         }
 
+        Vector seqs = new Vector();
+        int[] ids = groups[i].getSeq();
 
-        /////////////////////////////////
-        // LOAD VIEWPORT
-        Viewport[] views = jms.getViewport();
-        Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
+        for (int s = 0; s < ids.length; s++)
+        {
+          seqs.addElement( (jalview.datamodel.SequenceI) seqids.elementAt(
+              ids[s]));
+        }
 
-        AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight());
+        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());
 
-        af.setFileName(file, "Jalview");
+        sg.setOutlineColour(new java.awt.Color(
+            groups[i].getOutlineColour()));
 
-        for (int i = 0; i < JSEQ.length; i++)
+        if (groups[i].getConsThreshold() != 0)
         {
-          af.viewport.setSequenceColour(
-              af.viewport.alignment.getSequenceAt(i),
-              new java.awt.Color(
-                  JSEQ[i].getColour()));
+          jalview.analysis.Conservation c = new jalview.analysis.Conservation(
+              "All",
+              ResidueProperties.propHash, 3, sg.getSequences(null), 0,
+              sg.getWidth() - 1);
+          c.calculate();
+          c.verdict(false, 25);
+          sg.cs.setConservation(c);
         }
 
+        al.addGroup(sg);
+      }
+    }
 
+    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());
+    af.viewport.setAbovePIDThreshold(view.getPidSelected());
+    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.alignPanel.fontChanged();
+
+    af.viewport.setRenderGaps(view.getRenderGaps());
+    af.viewport.setWrapAlignment(view.getWrapAlignment());
+    af.alignPanel.setWrapAlignment(view.getWrapAlignment());
+    af.viewport.setShowAnnotation(view.getShowAnnotation());
+    af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
+    af.viewport.setShowBoxes(view.getShowBoxes());
+    af.viewport.setShowText(view.getShowText());
+
+    ColourSchemeI cs = null;
+
+    if (view.getBgColour() != null)
+    {
+      if (view.getBgColour().startsWith("ucs"))
+      {
+        cs = GetUserColourScheme(jms, view.getBgColour());
+      }
+      else
+      {
+        cs = ColourSchemeProperty.getColour(al, view.getBgColour());
+      }
+
+      if (cs != null)
+      {
+        cs.setThreshold(view.getPidThreshold(), true);
+        cs.setConsensus(af.viewport.hconsensus);
+      }
+    }
 
-        //  af.changeColour() );
-        /////////////////////////
-        //LOAD GROUPS
-        if (jms.getJGroupCount() > 0)
-        {
-            JGroup[] groups = jms.getJGroup();
-
-            for (int i = 0; i < groups.length; i++)
-            {
-                ColourSchemeI cs = null;
-
-                if (groups[i].getColour() != null)
-                {
-                    if (groups[i].getColour().startsWith("ucs"))
-                    {
-                        cs = GetUserColourScheme(jms, groups[i].getColour());
-                    }
-                    else
-                    {
-                        cs = ColourSchemeProperty.getColour(al,
-                                groups[i].getColour());
-                    }
-
-                    if(cs!=null)
-                      cs.setThreshold(groups[i].getPidThreshold(), true);
-
-                }
-
-                Vector seqs = new Vector();
-                int[] ids = groups[i].getSeq();
-
-                for (int s = 0; s < ids.length; 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());
-
-                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);
-                    c.calculate();
-                    c.verdict(false, 25);
-                    sg.cs.setConservation(c);
-                }
-
-                al.addGroup(sg);
-            }
-        }
+    af.viewport.setGlobalColourScheme(cs);
+    af.viewport.setColourAppliesToAllGroups(false);
+    af.changeColour(cs);
+    if (view.getConservationSelected() && cs != null)
+    {
+      cs.setConservationInc(view.getConsThreshold());
+    }
 
+    af.viewport.setColourAppliesToAllGroups(true);
+    af.viewport.showSequenceFeatures = view.getShowSequenceFeatures();
 
+    if (jms.getFeatureSettings() != null)
+    {
+      af.viewport.featuresDisplayed = new Hashtable();
+      String[] renderOrder = new String[jms.getFeatureSettings().
+          getSettingCount()];
+      for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
+      {
+        Setting setting = jms.getFeatureSettings().getSetting(fs);
 
-        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());
-        af.viewport.setAbovePIDThreshold(view.getPidSelected());
-        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.alignPanel.fontChanged();
-
-        af.viewport.setRenderGaps(view.getRenderGaps());
-        af.viewport.setWrapAlignment(view.getWrapAlignment());
-        af.alignPanel.setWrapAlignment(view.getWrapAlignment());
-        af.viewport.setShowAnnotation(view.getShowAnnotation());
-        af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
-        af.viewport.setShowBoxes(view.getShowBoxes());
-        af.viewport.setShowText(view.getShowText());
+        af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.
+            getType(),
+            new java.awt.Color(setting.getColour()));
 
-        ColourSchemeI cs = null;
+        renderOrder[fs] = setting.getType();
 
-        if (view.getBgColour() != null)
+        if (setting.getDisplay())
         {
-            if (view.getBgColour().startsWith("ucs"))
-            {
-                cs = GetUserColourScheme(jms, view.getBgColour());
-            }
-            else
-            {
-                cs = ColourSchemeProperty.getColour(al, view.getBgColour());
-            }
-
-            if(cs!=null)
-            {
-              cs.setThreshold(view.getPidThreshold(), true);
-              cs.setConsensus(af.viewport.hconsensus);
-            }
+          af.viewport.featuresDisplayed.put(
+              setting.getType(), new Integer(setting.getColour()));
         }
+      }
+      af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder =
+          renderOrder;
+    }
 
-        af.viewport.setGlobalColourScheme(cs);
-        af.viewport.setColourAppliesToAllGroups(false);
-        af.changeColour(cs);
-        if (view.getConservationSelected() && cs!=null)
+    af.setMenusFromViewport(af.viewport);
+
+    Desktop.addInternalFrame(af, view.getTitle(),
+                             view.getWidth(), view.getHeight());
+
+    //LOAD TREES
+    ///////////////////////////////////////
+    if (jms.getTreeCount() > 0)
+    {
+      try
+      {
+        for (int t = 0; t < jms.getTreeCount(); t++)
         {
-          cs.setConservationInc(view.getConsThreshold());
-        }
 
-        af.viewport.setColourAppliesToAllGroups(true);
-        af.viewport.showSequenceFeatures = view.getShowSequenceFeatures();
+          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());
 
-        if(jms.getFeatureSettings()!=null)
-        {
-          af.viewport.featuresDisplayed = new Hashtable();
-          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()));
-
-           renderOrder[fs] = setting.getType();
-
-           if(setting.getDisplay())
-             af.viewport.featuresDisplayed.put(
-                 setting.getType(), new Integer(setting.getColour()));
-         }
-         af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
-        }
+          tp.fitToWindow.setState(tree.getFitToWindow());
+          tp.fitToWindow_actionPerformed(null);
 
-        af.setMenusFromViewport(af.viewport);
+          if (tree.getFontName() != null)
+          {
+            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()));
+          }
 
-        Desktop.addInternalFrame(af, view.getTitle(),
-             view.getWidth(), view.getHeight());
+          tp.showPlaceholders(tree.getMarkUnlinked());
+          tp.showBootstrap(tree.getShowBootstrap());
+          tp.showDistances(tree.getShowDistances());
 
-        //LOAD TREES
-        ///////////////////////////////////////
-        if (jms.getTreeCount() > 0)
-        {
-            try
-            {
-                for (int t = 0; t < jms.getTreeCount(); t++)
-                {
-
-                    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());
-
-                    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()));
-                    else
-                      tp.setTreeFont(new java.awt.Font(view.getFontName(),
-                                            view.getFontStyle(),
-                                            tree.getFontSize()));
-
-                    tp.showPlaceholders(tree.getMarkUnlinked());
-                    tp.showBootstrap(tree.getShowBootstrap());
-                    tp.showDistances(tree.getShowDistances());
-
-                    tp.treeCanvas.threshold = tree.getThreshold();
-
-                    if (tree.getCurrentTree())
-                      af.viewport.setCurrentTree(tp.getTree());
-                }
-
-            }
-            catch (Exception ex)
-            {
-                ex.printStackTrace();
-            }
+          tp.treeCanvas.threshold = tree.getThreshold();
 
+          if (tree.getCurrentTree())
+          {
+            af.viewport.setCurrentTree(tp.getTree());
+          }
         }
 
-        return af;
+      }
+      catch (Exception ex)
+      {
+        ex.printStackTrace();
+      }
+
     }
-}
 
+    return af;
+  }
+}
diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index fd3c334..7500a93 100755
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -21,428 +21,431 @@ 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
+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)
+  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(av);
+
+    // scale the initial size of overviewpanel to shape of alignment
+    float initialScale = (float) av.alignment.getWidth() /
+        (float) av.alignment.getHeight();
+
+    if (av.conservation == null)
     {
-        this.av = ap.av;
-        this.ap = ap;
-        setLayout(null);
-
-        sr = new SequenceRenderer(av);
-        sr.renderGaps = false;
-        sr.forOverview = true;
-        fr = new FeatureRenderer(av);
-
-        // 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();
+      graphHeight = 0;
     }
 
-
-    /**
-     * DOCUMENT ME!
-     */
-    void checkValid()
+    if (av.alignment.getWidth() > av.alignment.getHeight())
     {
-        if (boxY < 0)
-        {
-            boxY = 0;
-        }
+      // wider
+      width = 400;
+      sequencesHeight = (int) (400f / initialScale);
+      if (sequencesHeight < 40)
+      {
+        sequencesHeight = 40;
+      }
+    }
+    else
+    {
+      // taller
+      width = (int) (400f * initialScale);
+      sequencesHeight = 300;
 
-        if (boxY > (sequencesHeight - boxHeight))
-        {
-            boxY = sequencesHeight - boxHeight + 1;
-        }
+      if (width < 120)
+      {
+        width = 120;
+      }
+    }
 
-        if (boxX < 0)
+    addComponentListener(new ComponentAdapter()
+    {
+      public void componentResized(ComponentEvent evt)
+      {
+        if ( (getWidth() != width) ||
+            (getHeight() != (sequencesHeight + graphHeight)))
         {
-            boxX = 0;
+          updateOverviewImage();
         }
+      }
+    });
 
-        if (boxX > (width - boxWidth))
+    addMouseMotionListener(new MouseMotionAdapter()
+    {
+      public void mouseDragged(MouseEvent evt)
+      {
+        if (!av.wrapAlignment)
         {
-          if(av.hasHiddenColumns)
-          {
-            //Try smallest possible box
-            boxWidth = (int) ( (av.endRes - av.startRes + 1) *
-                                   av.getCharWidth() * scalew);
-          }
-          boxX = width - boxWidth;
+          boxX = evt.getX();
+          boxY = evt.getY();
+          checkValid();
         }
+      }
+    });
 
-        int col = (int) (boxX / scalew / av.getCharWidth());
-        int row = (int) (boxY / scaleh / av.getCharHeight());
-
-        if (av.hasHiddenColumns)
+    addMouseListener(new MouseAdapter()
+    {
+      public void mousePressed(MouseEvent evt)
+      {
+        if (!av.wrapAlignment)
         {
-          if (!av.getColumnSelection().isVisible(col))
-          {
-            return;
-          }
-
-          col = av.getColumnSelection().findColumnPosition(col);
+          boxX = evt.getX();
+          boxY = evt.getY();
+          checkValid();
         }
+      }
+    });
 
-        if( av.hasHiddenRows )
-        {
-          row = av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(row);
-        }
+    updateOverviewImage();
+  }
 
-        ap.setScrollValues( col, row );
+  /**
+   * DOCUMENT ME!
+   */
+  void checkValid()
+  {
+    if (boxY < 0)
+    {
+      boxY = 0;
+    }
 
+    if (boxY > (sequencesHeight - boxHeight))
+    {
+      boxY = sequencesHeight - boxHeight + 1;
     }
 
-    /**
-     * DOCUMENT ME!
-     */
-    public void updateOverviewImage()
+    if (boxX < 0)
     {
-        if (resizing)
-        {
-            resizeAgain = true;
-            return;
-        }
+      boxX = 0;
+    }
 
-        resizing = true;
+    if (boxX > (width - boxWidth))
+    {
+      if (av.hasHiddenColumns)
+      {
+        //Try smallest possible box
+        boxWidth = (int) ( (av.endRes - av.startRes + 1) *
+                          av.getCharWidth() * scalew);
+      }
+      boxX = width - boxWidth;
+    }
 
-        if ( (getWidth() > 0) && (getHeight() > 0))
-        {
-          width = getWidth();
-          sequencesHeight = getHeight() - graphHeight;
-        }
+    int col = (int) (boxX / scalew / av.getCharWidth());
+    int row = (int) (boxY / scaleh / av.getCharHeight());
 
-        setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));
+    if (av.hasHiddenColumns)
+    {
+      if (!av.getColumnSelection().isVisible(col))
+      {
+        return;
+      }
 
-        Thread thread = new Thread(this);
-        thread.start();
-        repaint();
+      col = av.getColumnSelection().findColumnPosition(col);
     }
 
-    // This is set true if the user resizes whilst
-    // the overview is being calculated
-    boolean resizeAgain = false;
-
-    /**
-     * DOCUMENT ME!
-     */
-    public void run()
+    if (av.hasHiddenRows)
     {
-        miniMe = null;
+      row = av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(row);
+    }
 
-       if (av.showSequenceFeatures)
-       {
-         fr.transferSettings( ap.seqPanel.seqCanvas.getFeatureRenderer() );
-       }
+    ap.setScrollValues(col, row);
 
-        int alwidth = av.alignment.getWidth();
-        int alheight = av.alignment.getHeight()
-            +av.alignment.getHiddenSequences().getSize();
+  }
 
-        setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));
+  /**
+   * DOCUMENT ME!
+   */
+  public void updateOverviewImage()
+  {
+    if (resizing)
+    {
+      resizeAgain = true;
+      return;
+    }
 
-        int fullsizeWidth = alwidth * av.getCharWidth();
-        int fullsizeHeight = alheight * av.getCharHeight();
+    resizing = true;
 
-        scalew = (float) width / (float) fullsizeWidth;
-        scaleh = (float) sequencesHeight / (float) fullsizeHeight;
+    if ( (getWidth() > 0) && (getHeight() > 0))
+    {
+      width = getWidth();
+      sequencesHeight = getHeight() - graphHeight;
+    }
 
-        miniMe = new BufferedImage(width, sequencesHeight + graphHeight,
-                BufferedImage.TYPE_INT_RGB);
+    setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));
 
+    Thread thread = new Thread(this);
+    thread.start();
+    repaint();
+  }
 
-        Graphics mg = miniMe.getGraphics();
-        mg.setColor(Color.orange);
-        mg.fillRect(0,0,width, miniMe.getHeight());
+  // This is set true if the user resizes whilst
+  // the overview is being calculated
+  boolean resizeAgain = false;
 
-        float sampleCol = (float) alwidth / (float) width;
-        float sampleRow = (float) alheight / (float) sequencesHeight;
+  /**
+   * DOCUMENT ME!
+   */
+  public void run()
+  {
+    miniMe = null;
 
-        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;
-          }
+    if (av.showSequenceFeatures)
+    {
+      fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
+    }
 
-          lastrow = (int)(row*sampleRow);
+    int alwidth = av.alignment.getWidth();
+    int alheight = av.alignment.getHeight()
+        + av.alignment.getHiddenSequences().getSize();
 
-          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);
+    setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));
 
-          if(seq==null)
-          {
-            System.out.println(lastrow+" null");
-            continue;
-          }
+    int fullsizeWidth = alwidth * av.getCharWidth();
+    int fullsizeHeight = alheight * av.getCharHeight();
 
-            for (col = 0; col < width; col++)
-            {
-            if((int)(col*sampleCol) == lastcol && (int)(row*sampleRow)==lastrow)
-            {
-              miniMe.setRGB(col,row,color);
-              continue;
-            }
+    scalew = (float) width / (float) fullsizeWidth;
+    scaleh = (float) sequencesHeight / (float) fullsizeHeight;
 
+    miniMe = new BufferedImage(width, sequencesHeight + graphHeight,
+                               BufferedImage.TYPE_INT_RGB);
 
-            lastcol = (int)(col*sampleCol);
+    Graphics mg = miniMe.getGraphics();
+    mg.setColor(Color.orange);
+    mg.fillRect(0, 0, width, miniMe.getHeight());
 
-            if (seq.getLength() > lastcol)
-            {
-              color = sr.getResidueBoxColour(
-                  seq, lastcol).getRGB();
+    float sampleCol = (float) alwidth / (float) width;
+    float sampleRow = (float) alheight / (float) sequencesHeight;
 
-              if (av.showSequenceFeatures)
-                color = fr.findFeatureColour(color, seq, lastcol);
-            }
-            else
-            {
-              color = -1; //White
-            }
+    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;
+      }
 
-            if(hiddenRow ||
-               (av.hasHiddenColumns && !av.getColumnSelection().isVisible(lastcol)))
-            {
-              color = new Color(color).darker().darker().getRGB();
-            }
+      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);
 
-            miniMe.setRGB(col,row,color);
+          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;
         }
 
-        if (av.conservation != null)
+        lastcol = (int) (col * sampleCol);
+
+        if (seq.getLength() > lastcol)
         {
-          for (col = 0; col < width; col++)
+          color = sr.getResidueBoxColour(
+              seq, lastcol).getRGB();
+
+          if (av.showSequenceFeatures)
           {
-            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);
-            }
+            color = fr.findFeatureColour(color, seq, lastcol);
           }
         }
-        System.gc();
-
-        resizing = false;
-
-        setBoxPosition();
-
-        if(resizeAgain)
+        else
         {
-          resizeAgain = false;
-          updateOverviewImage();
+          color = -1; //White
         }
-    }
 
-    /**
-     * DOCUMENT ME!
-     */
-    public void setBoxPosition()
-    {
-      int fullsizeWidth = av.alignment.getWidth() * av.getCharWidth();
-      int fullsizeHeight = (av.alignment.getHeight()
-                   +av.alignment.getHiddenSequences().getSize()) * av.getCharHeight();
+        if (hiddenRow ||
+            (av.hasHiddenColumns && !av.getColumnSelection().isVisible(lastcol)))
+        {
+          color = new Color(color).darker().darker().getRGB();
+        }
 
-      int startRes = av.getStartRes();
-      int endRes = av.getEndRes();
+        miniMe.setRGB(col, row, color);
 
-      if(av.hasHiddenColumns)
-      {
-        startRes = av.getColumnSelection().adjustForHiddenColumns(startRes);
-        endRes = av.getColumnSelection().adjustForHiddenColumns(endRes);
       }
+    }
 
-      int startSeq = av.startSeq;
-      int endSeq = av.endSeq;
-
-      if (av.hasHiddenRows)
+    if (av.conservation != null)
+    {
+      for (col = 0; col < width; col++)
       {
-        startSeq =
-            av.alignment.getHiddenSequences().adjustForHiddenSeqs(startSeq);
-
-        endSeq =
-            av.alignment.getHiddenSequences().adjustForHiddenSeqs(endSeq);
-
+        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;
 
-      scalew = (float) width / (float) fullsizeWidth;
-      scaleh = (float) sequencesHeight / (float) fullsizeHeight;
+    setBoxPosition();
 
-        boxX = (int) (startRes * av.getCharWidth() * scalew);
-        boxY = (int) (startSeq * av.getCharHeight() * scaleh);
+    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);
 
-        if(av.hasHiddenColumns)
-          boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);
-        else
-          boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);
+      endSeq =
+          av.alignment.getHiddenSequences().adjustForHiddenSeqs(endSeq);
 
+    }
 
-        boxHeight = (int) ((endSeq - startSeq) * av.getCharHeight() * scaleh);
+    scalew = (float) width / (float) fullsizeWidth;
+    scaleh = (float) sequencesHeight / (float) fullsizeHeight;
 
+    boxX = (int) (startRes * av.getCharWidth() * scalew);
+    boxY = (int) (startSeq * av.getCharHeight() * scaleh);
 
-        repaint();
+    if (av.hasHiddenColumns)
+    {
+      boxWidth = (int) ( (endRes - startRes + 1) * av.getCharWidth() * scalew);
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param g DOCUMENT ME!
-     */
-    public void paintComponent(Graphics g)
+    else
     {
-        if (miniMe != null && !resizing)
-        {
-          g.drawImage(miniMe, 0, 0, this);
-        }
-        else
-        {
-          g.setColor(Color.white);
-          g.fillRect(0, 0, getWidth(), getHeight());
-          g.setColor(Color.black);
-          g.setFont(new Font("Verdana", Font.BOLD, 15));
-          g.drawString("Recalculating", 5, sequencesHeight / 2);
-          g.drawString("Overview.....", 5, (sequencesHeight / 2) + 20);
-        }
+      boxWidth = (int) ( (endRes - startRes + 1) * av.getCharWidth() * scalew);
+    }
 
+    boxHeight = (int) ( (endSeq - startSeq) * av.getCharHeight() * scaleh);
 
-        g.setColor(Color.red);
-        g.drawRect(boxX, boxY, boxWidth, boxHeight);
-        g.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);
+    repaint();
+  }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param g DOCUMENT ME!
+   */
+  public void paintComponent(Graphics g)
+  {
+    if (miniMe != null && !resizing)
+    {
+      g.drawImage(miniMe, 0, 0, this);
     }
+    else
+    {
+      g.setColor(Color.white);
+      g.fillRect(0, 0, getWidth(), getHeight());
+      g.setColor(Color.black);
+      g.setFont(new Font("Verdana", Font.BOLD, 15));
+      g.drawString("Recalculating", 5, sequencesHeight / 2);
+      g.drawString("Overview.....", 5, (sequencesHeight / 2) + 20);
+    }
+
+    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 d7e0cd7..772e67e 100755
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,19 +18,16 @@
  */
 package jalview.gui;
 
-import jalview.analysis.*;
-
-import jalview.datamodel.*;
-
-import jalview.jbgui.*;
+import java.util.*;
 
 import java.awt.*;
 import java.awt.event.*;
-
-import java.util.*;
-import javax.swing.*;
 import java.awt.print.*;
+import javax.swing.*;
 
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.jbgui.*;
 
 /**
  * DOCUMENT ME!
@@ -38,450 +35,450 @@ import java.awt.print.*;
  * @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!
-     */
-    public PCAPanel(AlignmentPanel ap)
+  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!
+   */
+  public PCAPanel(AlignmentPanel ap)
+  {
+    this.av = ap.av;
+    this.ap = ap;
+
+    boolean sameLength = true;
+
+    seqstrings = av.getAlignmentView(av.getSelectionGroup() != null);
+    if (av.getSelectionGroup() == null)
     {
-        this.av = ap.av;
-        this.ap = ap;
-
-        boolean sameLength = true;
-
-        seqstrings = av.getAlignmentView(av.getSelectionGroup()!=null);
-        if(av.getSelectionGroup()==null)
-        {
-          seqs = av.alignment.getSequencesArray();
-        }
-        else
-        {
-          seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
-        }
-        SeqCigar sq[]=seqstrings.getSequences();
-        int length = sq[0].getWidth();
-
-        for (int i = 0; i < seqs.length; i++)
-        {
-          if (sq[i].getWidth() != length)
-          {
-            sameLength = false;
-            break;
-          }
-        }
-
-        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);
-
-          return;
-        }
+      seqs = av.alignment.getSequencesArray();
+    }
+    else
+    {
+      seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
+    }
+    SeqCigar sq[] = seqstrings.getSequences();
+    int length = sq[0].getWidth();
 
+    for (int i = 0; i < seqs.length; i++)
+    {
+      if (sq[i].getWidth() != length)
+      {
+        sameLength = false;
+        break;
+      }
+    }
 
-        Desktop.addInternalFrame(this, "Principal component analysis",
-                               400, 400);
+    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);
+
+      return;
+    }
 
+    Desktop.addInternalFrame(this, "Principal component analysis",
+                             400, 400);
 
+    PaintRefresher.Register(this, av.getSequenceSetId());
 
-        PaintRefresher.Register(this, av.getSequenceSetId());
+    rc = new RotatableCanvas(ap);
+    this.getContentPane().add(rc, BorderLayout.CENTER);
+    Thread worker = new Thread(this);
+    worker.start();
+  }
 
-        rc = new RotatableCanvas(ap);
-        this.getContentPane().add(rc, BorderLayout.CENTER);
-        Thread worker = new Thread(this);
-        worker.start();
-    }
+  public void bgcolour_actionPerformed(ActionEvent e)
+  {
+    Color col = JColorChooser.showDialog(this, "Select Background Colour",
+                                         rc.bgColour);
 
-    public void bgcolour_actionPerformed(ActionEvent e)
+    if (col != null)
     {
-      Color col = JColorChooser.showDialog(this, "Select Background Colour",
-                rc.bgColour);
-
-      if(col!=null)
-        rc.bgColour = col;
-      rc.repaint();
+      rc.bgColour = col;
     }
+    rc.repaint();
+  }
 
-
-
-
-    /**
-     * DOCUMENT ME!
-     */
-    public void run()
+  /**
+   * DOCUMENT ME!
+   */
+  public void run()
+  {
+    try
     {
-      try{
-        pca = new PCA(seqstrings.getSequenceStrings(' '));
-        pca.run();
+      pca = new PCA(seqstrings.getSequenceStrings(' '));
+      pca.run();
 
-        // Now find the component coordinates
-        int ii = 0;
+      // Now find the component coordinates
+      int ii = 0;
 
-        while ( (ii < seqs.length) && (seqs[ii] != null))
-        {
-          ii++;
-        }
+      while ( (ii < seqs.length) && (seqs[ii] != null))
+      {
+        ii++;
+      }
 
-        double[][] comps = new double[ii][ii];
+      double[][] comps = new double[ii][ii];
 
-        for (int i = 0; i < ii; i++)
+      for (int i = 0; i < ii; i++)
+      {
+        if (pca.getEigenvalue(i) > 1e-4)
         {
-          if (pca.getEigenvalue(i) > 1e-4)
-          {
-            comps[i] = pca.component(i);
-          }
+          comps[i] = pca.component(i);
         }
+      }
 
-        //////////////////
-        xCombobox.setSelectedIndex(0);
-        yCombobox.setSelectedIndex(1);
-        zCombobox.setSelectedIndex(2);
-
-        top = pca.getM().rows - 1;
-
-        Vector points = new Vector();
-        float[][] scores = pca.getComponents(top - 1, top - 2, top - 3, 100);
-
-        for (int i = 0; i < pca.getM().rows; i++)
-        {
-          SequencePoint sp = new SequencePoint(seqs[i], scores[i]);
-          points.addElement(sp);
-        }
+      //////////////////
+      xCombobox.setSelectedIndex(0);
+      yCombobox.setSelectedIndex(1);
+      zCombobox.setSelectedIndex(2);
 
-        rc.setPoints(points, pca.getM().rows);
-        rc.repaint();
+      top = pca.getM().rows - 1;
 
-        addKeyListener(rc);
+      Vector points = new Vector();
+      float[][] scores = pca.getComponents(top - 1, top - 2, top - 3, 100);
 
+      for (int i = 0; i < pca.getM().rows; i++)
+      {
+        SequencePoint sp = new SequencePoint(seqs[i], scores[i]);
+        points.addElement(sp);
       }
-     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();
 
-      }
+      rc.setPoints(points, pca.getM().rows);
+      rc.repaint();
 
-    }
+      addKeyListener(rc);
 
-    /**
-     * DOCUMENT ME!
-     */
-    void doDimensionChange()
+    }
+    catch (OutOfMemoryError er)
     {
-        if (top == 0)
-        {
-            return;
-        }
-
-        int dim1 = top - xCombobox.getSelectedIndex();
-        int dim2 = top - yCombobox.getSelectedIndex();
-        int dim3 = top - zCombobox.getSelectedIndex();
+      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();
 
-        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];
-        }
-
-        rc.img = null;
-        rc.rotmat.setIdentity();
-        rc.initAxes();
-        rc.paint(rc.getGraphics());
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void xCombobox_actionPerformed(ActionEvent e)
-    {
-        doDimensionChange();
-    }
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void yCombobox_actionPerformed(ActionEvent e)
+  /**
+   * DOCUMENT ME!
+   */
+  void doDimensionChange()
+  {
+    if (top == 0)
     {
-        doDimensionChange();
+      return;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void zCombobox_actionPerformed(ActionEvent e)
+    int dim1 = top - xCombobox.getSelectedIndex();
+    int dim2 = top - yCombobox.getSelectedIndex();
+    int dim3 = top - zCombobox.getSelectedIndex();
+
+    float[][] scores = pca.getComponents(dim1, dim2, dim3, 100);
+
+    for (int i = 0; i < pca.getM().rows; i++)
     {
-        doDimensionChange();
+      ( (SequencePoint) rc.points.elementAt(i)).coord = scores[i];
     }
 
+    rc.img = null;
+    rc.rotmat.setIdentity();
+    rc.initAxes();
+    rc.paint(rc.getGraphics());
+  }
 
-    public void outputValues_actionPerformed(ActionEvent e)
-    {
-      CutAndPasteTransfer cap = new CutAndPasteTransfer();
-      Desktop.addInternalFrame(cap, "PCA details", 500,
-                500);
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void xCombobox_actionPerformed(ActionEvent e)
+  {
+    doDimensionChange();
+  }
 
-      cap.setText(pca.getDetails());
-     }
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void yCombobox_actionPerformed(ActionEvent e)
+  {
+    doDimensionChange();
+  }
 
-    public void showLabels_actionPerformed(ActionEvent e)
-    {
-      rc.showLabels(showLabels.getState());
-    }
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void zCombobox_actionPerformed(ActionEvent e)
+  {
+    doDimensionChange();
+  }
 
-    public void print_actionPerformed(ActionEvent e)
+  public void outputValues_actionPerformed(ActionEvent e)
+  {
+    CutAndPasteTransfer cap = new CutAndPasteTransfer();
+    Desktop.addInternalFrame(cap, "PCA details", 500,
+                             500);
+
+    cap.setText(pca.getDetails());
+  }
+
+  public void showLabels_actionPerformed(ActionEvent e)
+  {
+    rc.showLabels(showLabels.getState());
+  }
+
+  public void print_actionPerformed(ActionEvent e)
+  {
+    PCAPrinter printer = new PCAPrinter();
+    printer.start();
+  }
+
+  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
+    if (seqstrings == null)
     {
-      PCAPrinter printer = new PCAPrinter();
-      printer.start();
+      jalview.bin.Cache.log.info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
+      return;
     }
-
-    public void originalSeqData_actionPerformed(ActionEvent e)
+    // 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[])
+    Object[] alAndColsel = seqstrings.getAlignmentAndColumnSelection(av.
+        getGapCharacter());
+
+    if (alAndColsel != null && alAndColsel[0] != null)
     {
-      // 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)
+      // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
+
+      Alignment al = new Alignment( (SequenceI[]) alAndColsel[0]);
+      Alignment dataset = av.getAlignment().getDataset();
+      if (dataset != null)
       {
-        jalview.bin.Cache.log.info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
-        return;
+        al.setDataset(dataset);
       }
-      // 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[])
-      Object[] alAndColsel = seqstrings.getAlignmentAndColumnSelection(av.
-          getGapCharacter());
 
-
-      if (alAndColsel != null && alAndColsel[0]!=null)
+      if (true)
       {
-          // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
-
-          Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
-          Alignment dataset = av.getAlignment().getDataset();
-          if (dataset != null)
-          {
-            al.setDataset(dataset);
-          }
-
-          if (true)
-          {
-              // make a new frame!
-              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!!<<<
-              // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
-
-              //           af.addSortByOrderMenuItem(ServiceName + " Ordering",
-              //                                     msaorder);
-
-              Desktop.addInternalFrame(af, "Original Data for " + this.title,
+        // make a new frame!
+        AlignFrame af = new AlignFrame(al, (ColumnSelection) alAndColsel[1],
                                        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);
-           */
+                                       AlignFrame.DEFAULT_HEIGHT
+            );
+
+        //>>>This is a fix for the moment, until a better solution is found!!<<<
+        // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
+
+        //           af.addSortByOrderMenuItem(ServiceName + " Ordering",
+        //                                     msaorder);
+
+        Desktop.addInternalFrame(af, "Original Data for " + this.title,
+                                 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);
+     */
+  }
 
-    class PCAPrinter extends Thread implements Printable
+  class PCAPrinter
+      extends Thread implements Printable
+  {
+    public void run()
     {
-      public void run()
-      {
-        PrinterJob printJob = PrinterJob.getPrinterJob();
-        PageFormat pf = printJob.pageDialog(printJob.defaultPage());
+      PrinterJob printJob = PrinterJob.getPrinterJob();
+      PageFormat pf = printJob.pageDialog(printJob.defaultPage());
 
-        printJob.setPrintable(this, pf);
+      printJob.setPrintable(this, pf);
 
-        if (printJob.printDialog())
+      if (printJob.printDialog())
+      {
+        try
+        {
+          printJob.print();
+        }
+        catch (Exception PrintException)
         {
-          try
-          {
-            printJob.print();
-          }
-          catch (Exception PrintException)
-          {
-            PrintException.printStackTrace();
-          }
+          PrintException.printStackTrace();
         }
       }
+    }
 
-      public int print(Graphics pg, PageFormat pf, int pi)
-          throws PrinterException
-      {
-        pg.translate( (int) pf.getImageableX(), (int) pf.getImageableY());
+    public int print(Graphics pg, PageFormat pf, int pi)
+        throws PrinterException
+    {
+      pg.translate( (int) pf.getImageableX(), (int) pf.getImageableY());
 
-        rc.drawBackground(pg, rc.bgColour);
-        rc.drawScene(pg);
-        if (rc.drawAxes == true)
-        {
-          rc.drawAxes(pg);
-        }
+      rc.drawBackground(pg, rc.bgColour);
+      rc.drawScene(pg);
+      if (rc.drawAxes == true)
+      {
+        rc.drawAxes(pg);
+      }
 
-        if (pi == 0)
-          return Printable.PAGE_EXISTS;
-        else
-          return Printable.NO_SUCH_PAGE;
+      if (pi == 0)
+      {
+        return Printable.PAGE_EXISTS;
+      }
+      else
+      {
+        return Printable.NO_SUCH_PAGE;
       }
     }
+  }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void eps_actionPerformed(ActionEvent e)
+  {
+    makePCAImage(jalview.util.ImageMaker.EPS);
+  }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void png_actionPerformed(ActionEvent e)
+  {
+    makePCAImage(jalview.util.ImageMaker.PNG);
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void eps_actionPerformed(ActionEvent e)
-    {
-      makePCAImage(jalview.util.ImageMaker.EPS);
-    }
+  void makePCAImage(int type)
+  {
+    int width = rc.getWidth();
+    int height = rc.getHeight();
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void png_actionPerformed(ActionEvent e)
-    {
-       makePCAImage(jalview.util.ImageMaker.PNG);
-    }
+    jalview.util.ImageMaker im;
 
-    void makePCAImage(int type)
+    if (type == jalview.util.ImageMaker.PNG)
     {
-      int width = rc.getWidth();
-      int height = rc.getHeight();
-
-      jalview.util.ImageMaker im;
-
-      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);
-        else
-          im = new jalview.util.ImageMaker(this,
-                                 jalview.util.ImageMaker.EPS,
-                                 "Make EPS file from PCA",
-                                 width, height,
-                                 null, this.getTitle());
-
-      if(im.getGraphics()!=null)
-       {
-         rc.drawBackground(im.getGraphics(), Color.black);
-         rc.drawScene(im.getGraphics());
-         if (rc.drawAxes == true)
-         {
-           rc.drawAxes(im.getGraphics());
-         }
-         im.writeImage();
-       }
+      im = new jalview.util.ImageMaker(this,
+                                       jalview.util.ImageMaker.PNG,
+                                       "Make PNG image from PCA",
+                                       width, height,
+                                       null, null);
     }
-
-
-    public void viewMenu_menuSelected()
+    else
     {
-      buildAssociatedViewMenu();
+      im = new jalview.util.ImageMaker(this,
+                                       jalview.util.ImageMaker.EPS,
+                                       "Make EPS file from PCA",
+                                       width, height,
+                                       null, this.getTitle());
     }
 
-
-    void buildAssociatedViewMenu()
+    if (im.getGraphics() != null)
     {
-      AlignmentPanel [] aps = PaintRefresher.getAssociatedPanels(av.getSequenceSetId());
-      if(aps.length==1 && rc.av ==aps[0].av)
+      rc.drawBackground(im.getGraphics(), Color.black);
+      rc.drawScene(im.getGraphics());
+      if (rc.drawAxes == true)
       {
-        associateViewsMenu.setVisible(false);
-        return;
-      }
-
-      associateViewsMenu.setVisible(true);
-
-      if( (viewMenu.getItem(viewMenu.getItemCount()-2) instanceof JMenuItem))
-      {
-        viewMenu.insertSeparator(viewMenu.getItemCount()-1);
+        rc.drawAxes(im.getGraphics());
       }
+      im.writeImage();
+    }
+  }
 
-      associateViewsMenu.removeAll();
+  public void viewMenu_menuSelected()
+  {
+    buildAssociatedViewMenu();
+  }
 
+  void buildAssociatedViewMenu()
+  {
+    AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av.
+        getSequenceSetId());
+    if (aps.length == 1 && rc.av == aps[0].av)
+    {
+      associateViewsMenu.setVisible(false);
+      return;
+    }
 
-      JRadioButtonMenuItem item;
-      ButtonGroup buttonGroup = new ButtonGroup();
-      int i, iSize = aps.length;
-      final PCAPanel thisPCAPanel = this;
-      for(i=0; i<iSize; i++)
-      {
-          final AlignmentPanel ap = aps[i];
-          item = new JRadioButtonMenuItem(ap.av.viewName, ap.av==rc.av );
-          buttonGroup.add(item);
-          item.addActionListener(new ActionListener()
-              {
-                public void actionPerformed(ActionEvent evt)
-                {
-                  rc.applyToAllViews = false;
-                  rc.av = ap.av;
-                  rc.ap = ap;
-                  PaintRefresher.Register(thisPCAPanel, ap.av.getSequenceSetId());
-                }
-              });
-
-          associateViewsMenu.add(item);
-      }
+    associateViewsMenu.setVisible(true);
 
-      final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem("All Views");
+    if ( (viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
+    {
+      viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
+    }
 
-      buttonGroup.add(itemf);
+    associateViewsMenu.removeAll();
 
-      itemf.setSelected(rc.applyToAllViews);
-      itemf.addActionListener(new ActionListener()
+    JRadioButtonMenuItem item;
+    ButtonGroup buttonGroup = new ButtonGroup();
+    int i, iSize = aps.length;
+    final PCAPanel thisPCAPanel = this;
+    for (i = 0; i < iSize; i++)
+    {
+      final AlignmentPanel ap = aps[i];
+      item = new JRadioButtonMenuItem(ap.av.viewName, ap.av == rc.av);
+      buttonGroup.add(item);
+      item.addActionListener(new ActionListener()
       {
         public void actionPerformed(ActionEvent evt)
         {
-          rc.applyToAllViews = itemf.isSelected();
+          rc.applyToAllViews = false;
+          rc.av = ap.av;
+          rc.ap = ap;
+          PaintRefresher.Register(thisPCAPanel, ap.av.getSequenceSetId());
         }
       });
-      associateViewsMenu.add(itemf);
 
+      associateViewsMenu.add(item);
     }
 
+    final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem("All Views");
+
+    buttonGroup.add(itemf);
+
+    itemf.setSelected(rc.applyToAllViews);
+    itemf.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent evt)
+      {
+        rc.applyToAllViews = itemf.isSelected();
+      }
+    });
+    associateViewsMenu.add(itemf);
+
   }
+
+}
diff --git a/src/jalview/gui/PaintRefresher.java b/src/jalview/gui/PaintRefresher.java
index d283720..1b25385 100755
--- a/src/jalview/gui/PaintRefresher.java
+++ b/src/jalview/gui/PaintRefresher.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,12 +18,11 @@
  */
 package jalview.gui;
 
-import jalview.datamodel.*;
+import java.util.*;
 
 import java.awt.*;
 
-import java.util.*;
-
+import jalview.datamodel.*;
 
 /**
  * DOCUMENT ME!
@@ -33,186 +32,212 @@ import java.util.*;
  */
 public class PaintRefresher
 {
-    static Hashtable components;
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param comp DOCUMENT ME!
-     * @param al DOCUMENT ME!
-     */
-    public static void Register(Component comp, String seqSetId)
+  static Hashtable components;
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param comp DOCUMENT ME!
+   * @param al DOCUMENT ME!
+   */
+  public static void Register(Component comp, String seqSetId)
+  {
+    if (components == null)
     {
-      if (components == null)
-        components = new Hashtable();
+      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);
-        }
+    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)
+  public static void RemoveComponent(Component comp)
+  {
+    if (components == null)
     {
-      if (components == null)
-        return;
+      return;
+    }
 
-      Enumeration en = components.keys();
-      while(en.hasMoreElements())
+    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)
       {
-        String id = en.nextElement().toString();
-        Vector comps = (Vector) components.get(id);
-        comps.remove(comp);
-        if(comps.size()==0)
-        {
-          components.remove(id);
-        }
+        components.remove(id);
       }
     }
-
-    public static void Refresh(Component source, String 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)
     {
-      Refresh( source, id, false, false);
+      return;
     }
 
-    public static void Refresh(Component source,
-                               String id,
-                               boolean alignmentChanged,
-                               boolean validateSequences)
+    Component comp;
+    Vector comps = (Vector) components.get(id);
+
+    if (comps == null)
     {
-      if (components == null)
-        return;
+      return;
+    }
 
-      Component comp;
-      Vector comps = (Vector) components.get(id);
+    Enumeration e = comps.elements();
+    while (e.hasMoreElements())
+    {
+      comp = (Component) e.nextElement();
 
-      if(comps==null)
+      if (comp == source)
       {
-        return;
+        continue;
       }
 
-      Enumeration e = comps.elements();
-      while (e.hasMoreElements())
+      if (validateSequences
+          && comp instanceof AlignmentPanel
+          && source instanceof AlignmentPanel)
       {
-        comp = (Component) e.nextElement();
-
-        if(comp==source)
-        {
-          continue;
-        }
+        validateSequences( ( (AlignmentPanel) source).av.alignment,
+                          ( (AlignmentPanel) comp).av.alignment);
+      }
 
-        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();
+      }
 
-        if(comp instanceof AlignmentPanel && alignmentChanged)
-        {
-          ((AlignmentPanel)comp).alignmentChanged();
-        }
+      comp.repaint();
+    }
+  }
 
-        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();
     }
 
-    static void validateSequences(AlignmentI source, AlignmentI comp)
+    SequenceI[] a2;
+    if (comp.getHiddenSequences().getSize() > 0)
     {
-      SequenceI[] a1;
-      if(source.getHiddenSequences().getSize()>0)
-        a1 = source.getHiddenSequences().getFullAlignment().getSequencesArray();
-      else
-        a1 = source.getSequencesArray();
+      a2 = comp.getHiddenSequences().getFullAlignment().getSequencesArray();
+    }
+    else
+    {
+      a2 = comp.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;
 
-      int i, iSize=a1.length, j, jSize=a2.length;
+    if (iSize == jSize)
+    {
+      return;
+    }
 
-      if(iSize == jSize)
-        return;
+    boolean exists = false;
+    for (i = 0; i < iSize; i++)
+    {
+      exists = false;
 
-      boolean exists = false;
-      for(i=0; i<iSize; i++)
+      for (j = 0; j < jSize; j++)
       {
-        exists = false;
-
-        for(j=0; j<jSize; j++)
-          if (a2[j]==a1[i] )
-          {
-            exists = true;
-            break;
-          }
-
-        if(!exists)
+        if (a2[j] == a1[i])
         {
-          if (i < jSize)
-            comp.getSequences().insertElementAt(a1[i], i);
-          else
-            comp.addSequence(a1[i]);
-
-          jSize++;
-
-          if (comp.getHiddenSequences().getSize() > 0)
-            a2 = comp.getHiddenSequences().getFullAlignment().getSequencesArray();
-          else
-            a2 = comp.getSequencesArray();
+          exists = true;
+          break;
         }
       }
 
-      iSize=a1.length;
-      jSize=a2.length;
-
-      for(j=0; j<jSize; j++)
+      if (!exists)
       {
-        exists = false;
-        for(i=0; i<iSize; i++)
+        if (i < jSize)
+        {
+          comp.getSequences().insertElementAt(a1[i], i);
+        }
+        else
         {
-          if (a2[j]==a1[i])
-          {
-            exists = true;
-            break;
-          }
+          comp.addSequence(a1[i]);
         }
 
-        if(!exists)
+        jSize++;
+
+        if (comp.getHiddenSequences().getSize() > 0)
+        {
+          a2 = comp.getHiddenSequences().getFullAlignment().getSequencesArray();
+        }
+        else
         {
-          comp.deleteSequence(a2[j]);
+          a2 = comp.getSequencesArray();
         }
       }
     }
 
-    static AlignmentPanel [] getAssociatedPanels(String id)
+    iSize = a1.length;
+    jSize = a2.length;
+
+    for (j = 0; j < jSize; j++)
     {
-      Vector comps = (Vector)components.get(id);
-      Vector tmp = new Vector();
-      int i, iSize = comps.size();
+      exists = false;
       for (i = 0; i < iSize; i++)
       {
-        if (comps.elementAt(i) instanceof AlignmentPanel)
+        if (a2[j] == a1[i])
         {
-          tmp.addElement(((AlignmentPanel)comps.elementAt(i)));
+          exists = true;
+          break;
         }
       }
-      AlignmentPanel [] result = new AlignmentPanel[tmp.size()];
-      tmp.toArray(result);
 
-      return result;
+      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 30effb7..190dcb0 100755
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,16 +18,13 @@
  */
 package jalview.gui;
 
-import jalview.analysis.*;
-
-import jalview.datamodel.*;
-
-import jalview.jbgui.*;
+import java.util.*;
 
 import java.awt.event.*;
 
-import java.util.*;
-
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.jbgui.*;
 
 /**
  * DOCUMENT ME!
@@ -35,127 +32,128 @@ import java.util.*;
  * @author $author$
  * @version $Revision$
  */
-public class PairwiseAlignPanel extends GPairwiseAlignPanel
+public class PairwiseAlignPanel
+    extends GPairwiseAlignPanel
 {
 
-    AlignViewport av;
-    Vector sequences;
+  AlignViewport av;
+  Vector sequences;
+
+  /**
+   * Creates a new PairwiseAlignPanel object.
+   *
+   * @param av DOCUMENT ME!
+   */
+  public PairwiseAlignPanel(AlignViewport av)
+  {
+    super();
+    this.av = av;
 
-    /**
-     * Creates a new PairwiseAlignPanel object.
-     *
-     * @param av DOCUMENT ME!
-     */
-    public PairwiseAlignPanel(AlignViewport av)
+    sequences = new Vector();
+
+    SequenceI[] seqs;
+    String[] seqStrings = av.getViewAsString(true);
+
+    if (av.getSelectionGroup() == null)
+    {
+      seqs = av.alignment.getSequencesArray();
+    }
+    else
     {
-        super();
-        this.av = av;
+      seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
+    }
 
-        sequences = new Vector();
+    String type = (av.alignment.isNucleotide()) ? AlignSeq.DNA : AlignSeq.PEP;
 
-        SequenceI [] seqs;
-        String []  seqStrings = av.getViewAsString(true);
+    float[][] scores = new float[seqs.length][seqs.length];
+    double totscore = 0;
+    int count = seqs.length;
 
-        if(av.getSelectionGroup()==null)
-        {
-          seqs = av.alignment.getSequencesArray();
-        }
-        else
-        {
-          seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
-        }
+    Sequence seq;
 
-        String type=(av.alignment.isNucleotide()) ? AlignSeq.DNA : AlignSeq.PEP;
-        
-        float[][] scores = new float[seqs.length][seqs.length];
-        double totscore = 0;
-        int count = seqs.length;
+    for (int i = 1; i < count; i++)
+    {
+      for (int j = 0; j < i; j++)
+      {
 
-        Sequence seq;
+        AlignSeq as = new AlignSeq(seqs[i], seqStrings[i],
+                                   seqs[j], seqStrings[j], type);
 
-        for (int i = 1; i < count; i++)
+        if (as.s1str.length() == 0 || as.s2str.length() == 0)
         {
-            for (int j = 0; j < i; j++)
-            {
-
-                AlignSeq as = new AlignSeq(seqs[i], seqStrings[i],
-                        seqs[j], seqStrings[j], type);
-
-                if(as.s1str.length()==0 || as.s2str.length()==0)
-                {
-                  continue;
-                }
-
-                as.calcScoreMatrix();
-                as.traceAlignment();
-
-
-                as.printAlignment(System.out);
-                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()
-                );
-                sequences.add(seq);
-
-                seq = new Sequence(as.getS2().getName(),
-                                   as.getAStr2(),
-                                   as.getS2().getStart(),
-                                   as.getS2().getEnd() );
-                sequences.add(seq);
-            }
+          continue;
         }
 
-        if (count > 2)
-        {
-            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());
-            }
-
-            System.out.println("\n");
-
-            for (int i = 0; i < count; i++)
-            {
-                for (int j = 0; j < i; j++)
-                {
-                    jalview.util.Format.print(System.out, "%7.3f",
-                        scores[i][j] / totscore);
-                }
-            }
-
-            System.out.println("\n");
-        }
+        as.calcScoreMatrix();
+        as.traceAlignment();
+
+        as.printAlignment(System.out);
+        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()
+            );
+        sequences.add(seq);
+
+        seq = new Sequence(as.getS2().getName(),
+                           as.getAStr2(),
+                           as.getS2().getStart(),
+                           as.getS2().getEnd());
+        sequences.add(seq);
+      }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void viewInEditorButton_actionPerformed(ActionEvent e)
+    if (count > 2)
     {
-        Sequence[] seq = new Sequence[sequences.size()];
+      System.out.println(
+          "Pairwise alignment scaled similarity score matrix\n");
 
-        for (int i = 0; i < sequences.size(); i++)
+      for (int i = 0; i < count; i++)
+      {
+        jalview.util.Format.print(System.out, "%s \n",
+                                  ("" + i) + " " +
+                                  seqs[i].getName());
+      }
+
+      System.out.println("\n");
+
+      for (int i = 0; i < count; i++)
+      {
+        for (int j = 0; j < i; j++)
         {
-            seq[i] = (Sequence) sequences.elementAt(i);
+          jalview.util.Format.print(System.out, "%7.3f",
+                                    scores[i][j] / totscore);
         }
+      }
 
-        AlignFrame af = new AlignFrame(new Alignment(seq),
-                                           AlignFrame.DEFAULT_WIDTH,
-                                           AlignFrame.DEFAULT_HEIGHT);
-
-        Desktop.addInternalFrame(af, "Pairwise Aligned Sequences",
-            AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+      System.out.println("\n");
     }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void viewInEditorButton_actionPerformed(ActionEvent e)
+  {
+    Sequence[] seq = new Sequence[sequences.size()];
+
+    for (int i = 0; i < sequences.size(); i++)
+    {
+      seq[i] = (Sequence) sequences.elementAt(i);
+    }
+
+    AlignFrame af = new AlignFrame(new Alignment(seq),
+                                   AlignFrame.DEFAULT_WIDTH,
+                                   AlignFrame.DEFAULT_HEIGHT);
+
+    Desktop.addInternalFrame(af, "Pairwise Aligned Sequences",
+                             AlignFrame.DEFAULT_WIDTH,
+                             AlignFrame.DEFAULT_HEIGHT);
+  }
 }
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index d5ddd1b..f1a38f5 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,21 +18,18 @@
  */
 package jalview.gui;
 
-import MCview.*;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
-import jalview.commands.ChangeCaseCommand;
+import java.util.*;
 
 import java.awt.*;
 import java.awt.event.*;
-
 import javax.swing.*;
 
-import java.util.Vector;
-import jalview.io.FormatAdapter;
-
+import MCview.*;
+import jalview.analysis.*;
+import jalview.commands.*;
+import jalview.datamodel.*;
+import jalview.io.*;
+import jalview.schemes.*;
 
 /**
  * DOCUMENT ME!
@@ -40,35 +37,37 @@ import jalview.io.FormatAdapter;
  * @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 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 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 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();
@@ -85,358 +84,364 @@ public class PopupMenu extends JPopupMenu
   JMenu jMenu1 = new JMenu();
 
   /**
-     * Creates a new PopupMenu object.
-     *
-     * @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;
-
-        ButtonGroup colours = new ButtonGroup();
-        colours.add(noColourmenuItem);
-        colours.add(clustalColour);
-        colours.add(zappoColour);
-        colours.add(taylorColour);
-        colours.add(hydrophobicityColour);
-        colours.add(helixColour);
-        colours.add(strandColour);
-        colours.add(turnColour);
-        colours.add(buriedColour);
-        colours.add(abovePIDColour);
-        colours.add(userDefinedColour);
-        colours.add(PIDColour);
-        colours.add(BLOSUM62Colour);
-
-        for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
+   * Creates a new PopupMenu object.
+   *
+   * @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;
+
+    ButtonGroup colours = new ButtonGroup();
+    colours.add(noColourmenuItem);
+    colours.add(clustalColour);
+    colours.add(zappoColour);
+    colours.add(taylorColour);
+    colours.add(hydrophobicityColour);
+    colours.add(helixColour);
+    colours.add(strandColour);
+    colours.add(turnColour);
+    colours.add(buriedColour);
+    colours.add(abovePIDColour);
+    colours.add(userDefinedColour);
+    colours.add(PIDColour);
+    colours.add(BLOSUM62Colour);
+
+    for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
+    {
+      JMenuItem item = new JMenuItem(jalview.io.FormatAdapter.WRITEABLE_FORMATS[
+                                     i]);
+
+      item.addActionListener(new java.awt.event.ActionListener()
+      {
+        public void actionPerformed(ActionEvent e)
+        {
+          outputText_actionPerformed(e);
+        }
+      });
+
+      outputMenu.add(item);
+    }
+
+    try
+    {
+      jbInit();
+    }
+    catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+
+    if (seq != null)
+    {
+      sequenceMenu.setText(sequence.getName());
+
+      JMenuItem menuItem;
+      if (seq.getDatasetSequence().getPDBId() != null)
+      {
+        java.util.Enumeration e = seq.getDatasetSequence().getPDBId().
+            elements();
+
+        while (e.hasMoreElements())
         {
-          JMenuItem item = new JMenuItem( jalview.io.FormatAdapter.WRITEABLE_FORMATS[i] );
+          final PDBEntry pdb = (PDBEntry) e.nextElement();
 
-          item.addActionListener(new java.awt.event.ActionListener()
+          menuItem = new JMenuItem();
+          menuItem.setText("View PDB entry: " + pdb.getId());
+          menuItem.addActionListener(new java.awt.event.ActionListener()
           {
             public void actionPerformed(ActionEvent e)
             {
-              outputText_actionPerformed(e);
+              new PDBViewer(pdb, sequence, ap.seqPanel.seqCanvas);
             }
           });
-
-          outputMenu.add(item);
+          sequenceMenu.add(menuItem);
         }
+      }
 
-
-        try
-        {
-            jbInit();
-        }
-        catch (Exception e)
+      menuItem = new JMenuItem("Hide Sequences");
+      menuItem.addActionListener(new java.awt.event.ActionListener()
+      {
+        public void actionPerformed(ActionEvent e)
         {
-            e.printStackTrace();
+          hideSequences(false);
         }
+      });
+      add(menuItem);
 
-
-        if (seq != null)
+      if (ap.av.getSelectionGroup() != null
+          && ap.av.getSelectionGroup().getSize() > 1)
+      {
+        menuItem = new JMenuItem("Represent Group with " + seq.getName());
+        menuItem.addActionListener(new java.awt.event.ActionListener()
         {
-          sequenceMenu.setText(sequence.getName());
-
-          JMenuItem menuItem;
-          if( seq.getDatasetSequence().getPDBId() != null)
+          public void actionPerformed(ActionEvent e)
           {
-            java.util.Enumeration e = seq.getDatasetSequence().getPDBId().
-                elements();
-
-            while (e.hasMoreElements())
-            {
-              final PDBEntry pdb = (PDBEntry) e.nextElement();
-
-              menuItem = new JMenuItem();
-              menuItem.setText("View PDB entry: " + pdb.getId());
-              menuItem.addActionListener(new java.awt.event.ActionListener()
-              {
-                public void actionPerformed(ActionEvent e)
-                {
-                  new PDBViewer(pdb, sequence, ap.seqPanel.seqCanvas);
-                }
-              });
-              sequenceMenu.add(menuItem);
-            }
+            hideSequences(true);
           }
+        });
+        sequenceMenu.add(menuItem);
+      }
 
-          menuItem = new JMenuItem("Hide Sequences");
-          menuItem.addActionListener(new java.awt.event.ActionListener()
-              {
-                public void actionPerformed(ActionEvent e)
-                {
-                  hideSequences(false);
-                }
-              });
-          add(menuItem);
+      if (ap.av.hasHiddenRows)
+      {
+        final int index = ap.av.alignment.findIndex(seq);
 
-          if(ap.av.getSelectionGroup() !=null
-             && ap.av.getSelectionGroup().getSize()>1)
+        if (ap.av.adjustForHiddenSeqs(index) -
+            ap.av.adjustForHiddenSeqs(index - 1) > 1)
+        {
+          menuItem = new JMenuItem("Reveal Sequences");
+          menuItem.addActionListener(new ActionListener()
           {
-            menuItem = new JMenuItem("Represent Group with " + seq.getName());
-            menuItem.addActionListener(new java.awt.event.ActionListener()
+            public void actionPerformed(ActionEvent e)
             {
-              public void actionPerformed(ActionEvent e)
+              ap.av.showSequence(index);
+              if (ap.overviewPanel != null)
               {
-                hideSequences(true);
+                ap.overviewPanel.updateOverviewImage();
               }
-            });
-            sequenceMenu.add(menuItem);
-          }
+            }
+          });
+          add(menuItem);
+        }
 
-          if (ap.av.hasHiddenRows)
+        menuItem = new JMenuItem("Reveal All");
+        menuItem.addActionListener(new ActionListener()
+        {
+          public void actionPerformed(ActionEvent e)
           {
-            final int index = ap.av.alignment.findIndex(seq);
-
-            if (ap.av.adjustForHiddenSeqs(index) -
-                ap.av.adjustForHiddenSeqs(index - 1) > 1)
+            ap.av.showAllHiddenSeqs();
+            if (ap.overviewPanel != null)
             {
-              menuItem = new JMenuItem("Reveal Sequences");
-              menuItem.addActionListener(new ActionListener()
-              {
-                public void actionPerformed(ActionEvent e)
-                {
-                  ap.av.showSequence(index);
-                  if (ap.overviewPanel != null)
-                    ap.overviewPanel.updateOverviewImage();
-                }
-              });
-              add(menuItem);
+              ap.overviewPanel.updateOverviewImage();
             }
-
-            menuItem = new JMenuItem("Reveal All");
-            menuItem.addActionListener(new ActionListener()
-                {
-                  public void actionPerformed(ActionEvent e)
-                  {
-                    ap.av.showAllHiddenSeqs();
-                    if (ap.overviewPanel != null)
-                      ap.overviewPanel.updateOverviewImage();
-                    }
-                });
-
-            add(menuItem);
           }
+        });
 
+        add(menuItem);
+      }
 
-        }
+    }
+
+    SequenceGroup sg = ap.av.getSelectionGroup();
 
+    if (sg != null)
+    {
+      groupName.setText(sg.getName());
+
+      if (sg.cs instanceof ZappoColourScheme)
+      {
+        zappoColour.setSelected(true);
+      }
+      else if (sg.cs instanceof TaylorColourScheme)
+      {
+        taylorColour.setSelected(true);
+      }
+      else if (sg.cs instanceof PIDColourScheme)
+      {
+        PIDColour.setSelected(true);
+      }
+      else if (sg.cs instanceof Blosum62ColourScheme)
+      {
+        BLOSUM62Colour.setSelected(true);
+      }
+      else if (sg.cs instanceof UserColourScheme)
+      {
+        userDefinedColour.setSelected(true);
+      }
+      else if (sg.cs instanceof HydrophobicColourScheme)
+      {
+        hydrophobicityColour.setSelected(true);
+      }
+      else if (sg.cs instanceof HelixColourScheme)
+      {
+        helixColour.setSelected(true);
+      }
+      else if (sg.cs instanceof StrandColourScheme)
+      {
+        strandColour.setSelected(true);
+      }
+      else if (sg.cs instanceof TurnColourScheme)
+      {
+        turnColour.setSelected(true);
+      }
+      else if (sg.cs instanceof BuriedColourScheme)
+      {
+        buriedColour.setSelected(true);
+      }
+      else if (sg.cs instanceof ClustalxColourScheme)
+      {
+        clustalColour.setSelected(true);
+      }
+      else
+      {
+        noColourmenuItem.setSelected(true);
+      }
 
+      if (sg.cs != null && sg.cs.conservationApplied())
+      {
+        conservationMenuItem.setSelected(true);
+      }
 
-        SequenceGroup sg = ap.av.getSelectionGroup();
+      showText.setSelected(sg.getDisplayText());
+      showColourText.setSelected(sg.getColourText());
+      showBoxes.setSelected(sg.getDisplayBoxes());
+    }
+    else
+    {
+      groupMenu.setVisible(false);
+      editMenu.setVisible(false);
+    }
 
-        if (sg != null)
-        {
-            groupName.setText(sg.getName());
+    if (!ap.av.alignment.getGroups().contains(sg))
+    {
+      unGroupMenuItem.setVisible(false);
+    }
 
-            if (sg.cs instanceof ZappoColourScheme)
-            {
-                zappoColour.setSelected(true);
-            }
-            else if (sg.cs instanceof TaylorColourScheme)
-            {
-                taylorColour.setSelected(true);
-            }
-            else if (sg.cs instanceof PIDColourScheme)
-            {
-                PIDColour.setSelected(true);
-            }
-            else if (sg.cs instanceof Blosum62ColourScheme)
-            {
-                BLOSUM62Colour.setSelected(true);
-            }
-            else if (sg.cs instanceof UserColourScheme)
-            {
-                userDefinedColour.setSelected(true);
-            }
-            else if (sg.cs instanceof HydrophobicColourScheme)
-            {
-                hydrophobicityColour.setSelected(true);
-            }
-            else if (sg.cs instanceof HelixColourScheme)
-            {
-                helixColour.setSelected(true);
-            }
-            else if (sg.cs instanceof StrandColourScheme)
-            {
-                strandColour.setSelected(true);
-            }
-            else if (sg.cs instanceof TurnColourScheme)
-            {
-                turnColour.setSelected(true);
-            }
-            else if (sg.cs instanceof BuriedColourScheme)
-            {
-                buriedColour.setSelected(true);
-            }
-            else if (sg.cs instanceof ClustalxColourScheme)
-            {
-                clustalColour.setSelected(true);
-            }
-            else
-            {
-                noColourmenuItem.setSelected(true);
-            }
+    if (seq == null)
+    {
+      sequenceMenu.setVisible(false);
+      pdbMenu.setVisible(false);
+    }
 
-            if (sg.cs!=null && sg.cs.conservationApplied())
-            {
-                conservationMenuItem.setSelected(true);
-            }
+    if (links != null && links.size() > 0)
+    {
+      JMenu linkMenu = new JMenu("Link");
+      JMenuItem item;
+      for (int i = 0; i < links.size(); i++)
+      {
+        String link = links.elementAt(i).toString();
+        final String label = link.substring(0, link.indexOf("|"));
+        item = new JMenuItem(label);
+        final String url;
 
-            showText.setSelected(sg.getDisplayText());
-            showColourText.setSelected(sg.getColourText());
-            showBoxes.setSelected(sg.getDisplayBoxes());
-        }
-        else
+        if (link.indexOf("$SEQUENCE_ID$") > -1)
         {
-          groupMenu.setVisible(false);
-          editMenu.setVisible(false);
-        }
+          String id = seq.getName();
+          if (id.indexOf("|") > -1)
+          {
+            id = id.substring(id.lastIndexOf("|") + 1);
+          }
 
-        if (!ap.av.alignment.getGroups().contains(sg))
-        {
-            unGroupMenuItem.setVisible(false);
+          url = link.substring(link.indexOf("|") + 1,
+                               link.indexOf("$SEQUENCE_ID$"))
+              + id +
+              link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
         }
-
-
-        if (seq == null)
+        else
         {
-            sequenceMenu.setVisible(false);
-            pdbMenu.setVisible(false);
+          url = link.substring(link.lastIndexOf("|") + 1);
         }
 
-        if(links != null && links.size()>0)
+        item.addActionListener(new java.awt.event.ActionListener()
         {
-          JMenu linkMenu = new JMenu("Link");
-          JMenuItem item;
-          for(int i=0; i<links.size(); i++)
+          public void actionPerformed(ActionEvent e)
           {
-            String link = links.elementAt(i).toString();
-            final String label = link.substring(0, link.indexOf("|"));
-            item = new JMenuItem(label);
-            final String url;
-
-            if (link.indexOf("$SEQUENCE_ID$") > -1)
-            {
-              String id = seq.getName();
-              if (id.indexOf("|") > -1)
-                id = id.substring(id.lastIndexOf("|") + 1);
-
-              url = link.substring(link.indexOf("|") + 1,
-                                   link.indexOf("$SEQUENCE_ID$"))
-                  + id +
-                  link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
-            }
-            else
-              url = link.substring(link.lastIndexOf("|")+1);
-
-
-            item.addActionListener(new java.awt.event.ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    showLink(url);
-                }
-            });
-
-            linkMenu.add(item);
+            showLink(url);
           }
-          if(sequence!=null)
-            sequenceMenu.add(linkMenu);
-          else
-            add(linkMenu);
-        }
+        });
+
+        linkMenu.add(item);
+      }
+      if (sequence != null)
+      {
+        sequenceMenu.add(linkMenu);
+      }
+      else
+      {
+        add(linkMenu);
+      }
     }
+  }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @throws Exception DOCUMENT ME!
+   */
+  private void jbInit()
+      throws Exception
+  {
+    groupMenu.setText("Group");
+    groupMenu.setText("Selection");
+    groupName.setText("Name");
+    groupName.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        groupName_actionPerformed();
+      }
+    });
+    sequenceMenu.setText("Sequence");
+    sequenceName.setText("Edit Name/Description");
+    sequenceName.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        sequenceName_actionPerformed();
+      }
+    });
+    PIDColour.setFocusPainted(false);
+    unGroupMenuItem.setText("Remove Group");
+    unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        unGroupMenuItem_actionPerformed();
+      }
+    });
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @throws Exception DOCUMENT ME!
-     */
-    private void jbInit() throws Exception
+    outline.setText("Border colour");
+    outline.addActionListener(new java.awt.event.ActionListener()
     {
-        groupMenu.setText("Group");
-        groupMenu.setText("Selection");
-        groupName.setText("Name");
-        groupName.addActionListener(new java.awt.event.ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    groupName_actionPerformed();
-                }
-            });
-        sequenceMenu.setText("Sequence");
-        sequenceName.setText("Edit Name/Description");
-        sequenceName.addActionListener(new java.awt.event.ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    sequenceName_actionPerformed();
-                }
-            });
-        PIDColour.setFocusPainted(false);
-        unGroupMenuItem.setText("Remove Group");
-        unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    unGroupMenuItem_actionPerformed();
-                }
-            });
-
-        outline.setText("Border colour");
-        outline.addActionListener(new java.awt.event.ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    outline_actionPerformed();
-                }
-            });
-        nucleotideMenuItem.setText("Nucleotide");
-        nucleotideMenuItem.addActionListener(new ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    nucleotideMenuItem_actionPerformed();
-                }
-            });
-        colourMenu.setText("Group Colour");
-        showBoxes.setText("Boxes");
-        showBoxes.setState(true);
-        showBoxes.addActionListener(new ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    showBoxes_actionPerformed();
-                }
-            });
-        showText.setText("Text");
-        showText.setState(true);
-        showText.addActionListener(new ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    showText_actionPerformed();
-                }
-            });
-        showColourText.setText("Colour Text");
-        showColourText.addActionListener(new ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    showColourText_actionPerformed();
-                }
-            });
+      public void actionPerformed(ActionEvent e)
+      {
+        outline_actionPerformed();
+      }
+    });
+    nucleotideMenuItem.setText("Nucleotide");
+    nucleotideMenuItem.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        nucleotideMenuItem_actionPerformed();
+      }
+    });
+    colourMenu.setText("Group Colour");
+    showBoxes.setText("Boxes");
+    showBoxes.setState(true);
+    showBoxes.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        showBoxes_actionPerformed();
+      }
+    });
+    showText.setText("Text");
+    showText.setState(true);
+    showText.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        showText_actionPerformed();
+      }
+    });
+    showColourText.setText("Colour Text");
+    showColourText.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        showColourText_actionPerformed();
+      }
+    });
     editMenu.setText("Edit");
     cut.setText("Cut");
     cut.addActionListener(new ActionListener()
@@ -523,620 +528,633 @@ public class PopupMenu extends JPopupMenu
     jMenu1.setText("Group");
     add(groupMenu);
 
-    add(sequenceMenu);
-    groupMenu.add(editMenu);
-    groupMenu.add(outputMenu);
-    groupMenu.add(sequenceFeature);
-    groupMenu.add(jMenu1);
-    sequenceMenu.add(sequenceName);
-    sequenceMenu.add(pdbMenu);
-    colourMenu.add(textColour);
-    colourMenu.add(noColourmenuItem);
-        colourMenu.add(clustalColour);
-        colourMenu.add(BLOSUM62Colour);
-        colourMenu.add(PIDColour);
-        colourMenu.add(zappoColour);
-        colourMenu.add(taylorColour);
-        colourMenu.add(hydrophobicityColour);
-        colourMenu.add(helixColour);
-        colourMenu.add(strandColour);
-        colourMenu.add(turnColour);
-        colourMenu.add(buriedColour);
-        colourMenu.add(nucleotideMenuItem);
-        colourMenu.add(userDefinedColour);
-
-        if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)
-        {
-          java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
-              getUserColourSchemes().keys();
+    add(sequenceMenu);
+    groupMenu.add(editMenu);
+    groupMenu.add(outputMenu);
+    groupMenu.add(sequenceFeature);
+    groupMenu.add(jMenu1);
+    sequenceMenu.add(sequenceName);
+    sequenceMenu.add(pdbMenu);
+    colourMenu.add(textColour);
+    colourMenu.add(noColourmenuItem);
+    colourMenu.add(clustalColour);
+    colourMenu.add(BLOSUM62Colour);
+    colourMenu.add(PIDColour);
+    colourMenu.add(zappoColour);
+    colourMenu.add(taylorColour);
+    colourMenu.add(hydrophobicityColour);
+    colourMenu.add(helixColour);
+    colourMenu.add(strandColour);
+    colourMenu.add(turnColour);
+    colourMenu.add(buriedColour);
+    colourMenu.add(nucleotideMenuItem);
+    colourMenu.add(userDefinedColour);
+
+    if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
+    {
+      java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
+          getUserColourSchemes().keys();
+
+      while (userColours.hasMoreElements())
+      {
+        JMenuItem item = new JMenuItem(userColours.
+                                       nextElement().toString());
+        item.addActionListener(new ActionListener()
+        {
+          public void actionPerformed(ActionEvent evt)
+          {
+            userDefinedColour_actionPerformed(evt);
+          }
+        });
+        colourMenu.add(item);
+      }
+    }
+
+    colourMenu.addSeparator();
+    colourMenu.add(abovePIDColour);
+    colourMenu.add(conservationMenuItem);
+    editMenu.add(copy);
+    editMenu.add(cut);
+    editMenu.add(upperCase);
+    editMenu.add(lowerCase);
+    editMenu.add(toggle);
+    pdbMenu.add(pdbFromFile);
+    pdbMenu.add(enterPDB);
+    pdbMenu.add(discoverPDB);
+    jMenu1.add(groupName);
+    jMenu1.add(unGroupMenuItem);
+    jMenu1.add(colourMenu);
+    jMenu1.add(showBoxes);
+    jMenu1.add(showText);
+    jMenu1.add(showColourText);
+    jMenu1.add(outline);
+    noColourmenuItem.setText("None");
+    noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        noColourmenuItem_actionPerformed();
+      }
+    });
+
+    clustalColour.setText("Clustalx colours");
+    clustalColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        clustalColour_actionPerformed();
+      }
+    });
+    zappoColour.setText("Zappo");
+    zappoColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        zappoColour_actionPerformed();
+      }
+    });
+    taylorColour.setText("Taylor");
+    taylorColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        taylorColour_actionPerformed();
+      }
+    });
+    hydrophobicityColour.setText("Hydrophobicity");
+    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()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        helixColour_actionPerformed();
+      }
+    });
+    strandColour.setText("Strand propensity");
+    strandColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        strandColour_actionPerformed();
+      }
+    });
+    turnColour.setText("Turn propensity");
+    turnColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        turnColour_actionPerformed();
+      }
+    });
+    buriedColour.setText("Buried Index");
+    buriedColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        buriedColour_actionPerformed();
+      }
+    });
+    abovePIDColour.setText("Above % Identity");
+    abovePIDColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        abovePIDColour_actionPerformed();
+      }
+    });
+    userDefinedColour.setText("User Defined...");
+    userDefinedColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        userDefinedColour_actionPerformed(e);
+      }
+    });
+    PIDColour.setText("Percentage Identity");
+    PIDColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        PIDColour_actionPerformed();
+      }
+    });
+    BLOSUM62Colour.setText("BLOSUM62");
+    BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        BLOSUM62Colour_actionPerformed();
+      }
+    });
+    conservationMenuItem.setText("Conservation");
+    conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        conservationMenuItem_actionPerformed();
+      }
+    });
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  void refresh()
+  {
+    if (ap.overviewPanel != null)
+    {
+      ap.overviewPanel.updateOverviewImage();
+    }
+
+    PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
+  }
 
-          while (userColours.hasMoreElements())
-          {
-            JMenuItem item = new JMenuItem(userColours.
-                nextElement().toString());
-            item.addActionListener(new ActionListener()
-            {
-              public void actionPerformed(ActionEvent evt)
-              {
-                userDefinedColour_actionPerformed(evt);
-              }
-            });
-            colourMenu.add(item);
-          }
-        }
+  /**
+   * 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());
+    refresh();
+  }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void zappoColour_actionPerformed()
+  {
+    getGroup().cs = new ZappoColourScheme();
+    refresh();
+  }
 
-        colourMenu.addSeparator();
-        colourMenu.add(abovePIDColour);
-        colourMenu.add(conservationMenuItem);
-    editMenu.add(copy);
-    editMenu.add(cut);
-    editMenu.add(upperCase);
-    editMenu.add(lowerCase);
-    editMenu.add(toggle);
-    pdbMenu.add(pdbFromFile);
-    pdbMenu.add(enterPDB);
-    pdbMenu.add(discoverPDB);
-    jMenu1.add(groupName);
-    jMenu1.add(unGroupMenuItem);
-    jMenu1.add(colourMenu);
-    jMenu1.add(showBoxes);
-    jMenu1.add(showText);
-    jMenu1.add(showColourText);
-    jMenu1.add(outline);
-    noColourmenuItem.setText("None");
-        noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    noColourmenuItem_actionPerformed();
-                }
-            });
-
-        clustalColour.setText("Clustalx colours");
-        clustalColour.addActionListener(new java.awt.event.ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    clustalColour_actionPerformed();
-                }
-            });
-        zappoColour.setText("Zappo");
-        zappoColour.addActionListener(new java.awt.event.ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    zappoColour_actionPerformed();
-                }
-            });
-        taylorColour.setText("Taylor");
-        taylorColour.addActionListener(new java.awt.event.ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    taylorColour_actionPerformed();
-                }
-            });
-        hydrophobicityColour.setText("Hydrophobicity");
-        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()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    helixColour_actionPerformed();
-                }
-            });
-        strandColour.setText("Strand propensity");
-        strandColour.addActionListener(new java.awt.event.ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    strandColour_actionPerformed();
-                }
-            });
-        turnColour.setText("Turn propensity");
-        turnColour.addActionListener(new java.awt.event.ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    turnColour_actionPerformed();
-                }
-            });
-        buriedColour.setText("Buried Index");
-        buriedColour.addActionListener(new java.awt.event.ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    buriedColour_actionPerformed();
-                }
-            });
-        abovePIDColour.setText("Above % Identity");
-        abovePIDColour.addActionListener(new java.awt.event.ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    abovePIDColour_actionPerformed();
-                }
-            });
-        userDefinedColour.setText("User Defined...");
-        userDefinedColour.addActionListener(new java.awt.event.ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    userDefinedColour_actionPerformed(e);
-                }
-            });
-        PIDColour.setText("Percentage Identity");
-        PIDColour.addActionListener(new java.awt.event.ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    PIDColour_actionPerformed();
-                }
-            });
-        BLOSUM62Colour.setText("BLOSUM62");
-        BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    BLOSUM62Colour_actionPerformed();
-                }
-            });
-        conservationMenuItem.setText("Conservation");
-        conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    conservationMenuItem_actionPerformed();
-                }
-            });
-    }
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void taylorColour_actionPerformed()
+  {
+    getGroup().cs = new TaylorColourScheme();
+    refresh();
+  }
 
-    /**
-     * DOCUMENT ME!
-     */
-    void refresh()
-    {
-        if (ap.overviewPanel != null)
-          ap.overviewPanel.updateOverviewImage();
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void hydrophobicityColour_actionPerformed()
+  {
+    getGroup().cs = new HydrophobicColourScheme();
+    refresh();
+  }
 
-        PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
-    }
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void helixColour_actionPerformed()
+  {
+    getGroup().cs = new HelixColourScheme();
+    refresh();
+  }
 
-    /**
-     * 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());
-        refresh();
-    }
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void strandColour_actionPerformed()
+  {
+    getGroup().cs = new StrandColourScheme();
+    refresh();
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void zappoColour_actionPerformed()
-    {
-        getGroup().cs = new ZappoColourScheme();
-        refresh();
-    }
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void turnColour_actionPerformed()
+  {
+    getGroup().cs = new TurnColourScheme();
+    refresh();
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void taylorColour_actionPerformed()
-    {
-        getGroup().cs = new TaylorColourScheme();
-        refresh();
-    }
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void buriedColour_actionPerformed()
+  {
+    getGroup().cs = new BuriedColourScheme();
+    refresh();
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void hydrophobicityColour_actionPerformed()
-    {
-        getGroup().cs = new HydrophobicColourScheme();
-        refresh();
-    }
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void nucleotideMenuItem_actionPerformed()
+  {
+    getGroup().cs = new NucleotideColourScheme();
+    refresh();
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void helixColour_actionPerformed()
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void abovePIDColour_actionPerformed()
+  {
+    SequenceGroup sg = getGroup();
+    if (sg.cs == null)
     {
-        getGroup().cs = new HelixColourScheme();
-        refresh();
+      return;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void strandColour_actionPerformed()
+    if (abovePIDColour.isSelected())
     {
-        getGroup().cs = new StrandColourScheme();
-        refresh();
-    }
+      sg.cs.setConsensus(AAFrequency.calculate(
+          sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
+          sg.getEndRes() + 1));
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void turnColour_actionPerformed()
+      int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
+          getGroup().getName());
+
+      sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
+
+      SliderPanel.showPIDSlider();
+    }
+    else // remove PIDColouring
     {
-        getGroup().cs = new TurnColourScheme();
-        refresh();
+      sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void buriedColour_actionPerformed()
+    refresh();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void userDefinedColour_actionPerformed(ActionEvent e)
+  {
+    SequenceGroup sg = getGroup();
+
+    if (e.getActionCommand().equals("User Defined..."))
     {
-        getGroup().cs = new BuriedColourScheme();
-        refresh();
+      new UserDefinedColours(ap, sg);
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void nucleotideMenuItem_actionPerformed()
+    else
     {
-        getGroup().cs = new NucleotideColourScheme();
-        refresh();
+      UserColourScheme udc = (UserColourScheme) UserDefinedColours.
+          getUserColourSchemes().get(e.getActionCommand());
+
+      sg.cs = udc;
     }
+    refresh();
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void abovePIDColour_actionPerformed()
-    {
-        SequenceGroup sg = getGroup();
-        if(sg.cs==null)
-          return;
+  /**
+   * 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));
+    refresh();
+  }
 
-        if (abovePIDColour.isSelected())
-        {
-          sg.cs.setConsensus(AAFrequency.calculate(
-              sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
-              sg.getEndRes() + 1));
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void BLOSUM62Colour_actionPerformed()
+  {
+    SequenceGroup sg = getGroup();
 
-            int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
-                    getGroup().getName());
+    sg.cs = new Blosum62ColourScheme();
 
-           sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
+    sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
+        hiddenRepSequences),
+                                             sg.getStartRes(),
+                                             sg.getEndRes() + 1));
 
-            SliderPanel.showPIDSlider();
-        }
-        else // remove PIDColouring
-        {
-            sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
-        }
+    refresh();
+  }
 
-        refresh();
-    }
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void noColourmenuItem_actionPerformed()
+  {
+    getGroup().cs = null;
+    refresh();
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void userDefinedColour_actionPerformed(ActionEvent e)
-    {
-       SequenceGroup sg = getGroup();
-
-       if (e.getActionCommand().equals("User Defined..."))
-         new UserDefinedColours(ap, sg);
-       else
-       {
-         UserColourScheme udc = (UserColourScheme) UserDefinedColours.
-             getUserColourSchemes().get(e.getActionCommand());
-
-         sg.cs = udc;
-       }
-       refresh();
-     }
-    /**
-     * 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));
-        refresh();
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void conservationMenuItem_actionPerformed()
+  {
+    SequenceGroup sg = getGroup();
+    if (sg.cs == null)
+    {
+      return;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void BLOSUM62Colour_actionPerformed()
+    if (conservationMenuItem.isSelected())
     {
-        SequenceGroup sg = getGroup();
+      Conservation c = new Conservation("Group",
+                                        ResidueProperties.propHash, 3,
+                                        sg.getSequences(ap.av.
+          hiddenRepSequences),
+                                        sg.getStartRes(),
+                                        sg.getEndRes() + 1);
 
-        sg.cs = new Blosum62ColourScheme();
+      c.calculate();
+      c.verdict(false, ap.av.ConsPercGaps);
 
-        sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.hiddenRepSequences),
-                                                 sg.getStartRes(),
-                                                 sg.getEndRes() + 1));
+      sg.cs.setConservation(c);
 
-        refresh();
+      SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
+      SliderPanel.showConservationSlider();
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void noColourmenuItem_actionPerformed()
+    else // remove ConservationColouring
     {
-        getGroup().cs = null;
-        refresh();
+      sg.cs.setConservation(null);
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void conservationMenuItem_actionPerformed()
-    {
-        SequenceGroup sg = getGroup();
-        if(sg.cs==null)
-          return;
-
-        if (conservationMenuItem.isSelected())
-        {
-            Conservation c = new Conservation("Group",
-                    ResidueProperties.propHash, 3,
-                    sg.getSequences(ap.av.hiddenRepSequences),
-                    sg.getStartRes(),
-                    sg.getEndRes() + 1);
-
-            c.calculate();
-            c.verdict(false, ap.av.ConsPercGaps);
-
-            sg.cs.setConservation(c);
+    refresh();
+  }
 
-            SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
-            SliderPanel.showConservationSlider();
-        }
-        else // remove ConservationColouring
-        {
-            sg.cs.setConservation(null);
-        }
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void groupName_actionPerformed()
+  {
 
-        refresh();
-    }
+    SequenceGroup sg = getGroup();
+    EditNameDialog dialog = new EditNameDialog(sg.getName(),
+                                               sg.getDescription(),
+                                               "       Group Name ",
+                                               "Group Description ",
+                                               "Edit Group Name/Description");
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void groupName_actionPerformed()
+    if (!dialog.accept)
     {
+      return;
+    }
 
-      SequenceGroup sg = getGroup();
-      EditNameDialog dialog = new EditNameDialog(sg.getName(),
-                                                 sg.getDescription(),
-                                                 "       Group Name ",
-                                                 "Group Description ",
-                                                 "Edit Group Name/Description");
-
-      if (!dialog.accept)
-      {
-        return;
-      }
+    sg.setName(dialog.getName());
+    sg.setDescription(dialog.getDescription());
+  }
 
-      sg.setName(dialog.getName());
-      sg.setDescription(dialog.getDescription());
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  SequenceGroup getGroup()
+  {
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    // this method won't add a new group if it already exists
+    if (sg != null)
+    {
+      ap.av.alignment.addGroup(sg);
     }
 
+    return sg;
+  }
+
+  /**
+   * 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");
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    SequenceGroup getGroup()
+    if (!dialog.accept)
     {
-        SequenceGroup sg = ap.av.getSelectionGroup();
-      // this method won't add a new group if it already exists
-        if(sg!=null)
-          ap.av.alignment.addGroup(sg);
-
-        return sg;
+      return;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    void sequenceName_actionPerformed()
+    if (dialog.getName() != null)
     {
-      EditNameDialog dialog = new EditNameDialog(sequence.getName(),
-                                                 sequence.getDescription(),
-                                                 "       Sequence Name ",
-                                                 "Sequence Description ",
-                                                 "Edit Sequence Name/Description");
+      if (dialog.getName().indexOf(" ") > -1)
+      {
+        JOptionPane.showMessageDialog(ap,
+                                      "Spaces have been converted to \"_\"",
+                                      "No spaces allowed in Sequence Name",
+                                      JOptionPane.WARNING_MESSAGE);
+      }
 
-        if (!dialog.accept)
-        {
-            return;
-        }
+      sequence.setName(dialog.getName().replace(' ', '_'));
+      ap.repaint();
+    }
 
-        if (dialog.getName() != null)
-        {
-            if (dialog.getName().indexOf(" ") > -1)
-            {
-                JOptionPane.showMessageDialog(ap,
-                    "Spaces have been converted to \"_\"",
-                    "No spaces allowed in Sequence Name",
-                    JOptionPane.WARNING_MESSAGE);
-            }
+    sequence.setDescription(dialog.getDescription());
 
-            sequence.setName(dialog.getName().replace(' ', '_'));
-            ap.repaint();
-        }
+    ap.av.firePropertyChange("alignment", null,
+                             ap.av.getAlignment().getSequences());
 
-        sequence.setDescription(dialog.getDescription());
+  }
 
-        ap.av.firePropertyChange("alignment", null,
-                                  ap.av.getAlignment().getSequences());
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  void unGroupMenuItem_actionPerformed()
+  {
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    ap.av.alignment.deleteGroup(sg);
+    ap.av.setSelectionGroup(null);
+    refresh();
+  }
 
-    }
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void outline_actionPerformed()
+  {
+    SequenceGroup sg = getGroup();
+    Color col = JColorChooser.showDialog(this, "Select Outline Colour",
+                                         Color.BLUE);
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    void unGroupMenuItem_actionPerformed()
-    {
-        SequenceGroup sg = ap.av.getSelectionGroup();
-        ap.av.alignment.deleteGroup(sg);
-        ap.av.setSelectionGroup(null);
-        refresh();
+    if (col != null)
+    {
+      sg.setOutlineColour(col);
     }
 
+    refresh();
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void outline_actionPerformed()
-    {
-        SequenceGroup sg = getGroup();
-        Color col = JColorChooser.showDialog(this, "Select Outline Colour",
-                Color.BLUE);
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void showBoxes_actionPerformed()
+  {
+    getGroup().setDisplayBoxes(showBoxes.isSelected());
+    refresh();
+  }
 
-        if (col != null)
-        {
-            sg.setOutlineColour(col);
-        }
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void showText_actionPerformed()
+  {
+    getGroup().setDisplayText(showText.isSelected());
+    refresh();
+  }
 
-        refresh();
-    }
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void showColourText_actionPerformed()
+  {
+    getGroup().setColourText(showColourText.isSelected());
+    refresh();
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void showBoxes_actionPerformed()
+  public void showLink(String url)
+  {
+    try
     {
-        getGroup().setDisplayBoxes(showBoxes.isSelected());
-        refresh();
+      jalview.util.BrowserLauncher.openURL(url);
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void showText_actionPerformed()
+    catch (Exception ex)
     {
-        getGroup().setDisplayText(showText.isSelected());
-        refresh();
+      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!
-     */
-    public void showColourText_actionPerformed()
+  void hideSequences(boolean representGroup)
+  {
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    if (sg == null || sg.getSize() < 1)
     {
-        getGroup().setColourText(showColourText.isSelected());
-        refresh();
+      ap.av.hideSequence(new SequenceI[]
+                         {sequence});
+      return;
     }
 
-    public void showLink(String url)
-    {
-      try
-      {
-        jalview.util.BrowserLauncher.openURL(url);
-      }
-      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 );
-
-
-        ex.printStackTrace();
-      }
-    }
+    ap.av.setSelectionGroup(null);
 
-    void hideSequences(boolean representGroup)
+    if (representGroup)
     {
-      SequenceGroup sg = ap.av.getSelectionGroup();
-      if(sg==null || sg.getSize()<1)
-      {
-        ap.av.hideSequence(new SequenceI[]{sequence});
-        return;
-      }
-
-      ap.av.setSelectionGroup(null);
-
-      if (representGroup)
-      {
-        ap.av.hideRepSequences(sequence, sg);
+      ap.av.hideRepSequences(sequence, sg);
 
-        return;
-      }
-
-      int gsize = sg.getSize();
-      SequenceI[] hseqs;
+      return;
+    }
 
-      hseqs = new SequenceI[gsize];
+    int gsize = sg.getSize();
+    SequenceI[] hseqs;
 
-      int index = 0;
-      for (int i = 0; i < gsize; i++)
-      {
-        hseqs[index++] = sg.getSequenceAt(i);
-      }
+    hseqs = new SequenceI[gsize];
 
-      ap.av.hideSequence(hseqs);
+    int index = 0;
+    for (int i = 0; i < gsize; i++)
+    {
+      hseqs[index++] = sg.getSequenceAt(i);
     }
 
+    ap.av.hideSequence(hseqs);
+  }
+
   public void copy_actionPerformed()
   {
     ap.alignFrame.copy_actionPerformed(null);
@@ -1161,14 +1179,20 @@ public class PopupMenu extends JPopupMenu
       {
         if (ap.av.hasHiddenColumns)
         {
-          if(start==0)
+          if (start == 0)
+          {
             start = ap.av.colSel.adjustForHiddenColumns(start);
+          }
 
           end = ap.av.colSel.getHiddenBoundaryRight(start);
           if (start == end)
+          {
             end = sg.getEndRes() + 1;
+          }
           if (end > sg.getEndRes())
+          {
             end = sg.getEndRes() + 1;
+          }
         }
 
         regions.addElement(new int[]
@@ -1188,16 +1212,15 @@ public class PopupMenu extends JPopupMenu
         startEnd[i] = (int[]) regions.elementAt(i);
       }
 
-
       String description;
       int caseChange;
 
-      if(source==toggle)
+      if (source == toggle)
       {
         description = "Toggle Case";
         caseChange = ChangeCaseCommand.TOGGLE_CASE;
       }
-      else if(source==upperCase)
+      else if (source == upperCase)
       {
         description = "To Upper Case";
         caseChange = ChangeCaseCommand.TO_UPPER;
@@ -1215,9 +1238,8 @@ public class PopupMenu extends JPopupMenu
 
       ap.alignFrame.addHistoryItem(caseCommand);
 
-
       ap.av.firePropertyChange("alignment", null,
-                                ap.av.getAlignment().getSequences());
+                               ap.av.getAlignment().getSequences());
 
     }
   }
@@ -1230,9 +1252,9 @@ public class PopupMenu extends JPopupMenu
                              "Alignment output - " + e.getActionCommand(), 600,
                              500);
 
-    String [] omitHidden = null;
+    String[] omitHidden = null;
 
-    if(ap.av.hasHiddenColumns)
+    if (ap.av.hasHiddenColumns)
     {
       System.out.println("PROMPT USER HERE");
       omitHidden = ap.av.getViewAsString(true);
@@ -1244,52 +1266,55 @@ public class PopupMenu extends JPopupMenu
         omitHidden));
   }
 
-
   public void pdbFromFile_actionPerformed()
   {
-     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");
-
-     int value = chooser.showOpenDialog(null);
-
-     if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
-     {
-       PDBEntry entry = new PDBEntry();
-       String choice = chooser.getSelectedFile().getPath();
-       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
-       try
-       {
-         MCview.PDBfile pdbfile = new MCview.PDBfile(choice,
-                                       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);
-           if (reply == null)
-             return;
-
-           entry.setId(reply);
-         }
-         else
-           entry.setId(pdbfile.id);
-       }
-       catch (java.io.IOException ex)
-       {
-         ex.printStackTrace();
-       }
-
-       entry.setFile(choice);
-       sequence.getDatasetSequence().addPDBId(entry);
-     }
+    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");
+
+    int value = chooser.showOpenDialog(null);
+
+    if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
+    {
+      PDBEntry entry = new PDBEntry();
+      String choice = chooser.getSelectedFile().getPath();
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+      try
+      {
+        MCview.PDBfile pdbfile = new MCview.PDBfile(choice,
+            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);
+          if (reply == null)
+          {
+            return;
+          }
+
+          entry.setId(reply);
+        }
+        else
+        {
+          entry.setId(pdbfile.id);
+        }
+      }
+      catch (java.io.IOException ex)
+      {
+        ex.printStackTrace();
+      }
+
+      entry.setFile(choice);
+      sequence.getDatasetSequence().addPDBId(entry);
+    }
 
   }
 
@@ -1310,25 +1335,27 @@ public class PopupMenu extends JPopupMenu
   public void discoverPDB_actionPerformed()
   {
     new jalview.io.DBRefFetcher(
-             ap.av.getAlignment(), ap.alignFrame).fetchDBRefs(false);
+        ap.av.getAlignment(), ap.alignFrame).fetchDBRefs(false);
   }
 
   public void sequenceFeature_actionPerformed()
   {
     SequenceGroup sg = ap.av.getSelectionGroup();
-    if(sg==null)
+    if (sg == null)
+    {
       return;
+    }
 
-    int gSize= sg.getSize();
-    SequenceI [] seqs = new SequenceI[gSize];
-    SequenceFeature [] features = new SequenceFeature[gSize];
+    int gSize = sg.getSize();
+    SequenceI[] seqs = new SequenceI[gSize];
+    SequenceFeature[] features = new SequenceFeature[gSize];
 
     for (int i = 0; i < gSize; i++)
     {
       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()
@@ -1344,6 +1371,8 @@ public class PopupMenu extends JPopupMenu
   {
     SequenceGroup sg = getGroup();
     if (sg != null)
+    {
       new TextColourChooser().chooseColour(ap, sg);
+    }
   }
 }
diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index b58c72d..e16aa42 100755
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,21 +18,16 @@
  */
 package jalview.gui;
 
-import jalview.io.*;
-
-import jalview.jbgui.*;
-
-import jalview.schemes.*;
+import java.util.*;
 
 import java.awt.*;
 import java.awt.event.*;
-
 import javax.swing.*;
 
-import java.util.*;
-
-import jalview.bin.Cache;
-
+import jalview.bin.*;
+import jalview.io.*;
+import jalview.jbgui.*;
+import jalview.schemes.*;
 
 /**
  * DOCUMENT ME!
@@ -40,159 +35,161 @@ import jalview.bin.Cache;
  * @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 $SEQUENCE_ID$ */
-    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");
-      sequenceURLLinks = new Vector();
+  /** Holds name and link separated with | character. Sequence ID must be $SEQUENCE_ID$ */
+  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");
+    sequenceURLLinks = new Vector();
 
-      try
-      {
-        StringTokenizer st = new StringTokenizer(string, "|");
-        while (st.hasMoreElements())
-        {
-          sequenceURLLinks.addElement(st.nextToken() + "|" + st.nextToken());
-        }
-      }
-      catch (Exception ex)
+    try
+    {
+      StringTokenizer st = new StringTokenizer(string, "|");
+      while (st.hasMoreElements())
       {
-        System.out.println(ex + "\nError parsing sequence links");
+        sequenceURLLinks.addElement(st.nextToken() + "|" + st.nextToken());
       }
     }
-    Vector nameLinks, urlLinks;
+    catch (Exception ex)
+    {
+      System.out.println(ex + "\nError parsing sequence links");
+    }
+  }
 
-    JInternalFrame frame;
+  Vector nameLinks, urlLinks;
 
-    DasSourceBrowser dasSource;
+  JInternalFrame frame;
 
+  DasSourceBrowser dasSource;
 
-    /**
-     * Creates a new Preferences object.
-     */
-    public Preferences()
-    {
+  /**
+   * Creates a new Preferences object.
+   */
+  public Preferences()
+  {
 
-        frame = new JInternalFrame();
-        frame.setContentPane(this);
-        dasSource = new DasSourceBrowser();
-        dasPanel.add(dasSource, BorderLayout.CENTER);
+    frame = new JInternalFrame();
+    frame.setContentPane(this);
+    dasSource = new DasSourceBrowser();
+    dasPanel.add(dasSource, BorderLayout.CENTER);
 
-        int width = 500, height = 420;
-        if(System.getProperty("os.name").startsWith("Mac"))
-        {
-          width = 570;
-          height = 460;
-        }
+    int width = 500, height = 420;
+    if (System.getProperty("os.name").startsWith("Mac"))
+    {
+      width = 570;
+      height = 460;
+    }
 
-        Desktop.addInternalFrame(frame, "Preferences", width, height);
-        frame.setMinimumSize(new Dimension(width, height));
+    Desktop.addInternalFrame(frame, "Preferences", width, height);
+    frame.setMinimumSize(new Dimension(width, height));
 
-        seqLimit.setSelected(    Cache.getDefault("SHOW_JVSUFFIX", true));
-        rightAlign.setSelected(  Cache.getDefault("RIGHT_ALIGN_IDS", false));
-        fullScreen.setSelected(  Cache.getDefault("SHOW_FULLSCREEN", false));
-        annotations.setSelected( Cache.getDefault("SHOW_ANNOTATIONS", true));
+    seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
+    rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
+    fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
+    annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 
-        conservation.setEnabled( Cache.getDefault("SHOW_ANNOTATIONS", true));
-        quality.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
-        identity.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
+    conservation.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
+    quality.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
+    identity.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
 
-        conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
-        quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
-        identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
+    conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
+    quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
+    identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 
-        for (int i = 0; i < 13; i++)
-        {
-            colour.addItem(ColourSchemeProperty.getColourName(i));
-        }
+    for (int i = 0; i < 13; i++)
+    {
+      colour.addItem(ColourSchemeProperty.getColourName(i));
+    }
 
-        String string = Cache.getDefault("DEFAULT_COLOUR", "None");
+    String string = Cache.getDefault("DEFAULT_COLOUR", "None");
 
-        colour.setSelectedItem(string);
+    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++)
-        {
-            fontNameCB.addItem(fonts[i]);
-        }
+    for (int i = 0; i < fonts.length; i++)
+    {
+      fontNameCB.addItem(fonts[i]);
+    }
 
-        for (int i = 1; i < 31; i++)
-        {
-            fontSizeCB.addItem(i + "");
-        }
+    for (int i = 1; i < 31; i++)
+    {
+      fontSizeCB.addItem(i + "");
+    }
 
-        fontStyleCB.addItem("plain");
-        fontStyleCB.addItem("bold");
-        fontStyleCB.addItem("italic");
+    fontStyleCB.addItem("plain");
+    fontStyleCB.addItem("bold");
+    fontStyleCB.addItem("italic");
 
-        fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
-        fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
-        fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN + "") );
+    fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
+    fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
+    fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
 
-        smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
+    smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 
-        idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
+    idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 
-        wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
+    wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 
-        gapSymbolCB.addItem("-");
-        gapSymbolCB.addItem(".");
+    gapSymbolCB.addItem("-");
+    gapSymbolCB.addItem(".");
 
-        gapSymbolCB.setSelectedItem( Cache.getDefault("GAP_SYMBOL", "-"));
+    gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 
-        startupCheckbox.setSelected( Cache.getDefault("SHOW_STARTUP_FILE", true) );
-        startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
-         "http://www.jalview.org/examples/exampleFile.jar"));
+    startupCheckbox.setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
+    startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
+                                                  "http://www.jalview.org/examples/exampleFile.jar"));
 
-        sortby.addItem("No sort");
-        sortby.addItem("Id");
-        sortby.addItem("Pairwise Identity");
-        sortby.setSelectedItem( Cache.getDefault("SORT_ALIGNMENT", "No sort") );
+    sortby.addItem("No sort");
+    sortby.addItem("Id");
+    sortby.addItem("Pairwise Identity");
+    sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 
-        epsRendering.addItem("Prompt each time");
-        epsRendering.addItem("Lineart");
-        epsRendering.addItem("Text");
-        epsRendering.setSelectedItem( Cache.getDefault("EPS_RENDERING", "Prompt each time"));
+    epsRendering.addItem("Prompt each time");
+    epsRendering.addItem("Lineart");
+    epsRendering.addItem("Text");
+    epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING",
+                                                  "Prompt each time"));
 
-        blcjv.setSelected( Cache.getDefault("BLC_JVSUFFIX", true) );
-        clustaljv.setSelected( Cache.getDefault("CLUSTAL_JVSUFFIX", true) );
-        fastajv.setSelected( Cache.getDefault("FASTA_JVSUFFIX", true) );
-        msfjv.setSelected( Cache.getDefault("MSF_JVSUFFIX", true) );
-        pfamjv.setSelected( Cache.getDefault("PFAM_JVSUFFIX", true) );
-        pileupjv.setSelected( Cache.getDefault("PILEUP_JVSUFFIX", true) );
-        pirjv.setSelected( Cache.getDefault("PIR_JVSUFFIX", true) );
+    blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
+    clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
+    fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
+    msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
+    pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
+    pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
+    pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 
-        modellerOutput.setSelected( Cache.getDefault("PIR_MODELLER", false));
+    modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 
-        autoCalculateConsCheck.setSelected( Cache.getDefault("AUTO_CALC_CONSENSUS", true));
-        padGaps.setSelected( Cache.getDefault("PAD_GAPS", false));
+    autoCalculateConsCheck.setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
+    padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 
-  /****************************************************
-   * Set up Connections
-   */
-        nameLinks = new Vector();
-        urlLinks = new Vector();
-        for(int i=0; i<sequenceURLLinks.size(); i++)
-        {
-          String link = sequenceURLLinks.elementAt(i).toString();
-          nameLinks.addElement(link.substring(0, link.indexOf("|")) );
-          urlLinks.addElement(link.substring(link.indexOf("|")+1));
-        }
+    /****************************************************
+     * Set up Connections
+     */
+    nameLinks = new Vector();
+    urlLinks = new Vector();
+    for (int i = 0; i < sequenceURLLinks.size(); i++)
+    {
+      String link = sequenceURLLinks.elementAt(i).toString();
+      nameLinks.addElement(link.substring(0, link.indexOf("|")));
+      urlLinks.addElement(link.substring(link.indexOf("|") + 1));
+    }
 
-        updateLinkData();
+    updateLinkData();
 
-        useProxy.setSelected( Cache.getDefault("USE_PROXY", false));
-        proxyServerTB.setEnabled(useProxy.isSelected());
-        proxyPortTB.setEnabled(useProxy.isSelected());
-        proxyServerTB.setText( Cache.getDefault("PROXY_SERVER", ""));
-        proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
+    useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
+    proxyServerTB.setEnabled(useProxy.isSelected());
+    proxyPortTB.setEnabled(useProxy.isSelected());
+    proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
+    proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 
-        defaultBrowser.setText( Cache.getDefault("DEFAULT_BROWSER",""));
+    defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
     try
     {
       jbInit();
@@ -204,277 +201,351 @@ public class Preferences extends GPreferences
 
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void ok_actionPerformed(ActionEvent 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_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()));
+
+    Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
+                                            sortby.getSelectedItem().toString());
+
+    if (epsRendering.getSelectedItem().equals("Prompt each time"))
     {
+      Cache.applicationProperties.remove("EPS_RENDERING");
+    }
+    else
+    {
+      Cache.applicationProperties.setProperty("EPS_RENDERING",
+                                              epsRendering.getSelectedItem().
+                                              toString());
+    }
 
-      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_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()));
-
-      Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby.getSelectedItem().toString() );
-
-      if(epsRendering.getSelectedItem().equals("Prompt each time"))
-        Cache.applicationProperties.remove("EPS_RENDERING");
-      else
-        Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering.getSelectedItem().toString());
+    if (defaultBrowser.getText().trim().length() < 1)
+    {
+      Cache.applicationProperties.remove("DEFAULT_BROWSER");
+    }
+    else
+    {
+      Cache.applicationProperties.setProperty("DEFAULT_BROWSER",
+                                              defaultBrowser.getText());
+    }
 
-      if(defaultBrowser.getText().trim().length()<1)
-        Cache.applicationProperties.remove("DEFAULT_BROWSER");
-      else
-        Cache.applicationProperties.setProperty("DEFAULT_BROWSER",
-                                                defaultBrowser.getText());
+    jalview.util.BrowserLauncher.resetBrowser();
 
-        jalview.util.BrowserLauncher.resetBrowser();
+    if (nameLinks.size() > 0)
+    {
+      StringBuffer links = new StringBuffer();
+      sequenceURLLinks = new Vector();
+      for (int i = 0; i < nameLinks.size(); 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());
+    }
+    else
+    {
+      Cache.applicationProperties.remove("SEQUENCE_LINKS");
+    }
 
-        if(nameLinks.size()>0)
-        {
-          StringBuffer links = new StringBuffer();
-          sequenceURLLinks = new Vector();
-          for (int i = 0; i < nameLinks.size(); 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());
-        }
-        else
-          Cache.applicationProperties.remove("SEQUENCE_LINKS");
+    Cache.applicationProperties.setProperty("USE_PROXY",
+                                            Boolean.toString(useProxy.
+        isSelected()));
 
+    if (proxyServerTB.getText().trim().length() < 1)
+    {
+      Cache.applicationProperties.remove("PROXY_SERVER");
+    }
+    else
+    {
+      Cache.applicationProperties.setProperty("PROXY_SERVER",
+                                              proxyServerTB.getText());
+    }
 
-        Cache.applicationProperties.setProperty("USE_PROXY", Boolean.toString(useProxy.isSelected()));
+    if (proxyPortTB.getText().trim().length() < 1)
+    {
+      Cache.applicationProperties.remove("PROXY_PORT");
+    }
+    else
+    {
+      Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB.getText());
+    }
 
-        if (proxyServerTB.getText().trim().length() < 1)
-          Cache.applicationProperties.remove("PROXY_SERVER");
-        else
-          Cache.applicationProperties.setProperty("PROXY_SERVER",
-                                                  proxyServerTB.getText());
+    if (useProxy.isSelected())
+    {
+      System.setProperty("http.proxyHost", proxyServerTB.getText());
+      System.setProperty("http.proxyPort", proxyPortTB.getText());
+    }
+    else
+    {
+      System.setProperty("http.proxyHost", "");
+      System.setProperty("http.proxyPort", "");
+    }
 
-        if (proxyPortTB.getText().trim().length() < 1)
-          Cache.applicationProperties.remove("PROXY_PORT");
-        else
-          Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB.getText());
+    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()));
+
+    dasSource.saveProperties(Cache.applicationProperties);
+
+    Cache.saveProperties();
+    try
+    {
+      frame.setClosed(true);
+    }
+    catch (Exception ex)
+    {
+    }
+  }
 
-        if(useProxy.isSelected())
+  /**
+   * DOCUMENT ME!
+   */
+  public void startupFileTextfield_mouseClicked()
+  {
+    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+        getProperty(
+            "LAST_DIRECTORY"),
+        new String[]
         {
-          System.setProperty("http.proxyHost", proxyServerTB.getText());
-          System.setProperty("http.proxyPort", proxyPortTB.getText());
-        }
-        else
+        "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
+        "jar"
+    },
+        new String[]
         {
-          System.setProperty("http.proxyHost","");
-          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()) );
-        jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
+        "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"
+    }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
+    chooser.setFileView(new JalviewFileView());
+    chooser.setDialogTitle("Select startup file");
 
-        Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
-                                                Boolean.toString(autoCalculateConsCheck.isSelected()));
-        Cache.applicationProperties.setProperty("PAD_GAPS",
-                                                Boolean.toString(padGaps.isSelected()));
-
-        dasSource.saveProperties(Cache.applicationProperties);
-
-        Cache.saveProperties();
-        try
-        {
-            frame.setClosed(true);
-        }
-        catch (Exception ex)
-        {
-        }
-    }
+    int value = chooser.showOpenDialog(this);
 
-    /**
-     * DOCUMENT ME!
-     */
-    public void startupFileTextfield_mouseClicked()
+    if (value == JalviewFileChooser.APPROVE_OPTION)
     {
-        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");
-
-        int value = chooser.showOpenDialog(this);
-
-        if (value == JalviewFileChooser.APPROVE_OPTION)
-        {
-            jalview.bin.Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
-                chooser.getSelectedFormat());
-            startupFileTextfield.setText(chooser.getSelectedFile()
-                                                .getAbsolutePath());
-        }
+      jalview.bin.Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
+          chooser.getSelectedFormat());
+      startupFileTextfield.setText(chooser.getSelectedFile()
+                                   .getAbsolutePath());
     }
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void cancel_actionPerformed(ActionEvent e)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void cancel_actionPerformed(ActionEvent e)
+  {
+    try
     {
-        try
-        {
-            frame.setClosed(true);
-        }
-        catch (Exception ex)
-        {
-        }
+      frame.setClosed(true);
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void annotations_actionPerformed(ActionEvent e)
+    catch (Exception ex)
     {
-        conservation.setEnabled(annotations.isSelected());
-        quality.setEnabled(annotations.isSelected());
-        identity.setEnabled(annotations.isSelected());
     }
+  }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void annotations_actionPerformed(ActionEvent e)
+  {
+    conservation.setEnabled(annotations.isSelected());
+    quality.setEnabled(annotations.isSelected());
+    identity.setEnabled(annotations.isSelected());
+  }
 
-    public void newLink_actionPerformed(ActionEvent e) {
+  public void newLink_actionPerformed(ActionEvent e)
+  {
 
-      GSequenceLink link = new GSequenceLink();
-      boolean valid = false;
-      while( !valid )
+    GSequenceLink link = new GSequenceLink();
+    boolean valid = false;
+    while (!valid)
+    {
+      if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
+                                                "New sequence URL link",
+                                                JOptionPane.OK_CANCEL_OPTION
+                                                , -1, null)
+          == JOptionPane.OK_OPTION)
       {
-        if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
-                                                  "New sequence URL link",
-                                                  JOptionPane.OK_CANCEL_OPTION
-                                                  ,-1, null)
-            == JOptionPane.OK_OPTION)
+        if (link.checkValid())
         {
-          if (link.checkValid())
-          {
-            nameLinks.addElement(link.getName());
-            urlLinks.addElement(link.getURL());
-            updateLinkData();
-            valid = true;
-          }
+          nameLinks.addElement(link.getName());
+          urlLinks.addElement(link.getURL());
+          updateLinkData();
+          valid = true;
         }
-        else
-          break;
+      }
+      else
+      {
+        break;
       }
     }
+  }
 
-    public void editLink_actionPerformed(ActionEvent e) {
-      GSequenceLink link = new GSequenceLink();
+  public void editLink_actionPerformed(ActionEvent e)
+  {
+    GSequenceLink link = new GSequenceLink();
 
-      int index = linkNameList.getSelectedIndex();
-      if(index==-1)
-      {
-        JOptionPane.showInternalMessageDialog(Desktop.desktop, "No link selected!"
-            ,"No link selected", JOptionPane.WARNING_MESSAGE);
-        return;
-      }
+    int index = linkNameList.getSelectedIndex();
+    if (index == -1)
+    {
+      JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                                            "No link selected!"
+                                            , "No link selected",
+                                            JOptionPane.WARNING_MESSAGE);
+      return;
+    }
 
-      link.setName( nameLinks.elementAt(index).toString() );
-      link.setURL( urlLinks.elementAt(index).toString() );
+    link.setName(nameLinks.elementAt(index).toString());
+    link.setURL(urlLinks.elementAt(index).toString());
 
-      boolean valid = false;
-      while (!valid)
-      {
+    boolean valid = false;
+    while (!valid)
+    {
 
-        if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
-                                                  "New sequence URL link",
-                                                  JOptionPane.OK_CANCEL_OPTION
-                                                  ,-1, null)
-            == JOptionPane.OK_OPTION)
+      if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
+                                                "New sequence URL link",
+                                                JOptionPane.OK_CANCEL_OPTION
+                                                , -1, null)
+          == JOptionPane.OK_OPTION)
+      {
+        if (link.checkValid())
         {
-          if (link.checkValid())
-          {
-            nameLinks.setElementAt(link.getName(), index);
-            urlLinks.setElementAt(link.getURL(), index);
-            updateLinkData();
-            valid = true;
-          }
+          nameLinks.setElementAt(link.getName(), index);
+          urlLinks.setElementAt(link.getURL(), index);
+          updateLinkData();
+          valid = true;
         }
-
-        else
-          break;
       }
-    }
 
-    public void deleteLink_actionPerformed(ActionEvent e) {
-      int index = linkNameList.getSelectedIndex();
-      if(index==-1)
+      else
       {
-        JOptionPane.showInternalMessageDialog(Desktop.desktop, "No link selected!"
-            ,"No link selected", JOptionPane.WARNING_MESSAGE);
-        return;
+        break;
       }
-      nameLinks.removeElementAt(index);
-      urlLinks.removeElementAt(index);
-      updateLinkData();
     }
+  }
 
-    void updateLinkData()
+  public void deleteLink_actionPerformed(ActionEvent e)
+  {
+    int index = linkNameList.getSelectedIndex();
+    if (index == -1)
     {
-      linkNameList.setListData(nameLinks);
-      linkURLList.setListData(urlLinks);
+      JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                                            "No link selected!"
+                                            , "No link selected",
+                                            JOptionPane.WARNING_MESSAGE);
+      return;
     }
+    nameLinks.removeElementAt(index);
+    urlLinks.removeElementAt(index);
+    updateLinkData();
+  }
 
-    public void defaultBrowser_mouseClicked(MouseEvent e)
-    {
-      JFileChooser chooser = new JFileChooser(".");
-      chooser.setDialogTitle("Select default web browser");
+  void updateLinkData()
+  {
+    linkNameList.setListData(nameLinks);
+    linkURLList.setListData(urlLinks);
+  }
+
+  public void defaultBrowser_mouseClicked(MouseEvent e)
+  {
+    JFileChooser chooser = new JFileChooser(".");
+    chooser.setDialogTitle("Select default web browser");
 
-      int value = chooser.showOpenDialog(this);
+    int value = chooser.showOpenDialog(this);
 
-      if (value == JFileChooser.APPROVE_OPTION)
-      {
-        defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
-      }
+    if (value == JFileChooser.APPROVE_OPTION)
+    {
+      defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
+    }
 
   }
 
diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index 4ca114d..aa73383 100755
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,19 +18,16 @@
  */
 package jalview.gui;
 
-import jalview.datamodel.*;
-import jalview.jbgui.*;
-import jalview.util.Comparison;
-import jalview.commands.*;
-
-import java.awt.event.*;
-
 import java.util.*;
 
-import javax.swing.event.*;
-
+import java.awt.event.*;
 import javax.swing.*;
+import javax.swing.event.*;
 
+import jalview.commands.*;
+import jalview.datamodel.*;
+import jalview.jbgui.*;
+import jalview.util.*;
 
 /**
  * DOCUMENT ME!
@@ -38,289 +35,301 @@ import javax.swing.*;
  * @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!
-     */
-    public RedundancyPanel(final AlignmentPanel ap, AlignFrame af)
+  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!
+   */
+  public RedundancyPanel(final AlignmentPanel ap, AlignFrame af)
+  {
+    this.ap = ap;
+    this.af = af;
+    redundantSeqs = new Vector();
+
+    slider.addChangeListener(new ChangeListener()
     {
-        this.ap = ap;
-        this.af = af;
-        redundantSeqs = new Vector();
-
-        slider.addChangeListener(new ChangeListener()
-            {
-                public void stateChanged(ChangeEvent evt)
-                {
-                    valueField.setText(slider.getValue() + "");
-                    sliderValueChanged();
-                }
-            });
-
-        applyButton.setText("Remove");
-        allGroupsCheck.setVisible(false);
-        slider.setMinimum(0);
-        slider.setMaximum(100);
-        slider.setValue(100);
-
-        Thread worker = new Thread(this);
-        worker.start();
-
-        frame = new JInternalFrame();
-        frame.setContentPane(this);
-        Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400,
-                         100, false);
-        frame.addInternalFrameListener(new InternalFrameAdapter()
-            {
-              public void internalFrameClosing(InternalFrameEvent evt)
-              {
-               ap.idPanel.idCanvas.setHighlighted(null);
-              }
-            }
-            );
-
+      public void stateChanged(ChangeEvent evt)
+      {
+        valueField.setText(slider.getValue() + "");
+        sliderValueChanged();
+      }
+    });
+
+    applyButton.setText("Remove");
+    allGroupsCheck.setVisible(false);
+    slider.setMinimum(0);
+    slider.setMaximum(100);
+    slider.setValue(100);
+
+    Thread worker = new Thread(this);
+    worker.start();
+
+    frame = new JInternalFrame();
+    frame.setContentPane(this);
+    Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400,
+                             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!
+   *
+   * @return DOCUMENT ME!
+   */
+  public void run()
+  {
+    JProgressBar progress = new JProgressBar();
+    progress.setIndeterminate(true);
+    southPanel.add(progress, java.awt.BorderLayout.SOUTH);
 
+    label.setText("Calculating....");
 
-    /**
-     * 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()
+    slider.setVisible(false);
+    applyButton.setEnabled(false);
+    valueField.setVisible(false);
+
+    validate();
+
+    String[] omitHidden = null;
+
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    int height;
+
+    int start, end;
+
+    if ( (sg != null) && (sg.getSize() >= 1))
     {
-        JProgressBar progress = new JProgressBar();
-        progress.setIndeterminate(true);
-        southPanel.add(progress, java.awt.BorderLayout.SOUTH);
+      originalSequences = sg.getSequencesInOrder(ap.av.alignment);
+      start = sg.getStartRes();
+      end = sg.getEndRes();
+    }
+    else
+    {
+      originalSequences = ap.av.alignment.getSequencesArray();
+      start = 0;
+      end = ap.av.alignment.getWidth();
+    }
 
-        label.setText("Calculating....");
+    height = originalSequences.length;
 
-        slider.setVisible(false);
-        applyButton.setEnabled(false);
-        valueField.setVisible(false);
+    redundancy = new float[height];
+    for (int i = 0; i < height; i++)
+    {
+      redundancy[i] = 0f;
+    }
 
-        validate();
+    if (ap.av.hasHiddenColumns)
+    {
+      omitHidden = ap.av.getViewAsString(sg != null);
+    }
 
-        String[] omitHidden = null;
+    // long start = System.currentTimeMillis();
 
-        SequenceGroup sg = ap.av.getSelectionGroup();
-        int height;
+    float pid;
+    String seqi, seqj;
+    for (int i = 0; i < height; i++)
+    {
 
-        int start, end;
+      for (int j = 0; j < i; j++)
+      {
+        if (i == j)
+        {
+          continue;
+        }
 
-        if ( (sg != null) && (sg.getSize() >= 1))
+        if (omitHidden == null)
         {
-           originalSequences = sg.getSequencesInOrder(ap.av.alignment);
-           start = sg.getStartRes();
-           end = sg.getEndRes();
+          seqi = originalSequences[i].getSequenceAsString(start, end);
+          seqj = originalSequences[j].getSequenceAsString(start, end);
         }
         else
         {
-          originalSequences = ap.av.alignment.getSequencesArray();
-          start = 0;
-          end = ap.av.alignment.getWidth();
+          seqi = omitHidden[i];
+          seqj = omitHidden[j];
         }
 
-        height = originalSequences.length;
+        pid = Comparison.PID(seqi, seqj);
 
-        redundancy = new float[height];
-        for (int i = 0; i < height; i++)
+        if (seqj.length() < seqi.length())
         {
-          redundancy[i] = 0f;
+          redundancy[j] = Math.max(pid, redundancy[j]);
         }
-
-        if (ap.av.hasHiddenColumns)
+        else
         {
-          omitHidden = ap.av.getViewAsString(sg!=null);
+          redundancy[i] = Math.max(pid, redundancy[i]);
         }
 
+      }
+    }
 
-       // long start = System.currentTimeMillis();
+    progress.setIndeterminate(false);
+    progress.setVisible(false);
+    progress = null;
 
-        float pid;
-        String seqi, seqj;
-        for (int i = 0; i < height; i++)
-        {
+    label.setText("Enter the redundancy threshold");
+    slider.setVisible(true);
+    applyButton.setEnabled(true);
+    valueField.setVisible(true);
 
-            for (int j = 0; j < i; j++)
-            {
-              if(i==j)
-                continue;
-
-              if(omitHidden==null)
-              {
-                seqi = originalSequences[i].getSequenceAsString(start, end);
-                seqj = originalSequences[j].getSequenceAsString(start, end);
-              }
-              else
-              {
-                seqi = omitHidden[i];
-                seqj = omitHidden[j];
-              }
-
-              pid = Comparison.PID( seqi,  seqj );
-
-              if(seqj.length() < seqi.length())
-                redundancy[j] = Math.max(pid, redundancy[j]);
-              else
-                redundancy[i] = Math.max(pid, redundancy[i]);
-
-            }
-        }
+    validate();
+    // System.out.println((System.currentTimeMillis()-start));
+  }
+
+  void sliderValueChanged()
+  {
+    if (redundancy == null)
+    {
+      return;
+    }
 
-        progress.setIndeterminate(false);
-        progress.setVisible(false);
-        progress = null;
+    float value = slider.getValue();
 
-        label.setText("Enter the redundancy threshold");
-        slider.setVisible(true);
-        applyButton.setEnabled(true);
-        valueField.setVisible(true);
+    for (int i = 0; i < redundancy.length; i++)
+    {
+      if (value > redundancy[i])
+      {
+        redundantSeqs.remove(originalSequences[i]);
+      }
+      else if (!redundantSeqs.contains(originalSequences[i]))
+      {
+        redundantSeqs.add(originalSequences[i]);
+      }
 
-        validate();
-       // System.out.println((System.currentTimeMillis()-start));
     }
 
-    void sliderValueChanged()
-    {
-      if(redundancy==null)
-        return;
+    ap.idPanel.idCanvas.setHighlighted(redundantSeqs);
+  }
 
-      float value = slider.getValue();
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void applyButton_actionPerformed(ActionEvent e)
+  {
+    Vector del = new Vector();
 
-      for(int i=0; i<redundancy.length; i++)
-      {
-        if (value > redundancy[i])
-          redundantSeqs.remove(originalSequences[i]);
-        else if(!redundantSeqs.contains(originalSequences[i]))
-          redundantSeqs.add(originalSequences[i]);
+    undoButton.setEnabled(true);
 
-      }
+    float value = slider.getValue();
+    SequenceGroup sg = ap.av.getSelectionGroup();
 
-      ap.idPanel.idCanvas.setHighlighted(redundantSeqs);
+    for (int i = 0; i < redundancy.length; i++)
+    {
+      if (value <= redundancy[i])
+      {
+        del.addElement(originalSequences[i]);
+      }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void applyButton_actionPerformed(ActionEvent e)
+    // This has to be done before the restoreHistoryItem method of alignFrame will
+    // actually restore these sequences.
+    if (del.size() > 0)
     {
-        Vector del = new Vector();
-
-        undoButton.setEnabled(true);
-
-        float value = slider.getValue();
-        SequenceGroup sg = ap.av.getSelectionGroup();
+      SequenceI[] deleted = new SequenceI[del.size()];
 
-        for (int i = 0; i < redundancy.length; i++)
+      int width = 0;
+      for (int i = 0; i < del.size(); i++)
+      {
+        deleted[i] = (SequenceI) del.elementAt(i);
+        if (deleted[i].getLength() > width)
         {
-          if (value <= redundancy[i])
-          {
-            del.addElement(originalSequences[i]);
-          }
+          width = deleted[i].getLength();
         }
+      }
 
-        // This has to be done before the restoreHistoryItem method of alignFrame will
-        // actually restore these sequences.
-        if (del.size() > 0)
+      EditCommand cut = new EditCommand("Remove Redundancy",
+                                        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);
+        if (sg != null)
         {
-          SequenceI [] deleted = new SequenceI[del.size()];
-
-          int width = 0;
-          for (int i = 0; i < del.size(); i++)
-          {
-            deleted[i] = (SequenceI)del.elementAt(i);
-            if(deleted[i].getLength()>width)
-              width = deleted[i].getLength();
-          }
-
-          EditCommand cut = new EditCommand("Remove Redundancy",
-              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);
-            if (sg != null)
-            {
-              sg.deleteSequence(deleted[i], false);
-            }
-          }
-
-          historyList.push(cut);
-
-          ap.alignFrame.addHistoryItem(cut);
-
-          ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences());
+          sg.deleteSequence(deleted[i], false);
         }
+      }
 
+      historyList.push(cut);
 
+      ap.alignFrame.addHistoryItem(cut);
+
+      ap.av.firePropertyChange("alignment", null,
+                               ap.av.getAlignment().getSequences());
     }
 
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void undoButton_actionPerformed(ActionEvent e)
-    {
-      CommandI command = (CommandI) historyList.pop();
-      command.undoCommand();
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void undoButton_actionPerformed(ActionEvent e)
+  {
+    CommandI command = (CommandI) historyList.pop();
+    command.undoCommand();
 
-      if (ap.av.historyList.contains(command))
-      {
-        ap.av.historyList.remove(command);
-        af.updateEditMenuBar();
-      }
+    if (ap.av.historyList.contains(command))
+    {
+      ap.av.historyList.remove(command);
+      af.updateEditMenuBar();
+    }
 
-      ap.repaint();
+    ap.repaint();
 
-      if (historyList.size() == 0)
-      {
-        undoButton.setEnabled(false);
-      }
+    if (historyList.size() == 0)
+    {
+      undoButton.setEnabled(false);
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void valueField_actionPerformed(ActionEvent e)
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void valueField_actionPerformed(ActionEvent e)
+  {
+    try
     {
-        try
-        {
-            int i = Integer.parseInt(valueField.getText());
-            slider.setValue(i);
-        }
-        catch (Exception ex)
-        {
-            valueField.setText(slider.getValue() + "");
-        }
+      int i = Integer.parseInt(valueField.getText());
+      slider.setValue(i);
     }
-
+    catch (Exception ex)
+    {
+      valueField.setText(slider.getValue() + "");
+    }
+  }
 
 }
diff --git a/src/jalview/gui/RotatableCanvas.java b/src/jalview/gui/RotatableCanvas.java
index 5a963ec..32c4adc 100755
--- a/src/jalview/gui/RotatableCanvas.java
+++ b/src/jalview/gui/RotatableCanvas.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,17 +18,14 @@
  */
 package jalview.gui;
 
-import jalview.datamodel.*;
-
-import jalview.math.*;
+import java.util.*;
 
 import java.awt.*;
 import java.awt.event.*;
-
-import java.util.*;
-
 import javax.swing.*;
 
+import jalview.datamodel.*;
+import jalview.math.*;
 
 /**
  * DOCUMENT ME!
@@ -36,736 +33,737 @@ import javax.swing.*;
  * @author $author$
  * @version $Revision$
  */
-public class RotatableCanvas extends JPanel implements MouseListener,
+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)
+  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()
     {
-      this.av = ap.av;
-      this.ap = ap;
-
-      addMouseWheelListener(new MouseWheelListener()
+      public void mouseWheelMoved(MouseWheelEvent e)
       {
-        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++)
+        if (e.getWheelRotation() > 0)
         {
-            SequencePoint sp = (SequencePoint) points.elementAt(i);
-
-            for (int j = 0; j < 3; j++)
-            {
-                orig[i][j] = sp.coord[j];
-            }
+          scale = (float) (scale * 1.1);
+          repaint();
         }
 
-        //Initialize the matrices to identity
-        for (int i = 0; i < 3; i++)
+        else
         {
-            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);
-                }
-            }
+          scale = (float) (scale * 0.9);
+          repaint();
         }
+      }
+    });
 
-        axes = new float[3][3];
-        initAxes();
+  }
 
-        findCentre();
-        findWidth();
+  public void showLabels(boolean b)
+  {
+    showLabels = b;
+    repaint();
+  }
 
-        scale = findScale();
+  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);
 
-        addMouseListener(this);
+    prefsize = getPreferredSize();
+    orig = new float[npoint][3];
 
-        addMouseMotionListener(this);
+    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];
+      }
     }
 
-    public void initAxes()
+    //Initialize the matrices to identity
+    for (int i = 0; i < 3; i++)
     {
-        for (int i = 0; i < 3; i++)
+      for (int j = 0; j < 3; j++)
+      {
+        if (i != j)
         {
-            for (int j = 0; j < 3; j++)
-            {
-                if (i != j)
-                {
-                    axes[i][j] = 0;
-                }
-                else
-                {
-                    axes[i][j] = 1;
-                }
-            }
+          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);
+        }
+      }
     }
 
-    /**
-     * DOCUMENT ME!
-     */
-    public void findWidth()
-    {
-        max = new float[3];
-        min = new float[3];
+    axes = new float[3][3];
+    initAxes();
 
-        max[0] = (float) -1e30;
-        max[1] = (float) -1e30;
-        max[2] = (float) -1e30;
+    findCentre();
+    findWidth();
 
-        min[0] = (float) 1e30;
-        min[1] = (float) 1e30;
-        min[2] = (float) 1e30;
+    scale = findScale();
 
-        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];
-                }
-            }
-        }
+    addMouseListener(this);
 
-        //    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]);
+    addMouseMotionListener(this);
 
-        maxwidth = width[0];
+  }
 
-        if (width[1] > width[0])
+  public void initAxes()
+  {
+    for (int i = 0; i < 3; i++)
+    {
+      for (int j = 0; j < 3; j++)
+      {
+        if (i != j)
         {
-            maxwidth = width[1];
+          axes[i][j] = 0;
         }
-
-        if (width[2] > width[1])
+        else
         {
-            maxwidth = width[2];
+          axes[i][j] = 1;
         }
-
-        //System.out.println("Maxwidth = " + maxwidth);
+      }
     }
+  }
+
+  /**
+   * 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;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public float findScale()
+    min[0] = (float) 1e30;
+    min[1] = (float) 1e30;
+    min[2] = (float) 1e30;
+
+    for (int i = 0; i < 3; i++)
     {
-        int dim;
-        int width;
-        int height;
+      for (int j = 0; j < npoint; j++)
+      {
+        SequencePoint sp = (SequencePoint) points.elementAt(j);
 
-        if (getWidth() != 0)
-        {
-            width = getWidth();
-            height = getHeight();
-        }
-        else
+        if (sp.coord[i] >= max[i])
         {
-            width = prefsize.width;
-            height = prefsize.height;
+          max[i] = sp.coord[i];
         }
 
-        if (width < height)
-        {
-            dim = width;
-        }
-        else
+        if (sp.coord[i] <= min[i])
         {
-            dim = height;
+          min[i] = sp.coord[i];
         }
-
-        return (float) ((dim * scalefactor) / (2 * maxwidth));
+      }
     }
 
-    /**
-     * DOCUMENT ME!
-     */
-    public void findCentre()
-    {
-        //Find centre coordinate
-        findWidth();
+    //    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]);
 
-        centre[0] = (max[0] + min[0]) / 2;
-        centre[1] = (max[1] + min[1]) / 2;
-        centre[2] = (max[2] + min[2]) / 2;
+    maxwidth = width[0];
 
-        //    System.out.println("Centre x " + centre[0]);
-        //System.out.println("Centre y " + centre[1]);
-        //System.out.println("Centre z " + centre[2]);
+    if (width[1] > width[0])
+    {
+      maxwidth = width[1];
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Dimension getPreferredSize()
+    if (width[2] > width[1])
     {
-        if (prefsize != null)
-        {
-            return prefsize;
-        }
-        else
-        {
-            return new Dimension(400, 400);
-        }
+      maxwidth = width[2];
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Dimension getMinimumSize()
+    //System.out.println("Maxwidth = " + maxwidth);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public float findScale()
+  {
+    int dim;
+    int width;
+    int height;
+
+    if (getWidth() != 0)
     {
-        return getPreferredSize();
+      width = getWidth();
+      height = getHeight();
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param g DOCUMENT ME!
-     */
-    public void paintComponent(Graphics g1)
+    else
     {
+      width = prefsize.width;
+      height = prefsize.height;
+    }
 
-      Graphics2D g = (Graphics2D) g1;
+    if (width < height)
+    {
+      dim = width;
+    }
+    else
+    {
+      dim = height;
+    }
 
-      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
+    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()))
       {
-        //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();
-        }
+        prefsize.width = getWidth();
+        prefsize.height = getHeight();
 
+        scale = findScale();
 
-        drawBackground(ig, bgColour);
-        drawScene(ig);
+        //      System.out.println("New scale = " + scale);
+        img = createImage(getWidth(), getHeight());
+        ig = img.getGraphics();
+      }
 
-        if (drawAxes == true)
-        {
-          drawAxes(ig);
-        }
+      drawBackground(ig, bgColour);
+      drawScene(ig);
 
-        g.drawImage(img, 0, 0, this);
+      if (drawAxes == true)
+      {
+        drawAxes(ig);
       }
-    }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param g DOCUMENT ME!
-     */
-    public void drawAxes(Graphics g)
-    {
+      g.drawImage(img, 0, 0, this);
+    }
+  }
 
-        g.setColor(Color.yellow);
+  /**
+   * DOCUMENT ME!
+   *
+   * @param g DOCUMENT ME!
+   */
+  public void drawAxes(Graphics g)
+  {
 
-        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)));
-        }
-    }
+    g.setColor(Color.yellow);
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param g DOCUMENT ME!
-     * @param col DOCUMENT ME!
-     */
-    public void drawBackground(Graphics g, Color col)
+    for (int i = 0; i < 3; i++)
     {
-        g.setColor(col);
-        g.fillRect(0, 0, prefsize.width, prefsize.height);
+      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!
-     */
-    public void drawScene(Graphics g1)
+  }
+
+  /**
+   * 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));
+      }
 
-      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++)
+      if (av.getSelectionGroup() != null)
+      {
+        if (av.getSelectionGroup().getSequences(null).contains(
+            ( (SequencePoint) points.elementAt(i)).sequence))
         {
-            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);
-            }
+          g.setColor(Color.gray);
         }
+      }
 
-        //    //Now the rectangle
-        //    if (rectx2 != -1 && recty2 != -1) {
-        //      g.setColor(Color.white);
-        //
-        //      g.drawRect(rectx1,recty1,rectx2-rectx1,recty2-recty1);
-        //    }
-    }
+      if (z < 0)
+      {
+        g.setColor(g.getColor().darker());
+      }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Dimension minimumsize()
-    {
-        return prefsize;
+      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);
+      }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Dimension preferredsize()
+    //    //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)
     {
-        return prefsize;
+      scalefactor = (float) (scalefactor * 1.1);
+      scale = findScale();
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void keyTyped(KeyEvent evt)
+    else if (evt.getKeyCode() == KeyEvent.VK_DOWN)
     {
+      scalefactor = (float) (scalefactor * 0.9);
+      scale = findScale();
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void keyReleased(KeyEvent evt)
+    else if (evt.getKeyChar() == 's')
     {
+      System.err.println("DEBUG: Rectangle selection"); // log.debug
+
+      if ( (rectx2 != -1) && (recty2 != -1))
+      {
+        rectSelect(rectx1, recty1, rectx2, recty2);
+      }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void keyPressed(KeyEvent evt)
+    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)
     {
-        if (evt.getKeyCode() == KeyEvent.VK_UP)
-        {
-            scalefactor = (float) (scalefactor * 1.1);
-            scale = findScale();
-        }
-        else if (evt.getKeyCode() == KeyEvent.VK_DOWN)
+      AlignmentPanel[] aps = getAssociatedPanels();
+
+      for (int a = 0; a < aps.length; a++)
+      {
+        if (aps[a].av.getSelectionGroup() != null)
         {
-            scalefactor = (float) (scalefactor * 0.9);
-            scale = findScale();
+          aps[a].av.getSelectionGroup().addOrRemove(found, true);
         }
-        else if (evt.getKeyChar() == 's')
+        else
         {
-            System.err.println("DEBUG: Rectangle selection"); // log.debug
-
-            if ((rectx2 != -1) && (recty2 != -1))
-            {
-                rectSelect(rectx1, recty1, rectx2, recty2);
-            }
+          aps[a].av.setSelectionGroup(new SequenceGroup());
+          aps[a].av.getSelectionGroup().addOrRemove(found, true);
+          aps[a].av.getSelectionGroup().setEndRes(
+              aps[a].av.alignment.getWidth() - 1);
         }
+      }
 
-        repaint();
+      PaintRefresher.Refresh(this, av.getSequenceSetId());
     }
 
+    repaint();
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mouseClicked(MouseEvent evt)
-    {
-    }
+  // private void fireSequenceSelectionEvent(Selection sel) {
+  //   controller.handleSequenceSelectionEvent(new SequenceSelectionEvent(this,sel));
+  //}
+  public void mouseMoved(MouseEvent evt)
+  {
+    SequenceI found = findPoint(evt.getX(), evt.getY());
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mouseEntered(MouseEvent evt)
+    if (found != null)
     {
+      this.setToolTipText(found.getName());
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mouseExited(MouseEvent evt)
+    else
     {
+      this.setToolTipText(null);
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mouseReleased(MouseEvent evt)
+  }
+
+  /**
+   * 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();
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mousePressed(MouseEvent evt)
+    else
     {
-        int x = evt.getX();
-        int y = evt.getY();
-
-        mx = x;
-        my = y;
+      rotmat.setIdentity();
 
-        omx = mx;
-        omy = my;
+      rotmat.rotate( (float) (my - omy), 'x');
+      rotmat.rotate( (float) (mx - omx), 'y');
 
-        startx = x;
-        starty = 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];
+      }
 
-        rectx1 = x;
-        recty1 = y;
+      for (int i = 0; i < 3; i++)
+      {
+        axes[i] = rotmat.vectorMultiply(axes[i]);
+      }
 
-        rectx2 = -1;
-        recty2 = -1;
+      omx = mx;
+      omy = my;
 
-        SequenceI found = findPoint(x, y);
+      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 (found != null)
+      if ( (tmp1 > x1) && (tmp1 < x2) && (tmp2 > y1) && (tmp2 < y2))
+      {
+        if (av != null)
         {
-          AlignmentPanel[] aps = getAssociatedPanels();
-
-          for (int a = 0; a < aps.length; a++)
+          if (!av.getSelectionGroup().getSequences(null).contains(sp.sequence))
           {
-            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);
-            }
+            av.getSelectionGroup().addSequence(sp.sequence, true);
           }
-
-          PaintRefresher.Refresh(this, av.getSequenceSetId());
         }
-
-        repaint();
+      }
     }
 
-    // private void fireSequenceSelectionEvent(Selection sel) {
-    //   controller.handleSequenceSelectionEvent(new SequenceSelectionEvent(this,sel));
-    //}
-    public void mouseMoved(MouseEvent evt)
+    // 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++)
     {
-        SequenceI found = findPoint(evt.getX(), evt.getY());
+      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 (found != null)
-        {
-            this.setToolTipText(found.getName());
-        }
-        else
-        {
-            this.setToolTipText(null);
-        }
+      if ( (Math.abs(px - x) < 3) && (Math.abs(py - y) < 3))
+      {
+        found = i;
+      }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mouseDragged(MouseEvent evt)
+    if (found != -1)
     {
-        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());
-        }
+      return ( (SequencePoint) points.elementAt(found)).sequence;
     }
-
-    /**
-     * 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)
+    else
     {
-        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());
-        // }
+      return null;
     }
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param x DOCUMENT ME!
-     * @param y DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public SequenceI findPoint(int x, int y)
+  AlignmentPanel[] getAssociatedPanels()
+  {
+    if (applyToAllViews)
     {
-        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;
-        }
+      return PaintRefresher.getAssociatedPanels(av.getSequenceSetId());
     }
-
-    AlignmentPanel[] getAssociatedPanels()
+    else
     {
-      if (applyToAllViews)
-      {
-        return PaintRefresher.getAssociatedPanels(av.getSequenceSetId());
-      }
-      else
-        return new AlignmentPanel[]
-            { ap };
+      return new AlignmentPanel[]
+          {
+          ap};
     }
+  }
 }
diff --git a/src/jalview/gui/ScalePanel.java b/src/jalview/gui/ScalePanel.java
index 32283ce..ebf25bf 100755
--- a/src/jalview/gui/ScalePanel.java
+++ b/src/jalview/gui/ScalePanel.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,13 +18,11 @@
  */
 package jalview.gui;
 
-import jalview.datamodel.*;
-
 import java.awt.*;
 import java.awt.event.*;
-
 import javax.swing.*;
 
+import jalview.datamodel.*;
 
 /**
  * DOCUMENT ME!
@@ -32,420 +30,451 @@ import javax.swing.*;
  * @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
-    boolean mouseDragging = false;
-
-    // wants to delete columns
-    public ScalePanel(AlignViewport av, AlignmentPanel ap)
+  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
+  boolean mouseDragging = false;
+
+  // wants to delete columns
+  public ScalePanel(AlignViewport av, AlignmentPanel ap)
+  {
+    this.av = av;
+    this.ap = ap;
+
+    addMouseListener(this);
+    addMouseMotionListener(this);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void mousePressed(MouseEvent evt)
+  {
+    int x = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+    final int res;
+
+    if (av.hasHiddenColumns)
     {
-        this.av = av;
-        this.ap = ap;
-
-        addMouseListener(this);
-        addMouseMotionListener(this);
+      res = av.getColumnSelection().adjustForHiddenColumns(x);
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mousePressed(MouseEvent evt)
+    else
     {
-        int x = (evt.getX() / av.getCharWidth()) + av.getStartRes();
-        final int res;
-
-        if(av.hasHiddenColumns)
-          res = av.getColumnSelection().adjustForHiddenColumns(x);
-        else
-          res = x;
+      res = x;
+    }
 
-        min = res;
-        max = res;
+    min = res;
+    max = res;
 
-        if (SwingUtilities.isRightMouseButton(evt))
+    if (SwingUtilities.isRightMouseButton(evt))
+    {
+      JPopupMenu pop = new JPopupMenu();
+      if (reveal != null)
+      {
+        JMenuItem item = new JMenuItem("Reveal");
+        item.addActionListener(new ActionListener()
         {
-          JPopupMenu pop = new JPopupMenu();
-          if (reveal != null)
+          public void actionPerformed(ActionEvent e)
           {
-            JMenuItem item = new JMenuItem("Reveal");
-            item.addActionListener(new ActionListener()
-            {
-              public void actionPerformed(ActionEvent e)
-              {
-                av.showColumn(reveal[0]);
-                reveal = null;
-                ap.repaint();
-                if (ap.overviewPanel != null)
-                  ap.overviewPanel.updateOverviewImage();
-              }
-            });
-            pop.add(item);
-
-            if (av.getColumnSelection().getHiddenColumns().size() > 1)
+            av.showColumn(reveal[0]);
+            reveal = null;
+            ap.repaint();
+            if (ap.overviewPanel != null)
             {
-              item = new JMenuItem("Reveal All");
-              item.addActionListener(new ActionListener()
-              {
-                public void actionPerformed(ActionEvent e)
-                {
-                  av.showAllHiddenColumns();
-                  reveal = null;
-                  ap.repaint();
-                  if (ap.overviewPanel != null)
-                    ap.overviewPanel.updateOverviewImage();
-                }
-              });
-              pop.add(item);
+              ap.overviewPanel.updateOverviewImage();
             }
-            pop.show(this, evt.getX(), evt.getY());
           }
-          else if (av.getColumnSelection().contains(res))
+        });
+        pop.add(item);
+
+        if (av.getColumnSelection().getHiddenColumns().size() > 1)
+        {
+          item = new JMenuItem("Reveal All");
+          item.addActionListener(new ActionListener()
           {
-            JMenuItem item = new JMenuItem("Hide Columns");
-            item.addActionListener(new ActionListener()
+            public void actionPerformed(ActionEvent e)
             {
-              public void actionPerformed(ActionEvent e)
+              av.showAllHiddenColumns();
+              reveal = null;
+              ap.repaint();
+              if (ap.overviewPanel != null)
               {
-                av.hideColumns(res, res);
-                if(av.getSelectionGroup()!=null
-                   && av.getSelectionGroup().getSize()==av.alignment.getHeight())
-                  av.setSelectionGroup(null);
-
-                ap.repaint();
-                if (ap.overviewPanel != null)
-                  ap.overviewPanel.updateOverviewImage();
+                ap.overviewPanel.updateOverviewImage();
               }
-            });
-            pop.add(item);
-            pop.show(this, evt.getX(), evt.getY());
-          }
+            }
+          });
+          pop.add(item);
         }
-        else // LEFT MOUSE TO SELECT
+        pop.show(this, evt.getX(), evt.getY());
+      }
+      else if (av.getColumnSelection().contains(res))
+      {
+        JMenuItem item = new JMenuItem("Hide Columns");
+        item.addActionListener(new ActionListener()
         {
-          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++)
+          public void actionPerformed(ActionEvent e)
           {
-            sg.addSequence(av.alignment.getSequenceAt(i), false);
-          }
-
-          sg.setStartRes(res);
-          sg.setEndRes(res);
-          av.setSelectionGroup(sg);
+            av.hideColumns(res, res);
+            if (av.getSelectionGroup() != null
+                && av.getSelectionGroup().getSize() == av.alignment.getHeight())
+            {
+              av.setSelectionGroup(null);
+            }
 
-          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++)
+            ap.repaint();
+            if (ap.overviewPanel != null)
             {
-                av.getColumnSelection().addElement(i);
+              ap.overviewPanel.updateOverviewImage();
             }
-            sg.setStartRes(min);
-            sg.setEndRes(max);
           }
-
-
-        }
-
-
-        ap.repaint();
+        });
+        pop.add(item);
+        pop.show(this, evt.getX(), evt.getY());
+      }
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mouseReleased(MouseEvent evt)
+    else // LEFT MOUSE TO SELECT
     {
-        mouseDragging = false;
+      if (!evt.isControlDown() && !evt.isShiftDown())
+      {
+        av.getColumnSelection().clear();
+      }
 
-        int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+      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(res> av.alignment.getWidth())
+      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++)
         {
-          res = av.alignment.getWidth()-1;
+          av.getColumnSelection().addElement(i);
         }
+        sg.setStartRes(min);
+        sg.setEndRes(max);
+      }
 
-        if(av.hasHiddenColumns)
-          res = av.getColumnSelection().adjustForHiddenColumns(res);
+    }
 
-        if (!stretchingGroup)
-        {
-            ap.repaint();
+    ap.repaint();
+  }
 
-            return;
-        }
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void mouseReleased(MouseEvent evt)
+  {
+    mouseDragging = false;
 
-        SequenceGroup sg = av.getSelectionGroup();
+    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
 
-        if(sg!=null){
-          if (res > sg.getStartRes())
-          {
-            sg.setEndRes(res);
-          }
-          else if (res < sg.getStartRes())
-          {
-            sg.setStartRes(res);
-          }
-        }
-        stretchingGroup = false;
-        ap.repaint();
+    if (res > av.alignment.getWidth())
+    {
+      res = av.alignment.getWidth() - 1;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mouseDragged(MouseEvent evt)
+    if (av.hasHiddenColumns)
     {
-        mouseDragging = true;
-
-        int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
-        if(res<0)
-          res = 0;
+      res = av.getColumnSelection().adjustForHiddenColumns(res);
+    }
 
-        if(av.hasHiddenColumns)
-          res = av.getColumnSelection().adjustForHiddenColumns(res);
+    if (!stretchingGroup)
+    {
+      ap.repaint();
 
+      return;
+    }
 
-        if(res> av.alignment.getWidth())
-        {
-          res = av.alignment.getWidth()-1;
-        }
+    SequenceGroup sg = av.getSelectionGroup();
 
-        if (res < min)
-        {
-            min = res;
-        }
+    if (sg != null)
+    {
+      if (res > sg.getStartRes())
+      {
+        sg.setEndRes(res);
+      }
+      else if (res < sg.getStartRes())
+      {
+        sg.setStartRes(res);
+      }
+    }
+    stretchingGroup = false;
+    ap.repaint();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void mouseDragged(MouseEvent evt)
+  {
+    mouseDragging = true;
+
+    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+    if (res < 0)
+    {
+      res = 0;
+    }
 
-        if (res > max)
-        {
-            max = res;
-        }
+    if (av.hasHiddenColumns)
+    {
+      res = av.getColumnSelection().adjustForHiddenColumns(res);
+    }
 
+    if (res > av.alignment.getWidth())
+    {
+      res = av.alignment.getWidth() - 1;
+    }
 
+    if (res < min)
+    {
+      min = res;
+    }
 
-        SequenceGroup sg = av.getSelectionGroup();
+    if (res > max)
+    {
+      max = res;
+    }
 
-        if (sg != null)
-        {
-            stretchingGroup = true;
+    SequenceGroup sg = av.getSelectionGroup();
 
-            if (!av.getColumnSelection().contains(res))
-            {
-                av.getColumnSelection().addElement(res);
-            }
+    if (sg != null)
+    {
+      stretchingGroup = true;
 
-            if (res > sg.getStartRes())
-            {
-                sg.setEndRes(res);
-            }
-            if (res < sg.getStartRes())
-            {
-                sg.setStartRes(res);
-            }
+      if (!av.getColumnSelection().contains(res))
+      {
+        av.getColumnSelection().addElement(res);
+      }
 
-            for (int i = min; i <= max; i++)
-            {
-                if ((i < sg.getStartRes()) || (i > sg.getEndRes()))
-                {
-                    av.getColumnSelection().removeElement(i);
-                }
-                else
-                {
-                    av.getColumnSelection().addElement(i);
-                }
-            }
+      if (res > sg.getStartRes())
+      {
+        sg.setEndRes(res);
+      }
+      if (res < sg.getStartRes())
+      {
+        sg.setStartRes(res);
+      }
 
-            ap.repaint();
+      for (int i = min; i <= max; i++)
+      {
+        if ( (i < sg.getStartRes()) || (i > sg.getEndRes()))
+        {
+          av.getColumnSelection().removeElement(i);
         }
+        else
+        {
+          av.getColumnSelection().addElement(i);
+        }
+      }
+
+      ap.repaint();
     }
+  }
 
-    public void mouseEntered(MouseEvent evt)
+  public void mouseEntered(MouseEvent evt)
+  {
+    if (mouseDragging)
     {
-      if(mouseDragging)
-        ap.seqPanel.scrollCanvas(null);
+      ap.seqPanel.scrollCanvas(null);
     }
+  }
 
-    public void mouseExited(MouseEvent evt)
+  public void mouseExited(MouseEvent evt)
+  {
+    if (mouseDragging)
     {
-      if(mouseDragging)
-        ap.seqPanel.scrollCanvas(evt);
+      ap.seqPanel.scrollCanvas(evt);
     }
+  }
 
-    public void mouseClicked(MouseEvent evt){}
+  public void mouseClicked(MouseEvent evt)
+  {}
 
-    public void mouseMoved(MouseEvent evt)
+  public void mouseMoved(MouseEvent evt)
+  {
+    if (!av.hasHiddenColumns)
     {
-      if(!av.hasHiddenColumns)
-        return;
+      return;
+    }
 
-      int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
 
-      res = av.getColumnSelection().adjustForHiddenColumns(res);
+    res = av.getColumnSelection().adjustForHiddenColumns(res);
 
-      reveal = null;
-      for(int i=0; i<av.getColumnSelection().getHiddenColumns().size(); i++)
+    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])
       {
-        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");
-          break;
-        }
-        else
-          this.setToolTipText(null);
-
+        reveal = region;
+        ToolTipManager.sharedInstance().registerComponent(this);
+        this.setToolTipText("Reveal Hidden Columns with Right Mouse Button");
+        break;
+      }
+      else
+      {
+        this.setToolTipText(null);
       }
 
-      repaint();
     }
 
-    int [] reveal;
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param g DOCUMENT ME!
-     */
-    public void paintComponent(Graphics g)
+    repaint();
+  }
+
+  int[] reveal;
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param g DOCUMENT ME!
+   */
+  public void paintComponent(Graphics g)
+  {
+    drawScale(g, av.getStartRes(), av.getEndRes(), getWidth(), getHeight());
+  }
+
+  // scalewidth will normally be screenwidth,
+  public void drawScale(Graphics g, int startx, int endx, int width,
+                        int height)
+  {
+    Graphics2D gg = (Graphics2D) g;
+    gg.setFont(av.getFont());
+
+    if (av.antiAlias)
     {
-        drawScale(g, av.getStartRes(), av.getEndRes(), getWidth(), getHeight());
+      gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+                          RenderingHints.VALUE_ANTIALIAS_ON);
     }
 
-    // scalewidth will normally be screenwidth,
-    public void drawScale(Graphics g, int startx, int endx, int width,
-        int height)
-    {
-        Graphics2D gg = (Graphics2D) g;
-        gg.setFont(av.getFont());
-
-        if(av.antiAlias)
-          gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
-                              RenderingHints.VALUE_ANTIALIAS_ON);
+    //Fill in the background
+    gg.setColor(Color.white);
+    gg.fillRect(0, 0, width, height);
+    gg.setColor(Color.black);
 
-        //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));
 
-        //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);
+    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,
+      if ( (sel >= startx) && (sel <= endx))
+      {
+        gg.fillRect( (sel - startx) * av.charWidth, 0, av.charWidth,
                     getHeight());
-            }
-        }
+      }
+    }
 
-        // Draw the scale numbers
-        gg.setColor(Color.black);
+    // Draw the scale numbers
+    gg.setColor(Color.black);
 
-        int scalestartx = (startx / 10) * 10;
+    int scalestartx = (startx / 10) * 10;
 
-        FontMetrics fm = gg.getFontMetrics(av.getFont());
-        int y = av.charHeight - fm.getDescent();
+    FontMetrics fm = gg.getFontMetrics(av.getFont());
+    int y = av.charHeight - fm.getDescent();
 
-        if ((scalestartx % 10) == 0)
-        {
-            scalestartx += 5;
-        }
+    if ( (scalestartx % 10) == 0)
+    {
+      scalestartx += 5;
+    }
 
-        String string;
-        int maxX=0;
+    String string;
+    int maxX = 0;
 
-        for (int i = scalestartx; i < endx; i += 5)
+    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)
         {
-            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));
-            }
+          gg.drawString(string,
+                        (i - startx - 1) * av.charWidth, y);
+          maxX = (i - startx + 1) * av.charWidth + fm.stringWidth(string);
         }
 
-        if (av.hasHiddenColumns)
-        {
-          gg.setColor(Color.blue);
-          int res;
-          if(av.getShowHiddenMarkers())
-          {
-            for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size();
-                 i++)
-            {
+        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));
 
-              res = av.getColumnSelection().findHiddenRegionPosition(i) -
-                  startx;
-
-              if(res < 0 || res > endx-scalestartx)
-                continue;
+      }
+      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.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 (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 (reveal != null && reveal[0] > startx && reveal[0] < endx)
+          if (res < 0 || res > endx - scalestartx)
           {
-            gg.drawString("Reveal Columns", reveal[0] * av.charWidth, 0);
+            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/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 45bcf66..6a41772 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,13 +18,11 @@
  */
 package jalview.gui;
 
-import jalview.datamodel.*;
-
 import java.awt.*;
 import java.awt.image.*;
-
 import javax.swing.*;
 
+import jalview.datamodel.*;
 
 /**
  * DOCUMENT ME!
@@ -32,878 +30,908 @@ import javax.swing.*;
  * @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!
-     */
-    public SeqCanvas(AlignViewport av)
+  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!
+   */
+  public SeqCanvas(AlignViewport av)
+  {
+    this.av = av;
+    fr = new FeatureRenderer(av);
+    sr = new SequenceRenderer(av);
+    setLayout(new BorderLayout());
+    PaintRefresher.Register(this, av.getSequenceSetId());
+    setBackground(Color.white);
+  }
+
+  MCview.PDBCanvas pdbCanvas;
+  public SequenceRenderer getSequenceRenderer()
+  {
+    return sr;
+  }
+
+  public FeatureRenderer getFeatureRenderer()
+  {
+    return fr;
+  }
+
+  public void setPDBCanvas(MCview.PDBCanvas pc)
+  {
+    pdbCanvas = pc;
+  }
+
+  public AlignViewport getViewport()
+  {
+    return av;
+  }
+
+  /**
+   * 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)
+  {
+    int scalestartx = startx - (startx % 10) + 10;
+
+    g.setColor(Color.black);
+
+    // NORTH SCALE
+    for (int i = scalestartx; i < endx; i += 10)
     {
-        this.av = av;
-        fr = new FeatureRenderer(av);
-        sr = new SequenceRenderer(av);
-        setLayout(new BorderLayout());
-        PaintRefresher.Register(this, av.getSequenceSetId());
-        setBackground(Color.white);
-    }
+      int value = i;
+      if (av.hasHiddenColumns)
+      {
+        value = av.getColumnSelection().adjustForHiddenColumns(value);
+      }
 
-    MCview.PDBCanvas pdbCanvas;
-    public SequenceRenderer getSequenceRenderer()
-    {
-      return sr;
-    }
+      g.drawString(String.valueOf(value), (i - startx - 1) * av.charWidth,
+                   ypos - (av.charHeight / 2));
 
-    public FeatureRenderer getFeatureRenderer()
-    {
-      return fr;
+      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);
     }
-
-    public void setPDBCanvas(MCview.PDBCanvas pc)
+  }
+
+  /**
+   * 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)
+  {
+    FontMetrics fm = getFontMetrics(av.getFont());
+    ypos += av.charHeight;
+
+    if (av.hasHiddenColumns)
     {
-      pdbCanvas = pc;
+      startx = av.getColumnSelection().adjustForHiddenColumns(startx);
+      endx = av.getColumnSelection().adjustForHiddenColumns(endx);
     }
 
-    public AlignViewport getViewport()
+    int maxwidth = av.alignment.getWidth();
+    if (av.hasHiddenColumns)
     {
-      return av;
+      maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
     }
 
-
-    /**
-     * 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)
+    // WEST SCALE
+    for (int i = 0; i < av.alignment.getHeight(); i++)
     {
-        int scalestartx = startx - (startx % 10) + 10;
-
-        g.setColor(Color.black);
+      SequenceI seq = av.alignment.getSequenceAt(i);
+      int index = startx;
+      int value = -1;
 
-        // NORTH SCALE
-        for (int i = scalestartx; i < endx; i += 10)
+      while (index < endx)
+      {
+        if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
         {
-            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));
+          index++;
 
-            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);
+          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));
+      }
+    }
+  }
+
+  /**
+   * 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)
+  {
+    ypos += av.charHeight;
+
+    if (av.hasHiddenColumns)
+    {
+      endx = av.getColumnSelection().adjustForHiddenColumns(endx);
     }
 
-    /**
-     * 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)
+    SequenceI seq;
+    // EAST SCALE
+    for (int i = 0; i < av.alignment.getHeight(); i++)
     {
-        FontMetrics fm = getFontMetrics(av.getFont());
-        ypos += av.charHeight;
+      seq = av.alignment.getSequenceAt(i);
+      int index = endx;
+      int value = -1;
 
-        if(av.hasHiddenColumns)
+      while (index > startx)
+      {
+        if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
         {
-          startx = av.getColumnSelection().adjustForHiddenColumns(startx);
-          endx = av.getColumnSelection().adjustForHiddenColumns(endx);
+          index--;
+
+          continue;
         }
 
-        int maxwidth = av.alignment.getWidth();
-        if (av.hasHiddenColumns)
-            maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+        value = seq.findPosition(index);
 
-        // WEST SCALE
-        for (int i = 0; i < av.alignment.getHeight(); i++)
-        {
-            SequenceI seq = av.alignment.getSequenceAt(i);
-            int index = startx;
-            int value = -1;
+        break;
+      }
 
-            while (index < endx)
-            {
-                if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
-                {
-                    index++;
+      if (value != -1)
+      {
+        g.drawString(String.valueOf(value), 0,
+                     (ypos + (i * av.charHeight)) - (av.charHeight / 5));
+      }
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param horizontal DOCUMENT ME!
+   * @param vertical DOCUMENT ME!
+   */
+  public void fastPaint(int horizontal, int vertical)
+  {
+    if (gg == null)
+    {
+      return;
+    }
 
-                    continue;
-                }
+    fastPaint = true;
 
-                value = av.alignment.getSequenceAt(i).findPosition(index);
+    gg.copyArea(horizontal * av.charWidth,
+                vertical * av.charHeight,
+                imgWidth,
+                imgHeight,
+                -horizontal * av.charWidth,
+                -vertical * av.charHeight);
 
-                break;
-            }
+    int sr = av.startRes;
+    int er = av.endRes;
+    int ss = av.startSeq;
+    int es = av.endSeq;
+    int transX = 0;
+    int transY = 0;
 
-            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));
-            }
-        }
+    if (horizontal > 0) // scrollbar pulled right, image to the left
+    {
+      er++;
+      transX = (er - sr - horizontal) * av.charWidth;
+      sr = er - horizontal;
     }
-
-    /**
-     * 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)
+    else if (horizontal < 0)
     {
-        ypos += av.charHeight;
-
-        if(av.hasHiddenColumns)
-                endx = av.getColumnSelection().adjustForHiddenColumns(endx);
+      er = sr - horizontal - 1;
+    }
+    else if (vertical > 0) // scroll down
+    {
+      ss = es - vertical;
 
-        SequenceI seq;
-        // EAST SCALE
-        for (int i = 0; i < av.alignment.getHeight(); i++)
-        {
-            seq = av.alignment.getSequenceAt(i);
-            int index = endx;
-            int value = -1;
+      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;
 
-            while (index > startx)
-            {
-                if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
-                {
-                    index--;
+      if (es > av.endSeq)
+      {
+        es = av.endSeq;
+      }
+    }
 
-                    continue;
-                }
+    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.
+   */
+
+  // Set this to false to force a full panel paint
+  public void paintComponent(Graphics g)
+  {
+    super.paintComponent(g);
+
+    if (img != null && (fastPaint
+                        || (getVisibleRect().width != g.getClipBounds().width)
+                        || (getVisibleRect().height != g.getClipBounds().height)))
+    {
+      g.drawImage(img, 0, 0, this);
+      fastPaint = false;
+      return;
+    }
 
-                value = seq.findPosition(index);
+    // this draws the whole of the alignment
+    imgWidth = getWidth();
+    imgHeight = getHeight();
 
-                break;
-            }
+    imgWidth -= (imgWidth % av.charWidth);
+    imgHeight -= (imgHeight % av.charHeight);
 
-            if (value != -1)
-            {
-                g.drawString(String.valueOf(value), 0,
-                    (ypos + (i * av.charHeight)) - (av.charHeight / 5));
-            }
-        }
+    if ( (imgWidth < 1) || (imgHeight < 1))
+    {
+      return;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param horizontal DOCUMENT ME!
-     * @param vertical DOCUMENT ME!
-     */
-    public void fastPaint(int horizontal, int vertical)
+    if (img == null || imgWidth != img.getWidth() || imgHeight != img.getHeight())
     {
-        if (gg == null)
+      try
+      {
+        img = new BufferedImage(imgWidth, imgHeight,
+                                BufferedImage.TYPE_INT_RGB);
+        gg = (Graphics2D) img.getGraphics();
+        gg.setFont(av.getFont());
+      }
+      catch (OutOfMemoryError er)
+      {
+        System.gc();
+        System.out.println(er + " making image, SeqCanvas");
+        javax.swing.SwingUtilities.invokeLater(new Runnable()
         {
-            return;
-        }
+          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);
+          }
+        });
+
+        return;
+      }
+    }
 
+    if (av.antiAlias)
+    {
+      gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+                          RenderingHints.VALUE_ANTIALIAS_ON);
+    }
 
-        fastPaint = true;
+    gg.setColor(Color.white);
+    gg.fillRect(0, 0, imgWidth, imgHeight);
 
-        gg.copyArea(horizontal * av.charWidth,
-                    vertical * av.charHeight,
-                    imgWidth,
-                    imgHeight,
-                    -horizontal * av.charWidth,
-                    -vertical * av.charHeight);
+    if (av.getWrapAlignment())
+    {
+      drawWrappedPanel(gg, getWidth(), getHeight(), av.startRes);
+    }
+    else
+    {
+      drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0);
+    }
 
-        int sr = av.startRes;
-        int er = av.endRes;
-        int ss = av.startSeq;
-        int es = av.endSeq;
-        int transX = 0;
-        int transY = 0;
+    g.drawImage(img, 0, 0, this);
 
+    if (pdbCanvas != null)
+    {
+      pdbCanvas.updateSeqColours();
+    }
 
-        if (horizontal > 0) // scrollbar pulled right, image to the left
-        {
-            er ++;
-            transX = (er - sr - horizontal) * av.charWidth;
-            sr = er - horizontal;
-        }
-        else if (horizontal < 0)
-        {
-            er = sr - horizontal-1;
-        }
-        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;
+  /**
+   * DOCUMENT ME!
+   *
+   * @param cwidth DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public int getWrappedCanvasWidth(int cwidth)
+  {
+    FontMetrics fm = getFontMetrics(av.getFont());
 
-            if (es > av.endSeq)
-            {
-                es = av.endSeq;
-            }
-        }
+    LABEL_EAST = 0;
+    LABEL_WEST = 0;
 
-        gg.translate(transX, transY);
-        drawPanel(gg, sr, er, ss, es, 0);
-        gg.translate(-transX, -transY);
+    if (av.scaleRightWrapped)
+    {
+      LABEL_EAST = fm.stringWidth(getMask());
+    }
 
-        repaint();
+    if (av.scaleLeftWrapped)
+    {
+      LABEL_WEST = fm.stringWidth(getMask());
     }
 
-    /**
-     * 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.
-     */
+    return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
+  }
+
+  /**
+   * Generates a string of zeroes.
+   * @return String
+   */
+  String getMask()
+  {
+    String mask = "00";
+    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;
+      }
+    }
 
-    // Set this to false to force a full panel paint
-    public void paintComponent(Graphics g)
+    for (int i = maxWidth; i > 0; i /= 10)
     {
-        super.paintComponent(g);
+      mask += "0";
+    }
+    return mask;
+  }
+
+  /**
+   * 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)
+  {
+    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;
+    }
 
-        if ( img != null && (fastPaint
-             || (getVisibleRect().width != g.getClipBounds().width)
-             || (getVisibleRect().height != g.getClipBounds().height)))
-        {
-            g.drawImage(img, 0, 0, this);
-            fastPaint = false;
-            return;
-        }
+    int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
+    int cHeight = av.getAlignment().getHeight() * av.charHeight;
 
+    av.setWrappedWidth(cWidth);
 
-        // this draws the whole of the alignment
-        imgWidth = getWidth();
-        imgHeight = getHeight();
+    av.endRes = av.startRes + cWidth;
 
-        imgWidth -= (imgWidth % av.charWidth);
-        imgHeight -= (imgHeight % av.charHeight);
+    int endx;
+    int ypos = hgap;
+    int maxwidth = av.alignment.getWidth() - 1;
 
-        if ((imgWidth < 1) || (imgHeight < 1))
-        {
-            return;
-        }
+    if (av.hasHiddenColumns)
+    {
+      maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+    }
 
-        if (img == null || imgWidth != img.getWidth() || imgHeight != img.getHeight())
-        {
-          try{
-            img = new BufferedImage(imgWidth, imgHeight,
-                                    BufferedImage.TYPE_INT_RGB);
-            gg = (Graphics2D) img.getGraphics();
-            gg.setFont(av.getFont());
-          }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);
-              }
-            });
+    while ( (ypos <= canvasHeight) && (startRes < maxwidth))
+    {
+      endx = startRes + cWidth - 1;
 
-            return;
-          }
-        }
+      if (endx > maxwidth)
+      {
+        endx = maxwidth;
+      }
 
-        if (av.antiAlias)
-          gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
-                              RenderingHints.VALUE_ANTIALIAS_ON);
+      g.setFont(av.getFont());
+      g.setColor(Color.black);
 
-        gg.setColor(Color.white);
-        gg.fillRect(0, 0, imgWidth, imgHeight);
+      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);
+      }
 
-        if (av.getWrapAlignment())
-        {
-            drawWrappedPanel(gg, getWidth(), getHeight(), av.startRes);
-        }
-        else
-        {
-            drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0);
-        }
+      g.translate(LABEL_WEST, 0);
 
-        g.drawImage(img, 0, 0, this);
+      if (av.scaleAboveWrapped)
+      {
+        drawNorthScale(g, startRes, endx, ypos);
+      }
 
-        if (pdbCanvas != null)
+      if (av.hasHiddenColumns && av.showHiddenMarkers)
+      {
+        g.setColor(Color.blue);
+        int res;
+        for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size();
+             i++)
         {
-           pdbCanvas.updateSeqColours();
-        }
+          res = av.getColumnSelection().findHiddenRegionPosition(i) -
+              startRes;
 
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param cwidth DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getWrappedCanvasWidth(int cwidth)
-    {
-        FontMetrics fm = getFontMetrics(av.getFont());
-
-        LABEL_EAST = 0;
-        LABEL_WEST = 0;
+          if (res < 0 || res > endx - startRes)
+          {
+            continue;
+          }
 
-        if (av.scaleRightWrapped)
-        {
-            LABEL_EAST = fm.stringWidth(getMask());
-        }
+          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 (av.scaleLeftWrapped)
-        {
-            LABEL_WEST = fm.stringWidth(getMask());
         }
+      }
 
-        return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
-    }
-
+      // When printing we have an extra clipped region,
+      // the Printable page which we need to account for here
+      Shape clip = g.getClip();
 
-    /**
-     * Generates a string of zeroes.
-     * @return String
-     */
-    String getMask()
-    {
-      String mask = "00";
-      int maxWidth = 0;
-      int tmp;
-      for(int i=0; i<av.alignment.getHeight(); i++)
+      if (clip == null)
       {
-        tmp = av.alignment.getSequenceAt(i).getEnd();
-        if(tmp>maxWidth)
-          maxWidth = tmp;
+        g.setClip(0, 0, cWidth * av.charWidth, canvasHeight);
       }
-
-      for (int i = maxWidth; i > 0; i /= 10)
+      else
       {
-        mask += "0";
+        g.setClip(0, (int) clip.getBounds().getY(),
+                  cWidth * av.charWidth, (int) clip.getBounds().getHeight());
       }
-      return mask;
-    }
-
-    /**
-     * 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)
-    {
-        AlignmentI al = av.getAlignment();
 
-        FontMetrics fm = getFontMetrics(av.getFont());
+      drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);
 
-
-        if (av.scaleRightWrapped)
+      if (av.showAnnotation)
+      {
+        g.translate(0, cHeight + ypos + 3);
+        if (annotations == null)
         {
-            LABEL_EAST = fm.stringWidth(getMask());
+          annotations = new AnnotationPanel(av);
         }
 
+        annotations.drawComponent( (Graphics2D) g, startRes, endx + 1);
+        g.translate(0, -cHeight - ypos - 3);
+      }
+      g.setClip(clip);
+      g.translate( -LABEL_WEST, 0);
 
-        if (av.scaleLeftWrapped)
-        {
-            LABEL_WEST = fm.stringWidth(getMask());
-        }
-
-        int hgap = av.charHeight;
-        if(av.scaleAboveWrapped)
-          hgap += av.charHeight;
+      ypos += cHeight + getAnnotationHeight() + hgap;
 
-        int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
-        int cHeight = av.getAlignment().getHeight() * av.charHeight;
+      startRes += cWidth;
+    }
+  }
 
-        av.setWrappedWidth(cWidth);
+  AnnotationPanel annotations;
+  int getAnnotationHeight()
+  {
+    if (!av.showAnnotation)
+    {
+      return 0;
+    }
 
-        av.endRes = av.startRes + cWidth;
+    if (annotations == null)
+    {
+      annotations = new AnnotationPanel(av);
+    }
 
+    return annotations.adjustPanelHeight();
+  }
+
+  /**
+   * 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)
+  {
+    if (!av.hasHiddenColumns)
+    {
+      draw(g1, startRes, endRes, startSeq, endSeq, offset);
+    }
+    else
+    {
+      java.util.Vector regions = av.getColumnSelection().getHiddenColumns();
 
-        int endx;
-        int ypos = hgap;
-        int maxwidth = av.alignment.getWidth()-1;
+      int screenY = 0;
+      int blockStart = startRes;
+      int blockEnd = endRes;
 
-        if(av.hasHiddenColumns)
-          maxwidth = av.getColumnSelection().findColumnPosition(maxwidth)-1;
+      for (int i = 0; i < regions.size(); i++)
+      {
+        int[] region = (int[]) regions.elementAt(i);
+        int hideStart = region[0];
+        int hideEnd = region[1];
 
-        while ((ypos <= canvasHeight) && (startRes < maxwidth))
+        if (hideStart <= blockStart)
         {
-          endx = startRes + cWidth -1;
-
-          if (endx > maxwidth)
-          {
-            endx = maxwidth;
-          }
+          blockStart += (hideEnd - hideStart) + 1;
+          continue;
+        }
 
-            g.setFont(av.getFont());
-            g.setColor(Color.black);
+        blockEnd = hideStart - 1;
 
-            if (av.scaleLeftWrapped)
-            {
-                drawWestScale(g, startRes, endx, ypos);
-            }
+        g1.translate(screenY * av.charWidth, 0);
 
-            if (av.scaleRightWrapped)
-            {
-                g.translate(canvasWidth - LABEL_EAST, 0);
-                drawEastScale(g, startRes, endx, ypos);
-                g.translate(-(canvasWidth - LABEL_EAST), 0);
-            }
+        draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
 
-            g.translate(LABEL_WEST, 0);
-
-            if (av.scaleAboveWrapped)
-            {
-                drawNorthScale(g, startRes, endx, ypos);
-            }
+        if (av.getShowHiddenMarkers())
+        {
+          g1.setColor(Color.blue);
 
-            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);
+          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);
+      }
+    }
 
-            // When printing we have an extra clipped region,
-            // the Printable page which we need to account for here
-            Shape clip = g.getClip();
+  }
 
-            if (clip == null)
-            {
-                g.setClip(0, 0, cWidth * av.charWidth, canvasHeight);
-            }
-            else
-            {
-                g.setClip(0, (int) clip.getBounds().getY(),
-                    cWidth * av.charWidth, (int) clip.getBounds().getHeight());
-            }
+  //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);
 
-            drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);
+    SequenceI nextSeq;
 
-            if(av.showAnnotation)
-            {
-              g.translate(0, cHeight + ypos + 3);
-              if(annotations==null)
-                annotations = new AnnotationPanel(av);
+    /// First draw the sequences
+    /////////////////////////////
+    for (int i = startSeq; i < endSeq; i++)
+    {
+      nextSeq = av.alignment.getSequenceAt(i);
 
-              annotations.drawComponent( (Graphics2D) g, startRes, endx+1);
-              g.translate(0, -cHeight - ypos -3);
-            }
-            g.setClip(clip);
-            g.translate(-LABEL_WEST, 0);
+      sr.drawSequence(nextSeq, av.alignment.findAllGroups(nextSeq),
+                      startRes, endRes,
+                      offset + ( (i - startSeq) * av.charHeight));
 
-            ypos += cHeight+getAnnotationHeight()+hgap;
+      if (av.showSequenceFeatures)
+      {
+        fr.drawSequence(g, nextSeq, startRes, endRes,
+                        offset + ( (i - startSeq) * av.charHeight));
+      }
 
-            startRes += cWidth;
+      /// 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));
+      }
     }
 
-    AnnotationPanel annotations;
-    int getAnnotationHeight()
+    if (av.getSelectionGroup() != null || av.alignment.getGroups().size() > 0)
     {
-      if(!av.showAnnotation)
-        return 0;
-
-      if(annotations==null)
-        annotations = new AnnotationPanel(av);
+      drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset);
+    }
 
-      return annotations.adjustPanelHeight();
+  }
+
+  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;
+    int sy = -1;
+    int ex = -1;
+    int groupIndex = -1;
+    int visWidth = (endRes - startRes + 1) * av.charWidth;
+
+    if ( (group == null) && (av.alignment.getGroups().size() > 0))
+    {
+      group = (SequenceGroup) av.alignment.getGroups().elementAt(0);
+      groupIndex = 0;
     }
 
-    /**
-     * 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)
+    if (group != null)
     {
-      if(!av.hasHiddenColumns)
-      {
-        draw(g1, startRes, endRes, startSeq, endSeq, offset);
-      }
-      else
+      do
       {
-        java.util.Vector regions = av.getColumnSelection().getHiddenColumns();
+        int oldY = -1;
+        int i = 0;
+        boolean inGroup = false;
+        int top = -1;
+        int bottom = -1;
 
-        int screenY = 0;
-        int blockStart = startRes;
-        int blockEnd = endRes;
-
-        for (int i = 0; i < regions.size(); i++)
+        for (i = startSeq; i < endSeq; i++)
         {
-          int[] region = (int[]) regions.elementAt(i);
-          int hideStart = region[0];
-          int hideEnd = region[1];
+          sx = (group.getStartRes() - startRes) * av.charWidth;
+          sy = offset + ( (i - startSeq) * av.charHeight);
+          ex = ( ( (group.getEndRes() + 1) - group.getStartRes()) *
+                av.charWidth) -
+              1;
 
-          if (hideStart <= blockStart)
+          if (sx + ex < 0 || sx > visWidth)
           {
-            blockStart += (hideEnd - hideStart) + 1;
             continue;
           }
 
-          blockEnd = hideStart - 1;
-
-          g1.translate(screenY * av.charWidth, 0);
-
-          draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
-
-          if(av.getShowHiddenMarkers())
+          if ( (sx <= (endRes - startRes) * av.charWidth) &&
+              group.getSequences(null).
+              contains(av.alignment.getSequenceAt(i)))
           {
-            g1.setColor(Color.blue);
+            if ( (bottom == -1) &&
+                !group.getSequences(null).contains(
+                    av.alignment.getSequenceAt(i + 1)))
+            {
+              bottom = sy + av.charHeight;
+            }
 
-            g1.drawLine( (blockEnd - blockStart + 1) * av.charWidth - 1,
-                        0 + offset,
-                        (blockEnd - blockStart + 1) * av.charWidth - 1,
-                        (endSeq - startSeq) * av.charHeight + offset);
-          }
+            if (!inGroup)
+            {
+              if ( ( (top == -1) && (i == 0)) ||
+                  !group.getSequences(null).contains(
+                      av.alignment.getSequenceAt(i - 1)))
+              {
+                top = sy;
+              }
 
-          g1.translate( -screenY * av.charWidth, 0);
-          screenY += blockEnd - blockStart + 1;
-          blockStart = hideEnd + 1;
-        }
+              oldY = sy;
+              inGroup = true;
 
-        if (screenY <= (endRes - startRes))
-        {
-          blockEnd = blockStart + (endRes - startRes) - screenY;
-          g1.translate(screenY * av.charWidth, 0);
-          draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
+              if (group == av.getSelectionGroup())
+              {
+                g.setStroke(new BasicStroke(1,
+                                            BasicStroke.CAP_BUTT,
+                                            BasicStroke.JOIN_ROUND, 3f,
+                                            new float[]
+                                            {5f, 3f}, 0f));
+                g.setColor(Color.RED);
+              }
+              else
+              {
+                g.setStroke(new BasicStroke());
+                g.setColor(group.getOutlineColour());
+              }
+            }
+          }
+          else
+          {
+            if (inGroup)
+            {
+              if (sx >= 0 && sx < visWidth)
+              {
+                g.drawLine(sx, oldY, sx, sy);
+              }
 
-          g1.translate( -screenY * av.charWidth, 0);
-        }
-      }
+              if (sx + ex < visWidth)
+              {
+                g.drawLine(sx + ex, oldY, sx + ex, sy);
+              }
 
-    }
+              if (sx < 0)
+              {
+                ex += sx;
+                sx = 0;
+              }
 
+              if (sx + ex > visWidth)
+              {
+                ex = visWidth;
+              }
 
+              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;
+              }
 
-    //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);
+              if (bottom != -1)
+              {
+                g.drawLine(sx, bottom, sx + ex, bottom);
+                bottom = -1;
+              }
 
-      SequenceI nextSeq;
+              inGroup = false;
+            }
+          }
+        }
 
-        /// First draw the sequences
-        /////////////////////////////
-        for (int i = startSeq; i < endSeq; i++)
+        if (inGroup)
         {
-            nextSeq = av.alignment.getSequenceAt(i);
-
-            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));
-            }
+          sy = offset + ( (i - startSeq) * av.charHeight);
+          if (sx >= 0 && sx < visWidth)
+          {
+            g.drawLine(sx, oldY, sx, sy);
+          }
 
-            /// 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 (sx + ex < visWidth)
+          {
+            g.drawLine(sx + ex, oldY, sx + ex, sy);
+          }
 
-            if(av.cursorMode && cursorY==i
-               && cursorX>=startRes && cursorX<=endRes)
-            {
-              sr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * av.charWidth,
-                            offset + ( (i - startSeq) * av.charHeight));
-            }
+          if (sx < 0)
+          {
+            ex += sx;
+            sx = 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)
-   {
-       Graphics2D g = (Graphics2D)g1;
-        //
-        /////////////////////////////////////
-        // Now outline any areas if necessary
-        /////////////////////////////////////
-        SequenceGroup group = av.getSelectionGroup();
-
-        int sx = -1;
-        int sy = -1;
-        int ex = -1;
-        int groupIndex = -1;
-        int visWidth = (endRes - startRes +1) * av.charWidth;
-
-        if ((group == null) && (av.alignment.getGroups().size() > 0))
-        {
-            group = (SequenceGroup) av.alignment.getGroups().elementAt(0);
-            groupIndex = 0;
-        }
+          if (sx + ex > visWidth)
+          {
+            ex = visWidth;
+          }
+          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 (group != null)
-        {
-            do
-            {
-                int oldY = -1;
-                int i = 0;
-                boolean inGroup = false;
-                int top = -1;
-                int bottom = -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>visWidth)
-                    {
-                      continue;
-                    }
-
-                    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)))
-                        {
-                            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.setStroke(new BasicStroke(1,
-                                        BasicStroke.CAP_BUTT,
-                                        BasicStroke.JOIN_ROUND, 3f,
-                                        new float[] { 5f, 3f }, 0f));
-                                g.setColor(Color.RED);
-                            }
-                            else
-                            {
-                                g.setStroke(new BasicStroke());
-                                g.setColor(group.getOutlineColour());
-                            }
-                        }
-                    }
-                    else
-                    {
-                      if (inGroup)
-                      {
-                        if (sx >= 0 && sx < visWidth)
-                          g.drawLine(sx, oldY, sx, sy);
-
-                        if (sx + ex < visWidth)
-                          g.drawLine(sx + ex, oldY, sx + ex, sy);
-
-                        if (sx < 0)
-                        {
-                          ex += sx;
-                          sx = 0;
-                        }
-
-                        if (sx + ex > visWidth)
-                          ex = visWidth;
-
-                        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 < visWidth)
-                    g.drawLine(sx, oldY, sx, sy);
-
-                  if (sx + ex < visWidth)
-                    g.drawLine(sx + ex, oldY, sx + ex, sy);
-
-                  if (sx < 0)
-                  {
-                    ex += sx;
-                    sx = 0;
-                  }
-
-                  if (sx + ex > visWidth)
-                    ex = visWidth;
-                  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 (bottom != -1)
+          {
+            g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);
+            bottom = -1;
+          }
 
-                g.setStroke(new BasicStroke());
+          inGroup = false;
+        }
 
-                if (groupIndex >= av.alignment.getGroups().size())
-                {
-                    break;
-                }
+        groupIndex++;
 
-                group = (SequenceGroup) av.alignment.getGroups().elementAt(groupIndex);
+        g.setStroke(new BasicStroke());
 
+        if (groupIndex >= av.alignment.getGroups().size())
+        {
+          break;
+        }
 
-            }
-            while (groupIndex < av.alignment.getGroups().size());
+        group = (SequenceGroup) av.alignment.getGroups().elementAt(groupIndex);
 
-        }
+      }
+      while (groupIndex < av.alignment.getGroups().size());
 
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param results DOCUMENT ME!
-     */
-    public void highlightSearchResults(SearchResults results)
-    {
-        img = null;
+  }
 
-        searchResults = results;
+  /**
+   * DOCUMENT ME!
+   *
+   * @param results DOCUMENT ME!
+   */
+  public void highlightSearchResults(SearchResults results)
+  {
+    img = null;
 
-        repaint();
-    }
+    searchResults = results;
+
+    repaint();
+  }
 }
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 08bf7df..a20165a 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,15 +18,15 @@
  */
 package jalview.gui;
 
-import jalview.datamodel.*;
-import jalview.commands.EditCommand;
-import jalview.schemes.*;
+import java.util.*;
 
 import java.awt.*;
 import java.awt.event.*;
 import javax.swing.*;
-import java.util.Vector;
 
+import jalview.commands.*;
+import jalview.datamodel.*;
+import jalview.schemes.*;
 
 /**
  * DOCUMENT ME!
@@ -34,7 +34,8 @@ import java.util.Vector;
  * @author $author$
  * @version $Revision$
  */
-public class SeqPanel extends JPanel implements MouseListener,
+public class SeqPanel
+    extends JPanel implements MouseListener,
     MouseMotionListener, MouseWheelListener
 
 {
@@ -116,7 +117,9 @@ public class SeqPanel extends JPanel implements MouseListener,
 
       int hgap = av.charHeight;
       if (av.scaleAboveWrapped)
+      {
         hgap += av.charHeight;
+      }
 
       int cHeight = av.getAlignment().getHeight() * av.charHeight
           + hgap + seqCanvas.getAnnotationHeight();
@@ -127,7 +130,9 @@ public class SeqPanel extends JPanel implements MouseListener,
 
       int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());
       if (cwidth < 1)
+      {
         return 0;
+      }
 
       wrappedBlock = y / cHeight;
       wrappedBlock += av.getStartRes() / cwidth;
@@ -141,7 +146,9 @@ public class SeqPanel extends JPanel implements MouseListener,
     }
 
     if (av.hasHiddenColumns)
+    {
       res = av.getColumnSelection().adjustForHiddenColumns(res);
+    }
 
     return res;
 
@@ -156,7 +163,9 @@ public class SeqPanel extends JPanel implements MouseListener,
     {
       int hgap = av.charHeight;
       if (av.scaleAboveWrapped)
+      {
         hgap += av.charHeight;
+      }
 
       int cHeight = av.getAlignment().getHeight() * av.charHeight
           + hgap + seqCanvas.getAnnotationHeight();
@@ -185,7 +194,9 @@ public class SeqPanel extends JPanel implements MouseListener,
       {
         if (av.featuresDisplayed == null
             || !av.featuresDisplayed.containsKey(features[i].getType()))
+        {
           continue;
+        }
 
         if ( (features[i].getBegin() <= res) &&
             (features[i].getEnd() >= res))
@@ -196,1484 +207,1572 @@ public class SeqPanel extends JPanel implements MouseListener,
     }
 
     features = new SequenceFeature[tmp.size()];
-    for(int i=0; i<tmp.size(); i++)
+    for (int i = 0; i < tmp.size(); i++)
     {
-      features[i] = (SequenceFeature)tmp.elementAt(i);
+      features[i] = (SequenceFeature) tmp.elementAt(i);
     }
 
     return features;
   }
 
-   Vector getAllFeaturesAtRes(SequenceI seq, int res)
-   {
-     Vector allFeatures = new Vector();
-     int index = 0;
-     if(seq.getSequenceFeatures()!=null && av.featuresDisplayed!=null)
-     {
-       while (index < seq.getSequenceFeatures().length)
-       {
-         SequenceFeature sf = seq.getSequenceFeatures()[index];
-         if (sf.getBegin() <= res &&
-             sf.getEnd() >= res)
-         {
-           if (av.featuresDisplayed.containsKey(sf.getType()))
-           {
-             allFeatures.addElement(sf);
-           }
-         }
-         index++;
-       }
-     }
-     return allFeatures;
+  Vector getAllFeaturesAtRes(SequenceI seq, int res)
+  {
+    Vector allFeatures = new Vector();
+    int index = 0;
+    if (seq.getSequenceFeatures() != null && av.featuresDisplayed != null)
+    {
+      while (index < seq.getSequenceFeatures().length)
+      {
+        SequenceFeature sf = seq.getSequenceFeatures()[index];
+        if (sf.getBegin() <= res &&
+            sf.getEnd() >= res)
+        {
+          if (av.featuresDisplayed.containsKey(sf.getType()))
+          {
+            allFeatures.addElement(sf);
+          }
+        }
+        index++;
+      }
+    }
+    return allFeatures;
   }
 
-   void endEditing()
-   {
-     if (editCommand!=null && editCommand.getSize() > 0)
-     {
-       ap.alignFrame.addHistoryItem(editCommand);
-       av.firePropertyChange("alignment", null,
-                             av.getAlignment().getSequences());
-     }
-
-     startseq = -1;
-     lastres = -1;
-     editingSeqs = false;
-     groupEditing = false;
-     keyboardNo1 = null;
-     keyboardNo2 = null;
-     editCommand = null;
+  void endEditing()
+  {
+    if (editCommand != null && editCommand.getSize() > 0)
+    {
+      ap.alignFrame.addHistoryItem(editCommand);
+      av.firePropertyChange("alignment", null,
+                            av.getAlignment().getSequences());
     }
 
-    void setCursorRow()
+    startseq = -1;
+    lastres = -1;
+    editingSeqs = false;
+    groupEditing = false;
+    keyboardNo1 = null;
+    keyboardNo2 = null;
+    editCommand = null;
+  }
+
+  void setCursorRow()
+  {
+    seqCanvas.cursorY = getKeyboardNo(keyboardNo1) - 1;
+    scrollToVisible();
+  }
+
+  void setCursorColumn()
+  {
+    seqCanvas.cursorX = getKeyboardNo(keyboardNo1) - 1;
+    scrollToVisible();
+  }
+
+  void setCursorRowAndColumn()
+  {
+    if (keyboardNo2 == null)
     {
-      seqCanvas.cursorY = getKeyboardNo(keyboardNo1)-1;
-      scrollToVisible();
+      keyboardNo2 = new StringBuffer();
     }
-
-    void setCursorColumn()
+    else
     {
-      seqCanvas.cursorX = getKeyboardNo(keyboardNo1)-1;
+      seqCanvas.cursorX = getKeyboardNo(keyboardNo1) - 1;
+      seqCanvas.cursorY = getKeyboardNo(keyboardNo2) - 1;
       scrollToVisible();
     }
+  }
+
+  void setCursorPosition()
+  {
+    SequenceI sequence =
+        (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
+
+    seqCanvas.cursorX = sequence.findIndex(
+        getKeyboardNo(keyboardNo1) - 1
+        );
+    scrollToVisible();
+  }
 
-    void setCursorRowAndColumn()
+  void moveCursor(int dx, int dy)
+  {
+    seqCanvas.cursorX += dx;
+    seqCanvas.cursorY += dy;
+    if (av.hasHiddenColumns && !av.colSel.isVisible(seqCanvas.cursorX))
     {
-      if(keyboardNo2==null)
+      int original = seqCanvas.cursorX - dx;
+      int maxWidth = av.alignment.getWidth();
+
+      while (!av.colSel.isVisible(seqCanvas.cursorX)
+             && seqCanvas.cursorX < maxWidth
+             && seqCanvas.cursorX > 0)
       {
-        keyboardNo2 = new StringBuffer();
+        seqCanvas.cursorX += dx;
       }
-      else
+
+      if (seqCanvas.cursorX >= maxWidth
+          || !av.colSel.isVisible(seqCanvas.cursorX))
       {
-        seqCanvas.cursorX = getKeyboardNo(keyboardNo1) - 1;
-        seqCanvas.cursorY = getKeyboardNo(keyboardNo2) - 1;
-        scrollToVisible();
+        seqCanvas.cursorX = original;
       }
     }
 
-    void setCursorPosition()
+    scrollToVisible();
+  }
+
+  void scrollToVisible()
+  {
+    if (seqCanvas.cursorX < 0)
+    {
+      seqCanvas.cursorX = 0;
+    }
+    else if (seqCanvas.cursorX > av.alignment.getWidth() - 1)
     {
-      SequenceI sequence =
-          (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
+      seqCanvas.cursorX = av.alignment.getWidth() - 1;
+    }
 
-      seqCanvas.cursorX = sequence.findIndex(
-          getKeyboardNo(keyboardNo1)-1
-          );
-      scrollToVisible();
+    if (seqCanvas.cursorY < 0)
+    {
+      seqCanvas.cursorY = 0;
+    }
+    else if (seqCanvas.cursorY > av.alignment.getHeight() - 1)
+    {
+      seqCanvas.cursorY = av.alignment.getHeight() - 1;
     }
 
-    void moveCursor(int dx, int dy)
+    endEditing();
+    if (av.wrapAlignment)
+    {
+      ap.scrollToWrappedVisible(seqCanvas.cursorX);
+    }
+    else
     {
-      seqCanvas.cursorX += dx;
-      seqCanvas.cursorY += dy;
-      if (av.hasHiddenColumns && !av.colSel.isVisible(seqCanvas.cursorX))
+      while (seqCanvas.cursorY < av.startSeq)
       {
-        int original = seqCanvas.cursorX - dx;
-        int maxWidth = av.alignment.getWidth();
-
-        while(!av.colSel.isVisible(seqCanvas.cursorX)
-              && seqCanvas.cursorX<maxWidth
-              && seqCanvas.cursorX>0)
+        ap.scrollUp(true);
+      }
+      while (seqCanvas.cursorY + 1 > av.endSeq)
+      {
+        ap.scrollUp(false);
+      }
+      if (!av.wrapAlignment)
+      {
+        while (seqCanvas.cursorX < av.colSel.adjustForHiddenColumns(av.startRes))
         {
-          seqCanvas.cursorX += dx;
+          if (!ap.scrollRight(false))
+          {
+            break;
+          }
         }
-
-        if(seqCanvas.cursorX>=maxWidth
-           || !av.colSel.isVisible(seqCanvas.cursorX) )
+        while (seqCanvas.cursorX > av.colSel.adjustForHiddenColumns(av.endRes))
         {
-          seqCanvas.cursorX = original;
+          if (!ap.scrollRight(true))
+          {
+            break;
+          }
         }
       }
-
-      scrollToVisible();
     }
+    setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),
+                     seqCanvas.cursorX, seqCanvas.cursorY);
 
-    void scrollToVisible()
-    {
-      if (seqCanvas.cursorX < 0)
-        seqCanvas.cursorX = 0;
-      else if (seqCanvas.cursorX > av.alignment.getWidth() - 1)
-        seqCanvas.cursorX = av.alignment.getWidth() - 1;
-
-      if (seqCanvas.cursorY < 0)
-        seqCanvas.cursorY = 0;
-      else if (seqCanvas.cursorY > av.alignment.getHeight() - 1)
-        seqCanvas.cursorY = av.alignment.getHeight() - 1;
+    seqCanvas.repaint();
+  }
 
+  void setSelectionAreaAtCursor(boolean topLeft)
+  {
+    SequenceI sequence =
+        (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
 
-      endEditing();
-      if(av.wrapAlignment)
-      {
-        ap.scrollToWrappedVisible(seqCanvas.cursorX);
-      }
-      else
+    if (av.getSelectionGroup() != null)
+    {
+      SequenceGroup sg = av.selectionGroup;
+      //Find the top and bottom of this group
+      int min = av.alignment.getHeight(), max = 0;
+      for (int i = 0; i < sg.getSize(); i++)
       {
-        while (seqCanvas.cursorY < av.startSeq)
+        int index = av.alignment.findIndex(sg.getSequenceAt(i));
+        if (index > max)
         {
-          ap.scrollUp(true);
+          max = index;
         }
-        while (seqCanvas.cursorY + 1 > av.endSeq)
+        if (index < min)
         {
-          ap.scrollUp(false);
-        }
-        if (!av.wrapAlignment)
-        {
-          while (seqCanvas.cursorX < av.colSel.adjustForHiddenColumns(av.startRes))
-          {
-            if (!ap.scrollRight(false))
-              break;
-          }
-          while (seqCanvas.cursorX > av.colSel.adjustForHiddenColumns(av.endRes))
-          {
-            if (!ap.scrollRight(true))
-              break;
-          }
+          min = index;
         }
       }
-      setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),
-                       seqCanvas.cursorX, seqCanvas.cursorY);
 
-      seqCanvas.repaint();
-    }
-
-    void setSelectionAreaAtCursor(boolean topLeft)
-    {
-      SequenceI sequence =
-          (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
+      max++;
 
-      if(av.getSelectionGroup()!=null)
+      if (topLeft)
       {
-        SequenceGroup sg = av.selectionGroup;
-        //Find the top and bottom of this group
-        int min = av.alignment.getHeight(), max = 0;
-        for(int i=0; i<sg.getSize(); i++)
+        sg.setStartRes(seqCanvas.cursorX);
+        if (sg.getEndRes() < seqCanvas.cursorX)
         {
-          int index = av.alignment.findIndex( sg.getSequenceAt(i) );
-          if(index > max)
-            max = index;
-          if(index < min)
-            min = index;
+          sg.setEndRes(seqCanvas.cursorX);
         }
 
-        max ++;
-
-        if(topLeft)
+        min = seqCanvas.cursorY;
+      }
+      else
+      {
+        sg.setEndRes(seqCanvas.cursorX);
+        if (sg.getStartRes() > seqCanvas.cursorX)
         {
           sg.setStartRes(seqCanvas.cursorX);
-          if(sg.getEndRes()<seqCanvas.cursorX)
-            sg.setEndRes(seqCanvas.cursorX);
-
-          min = seqCanvas.cursorY;
         }
-        else
-        {
-          sg.setEndRes(seqCanvas.cursorX);
-          if(sg.getStartRes()>seqCanvas.cursorX)
-            sg.setStartRes(seqCanvas.cursorX);
 
-          max = seqCanvas.cursorY+1;
-        }
+        max = seqCanvas.cursorY + 1;
+      }
 
-        if(min>max)
-        {
-          // Only the user can do this
-          av.setSelectionGroup(null);
-        }
-        else
+      if (min > max)
+      {
+        // Only the user can do this
+        av.setSelectionGroup(null);
+      }
+      else
+      {
+        // Now add any sequences between min and max
+        sg.getSequences(null).clear();
+        for (int i = min; i < max; i++)
         {
-          // Now add any sequences between min and max
-          sg.getSequences(null).clear();
-          for (int i = min; i < max; i++)
-          {
-            sg.addSequence(av.alignment.getSequenceAt(i), false);
-          }
+          sg.addSequence(av.alignment.getSequenceAt(i), false);
         }
       }
+    }
 
-      if (av.getSelectionGroup() == null)
-      {
-        SequenceGroup sg = new SequenceGroup();
-        sg.setStartRes(seqCanvas.cursorX);
-        sg.setEndRes(seqCanvas.cursorX);
-        sg.addSequence(sequence, false);
-        av.setSelectionGroup(sg);
-      }
+    if (av.getSelectionGroup() == null)
+    {
+      SequenceGroup sg = new SequenceGroup();
+      sg.setStartRes(seqCanvas.cursorX);
+      sg.setEndRes(seqCanvas.cursorX);
+      sg.addSequence(sequence, false);
+      av.setSelectionGroup(sg);
+    }
 
+    ap.repaint();
+  }
 
-      ap.repaint();
-    }
+  void insertGapAtCursor(boolean group)
+  {
+    groupEditing = group;
+    startseq = seqCanvas.cursorY;
+    lastres = seqCanvas.cursorX;
+    editSequence(true, seqCanvas.cursorX + getKeyboardNo(keyboardNo1));
+    endEditing();
+  }
+
+  void deleteGapAtCursor(boolean group)
+  {
+    groupEditing = group;
+    startseq = seqCanvas.cursorY;
+    lastres = seqCanvas.cursorX + getKeyboardNo(keyboardNo1);
+    editSequence(false, seqCanvas.cursorX);
+    endEditing();
+  }
 
-    void insertGapAtCursor(boolean group)
+  void numberPressed(char value)
+  {
+    if (keyboardNo1 == null)
     {
-      groupEditing = group;
-      startseq = seqCanvas.cursorY;
-      lastres = seqCanvas.cursorX;
-      editSequence(true, seqCanvas.cursorX+getKeyboardNo(keyboardNo1));
-      endEditing();
+      keyboardNo1 = new StringBuffer();
     }
 
-    void deleteGapAtCursor(boolean group)
+    if (keyboardNo2 != null)
     {
-      groupEditing = group;
-      startseq = seqCanvas.cursorY;
-      lastres = seqCanvas.cursorX+getKeyboardNo(keyboardNo1);
-      editSequence(false, seqCanvas.cursorX);
-      endEditing();
+      keyboardNo2.append(value);
     }
-
-    void numberPressed(char value)
+    else
     {
-      if(keyboardNo1==null)
-        keyboardNo1 = new StringBuffer();
-
-      if(keyboardNo2!=null)
-        keyboardNo2.append(value);
-      else
-        keyboardNo1.append(value);
+      keyboardNo1.append(value);
     }
+  }
 
-    int getKeyboardNo(StringBuffer kb)
+  int getKeyboardNo(StringBuffer kb)
+  {
+    if (kb == null)
     {
-      if(kb==null)
-        return 1;
-      else
-        return Integer.parseInt(kb.toString());
+      return 1;
     }
-
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mouseReleased(MouseEvent evt)
+    else
     {
-      mouseDragging = false;
-      mouseWheelPressed = false;
-
-      if (!editingSeqs)
-      {
-         doMouseReleasedDefineMode(evt);
-         return;
-      }
+      return Integer.parseInt(kb.toString());
+    }
+  }
 
-       endEditing();
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void mouseReleased(MouseEvent evt)
+  {
+    mouseDragging = false;
+    mouseWheelPressed = false;
 
-       ap.repaint();
+    if (!editingSeqs)
+    {
+      doMouseReleasedDefineMode(evt);
+      return;
     }
 
+    endEditing();
 
+    ap.repaint();
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mousePressed(MouseEvent evt)
-    {
-      lastMousePress = evt.getPoint();
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void mousePressed(MouseEvent evt)
+  {
+    lastMousePress = evt.getPoint();
 
-      if (javax.swing.SwingUtilities.isMiddleMouseButton(evt))
-      {
-        mouseWheelPressed = true;
-        return;
-      }
+    if (javax.swing.SwingUtilities.isMiddleMouseButton(evt))
+    {
+      mouseWheelPressed = true;
+      return;
+    }
 
-      if (evt.isShiftDown() || evt.isAltDown() ||
-          evt.isControlDown())
-      {
-        if (evt.isAltDown() || evt.isControlDown())
-        {
-          groupEditing = true;
-        }
-        editingSeqs = true;
-      }
-      else
+    if (evt.isShiftDown() || evt.isAltDown() ||
+        evt.isControlDown())
+    {
+      if (evt.isAltDown() || evt.isControlDown())
       {
-        doMousePressedDefineMode(evt);
-        return;
+        groupEditing = true;
       }
+      editingSeqs = true;
+    }
+    else
+    {
+      doMousePressedDefineMode(evt);
+      return;
+    }
 
-      int seq = findSeq(evt);
-      int res = findRes(evt);
-
-      if(seq<0 || res<0)
-        return;
-
-        if ((seq < av.getAlignment().getHeight()) &&
-                (res < av.getAlignment().getSequenceAt(seq).getLength()))
-        {
-            startseq = seq;
-            lastres = res;
-        }
-        else
-        {
-            startseq = -1;
-            lastres = -1;
-        }
+    int seq = findSeq(evt);
+    int res = findRes(evt);
 
-        return;
+    if (seq < 0 || res < 0)
+    {
+      return;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mouseMoved(MouseEvent evt)
+    if ( (seq < av.getAlignment().getHeight()) &&
+        (res < av.getAlignment().getSequenceAt(seq).getLength()))
     {
-      if (editingSeqs)
-      {
-       // This is because MacOSX creates a mouseMoved
-       // If control is down, other platforms will not.
-       mouseDragged(evt);
-      }
-
-      int res = findRes(evt);
-      int seq = findSeq(evt);
+      startseq = seq;
+      lastres = res;
+    }
+    else
+    {
+      startseq = -1;
+      lastres = -1;
+    }
 
+    return;
+  }
 
-      if(res<0 || seq<0 || seq >= av.getAlignment().getHeight())
-            return;
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void mouseMoved(MouseEvent evt)
+  {
+    if (editingSeqs)
+    {
+      // This is because MacOSX creates a mouseMoved
+      // If control is down, other platforms will not.
+      mouseDragged(evt);
+    }
 
-      SequenceI sequence = av.getAlignment().getSequenceAt(seq);
+    int res = findRes(evt);
+    int seq = findSeq(evt);
 
-      if (res > sequence.getLength())
-      {
-        return;
-      }
+    if (res < 0 || seq < 0 || seq >= av.getAlignment().getHeight())
+    {
+      return;
+    }
 
-      if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence)
-      {
-        seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));
-      }
+    SequenceI sequence = av.getAlignment().getSequenceAt(seq);
 
-      setStatusMessage(sequence, res, seq);
+    if (res > sequence.getLength())
+    {
+      return;
+    }
 
+    if (seqCanvas.pdbCanvas != null && sequence == seqCanvas.pdbCanvas.sequence)
+    {
+      seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));
+    }
 
+    setStatusMessage(sequence, res, seq);
 
-      tooltipText.setLength(6); // Cuts the buffer back to <html>
+    tooltipText.setLength(6); // Cuts the buffer back to <html>
 
-      SequenceGroup []  groups = av.alignment.findAllGroups(sequence);
-      if(groups!=null)
+    SequenceGroup[] groups = av.alignment.findAllGroups(sequence);
+    if (groups != null)
+    {
+      for (int g = 0; g < groups.length; g++)
       {
-        for(int g=0; g<groups.length; g++)
+        if (groups[g].getStartRes() <= res && groups[g].getEndRes() >= res)
         {
-          if(groups[g].getStartRes()<=res && groups[g].getEndRes()>=res)
+          if (tooltipText.length() > 6)
           {
-            if (tooltipText.length() > 6)
-                    tooltipText.append("<br>");
+            tooltipText.append("<br>");
+          }
 
-            if (!groups[g].getName().startsWith("JTreeGroup") &&
-                !groups[g].getName().startsWith("JGroup"))
-              tooltipText.append(groups[g].getName());
+          if (!groups[g].getName().startsWith("JTreeGroup") &&
+              !groups[g].getName().startsWith("JGroup"))
+          {
+            tooltipText.append(groups[g].getName());
+          }
 
-            if(groups[g].getDescription()!=null)
-              tooltipText.append(": "+groups[g].getDescription());
+          if (groups[g].getDescription() != null)
+          {
+            tooltipText.append(": " + groups[g].getDescription());
           }
         }
       }
+    }
 
+    // use aa to see if the mouse pointer is on a
+    if (av.showSequenceFeatures)
+    {
+      SequenceFeature[] features = findFeaturesAtRes(
+          sequence.getDatasetSequence(), sequence.findPosition(res));
 
-        // use aa to see if the mouse pointer is on a
-        if (av.showSequenceFeatures)
+      if (features != null)
+      {
+        for (int i = 0; i < features.length; i++)
         {
-          SequenceFeature[] features = findFeaturesAtRes(
-              sequence.getDatasetSequence(), sequence.findPosition(res));
-
-          if (features != null)
+          if (features[i].getType().equals("disulfide bond"))
           {
-            for (int i = 0; i < features.length; i++)
+            if (features[i].getBegin() == sequence.findPosition(res)
+                || features[i].getEnd() == sequence.findPosition(res))
             {
-              if (features[i].getType().equals("disulfide bond"))
+              if (tooltipText.length() > 6)
               {
-                if (features[i].getBegin() == 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());
-                  if (features[i].links != null)
-                    tooltipText.append(" <img src=\"" + linkImageURL + "\">");
-                }
+                tooltipText.append("<br>");
               }
-              else
+              tooltipText.append("disulfide bond " + features[i].getBegin() +
+                                 ":" +
+                                 features[i].getEnd());
+              if (features[i].links != null)
               {
-                if (tooltipText.length() > 6)
-                  tooltipText.append("<br>");
+                tooltipText.append(" <img src=\"" + linkImageURL + "\">");
+              }
+            }
+          }
+          else
+          {
+            if (tooltipText.length() > 6)
+            {
+              tooltipText.append("<br>");
+            }
+
+            tooltipText.append(features[i].getType() + " " +
+                               features[i].begin);
+            if (features[i].begin != features[i].end)
+            {
+              tooltipText.append(" " + features[i].end);
+            }
 
-                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()))
+            {
+              tmpString = features[i].getDescription();
+              int startTag = tmpString.toUpperCase().indexOf("<HTML>");
+              if (startTag > -1)
+              {
+                tmpString = tmpString.substring(startTag + 6);
+              }
+              int endTag = tmpString.toUpperCase().indexOf("</BODY>");
+              if (endTag > -1)
+              {
+                tmpString = tmpString.substring(0, endTag);
+              }
+              endTag = tmpString.toUpperCase().indexOf("</HTML>");
+              if (endTag > -1)
+              {
+                tmpString = tmpString.substring(0, endTag);
+              }
 
-                if (features[i].getDescription() != null
-                    && !features[i].description.equals(features[i].getType()))
+              if (startTag > -1)
+              {
+                tooltipText.append("; " + tmpString);
+              }
+              else
+              {
+                if (tmpString.indexOf("<") > -1 || tmpString.indexOf(">") > -1)
                 {
-                  tmpString = features[i].getDescription();
-                  int startTag = tmpString.toUpperCase().indexOf("<HTML>");
-                  if (startTag > -1)
-                  {
-                    tmpString = tmpString.substring(startTag + 6);
-                  }
-                  int endTag = tmpString.toUpperCase().indexOf("</BODY>");
-                  if (endTag > -1)
-                  {
-                    tmpString = tmpString.substring(0, endTag);
-                  }
-                  endTag = tmpString.toUpperCase().indexOf("</HTML>");
-                  if (endTag > -1)
-                  {
-                    tmpString = tmpString.substring(0, endTag);
-                  }
-
-                  if (startTag > -1)
-                  {
-                    tooltipText.append("; " + tmpString);
-                  }
-                  else
-                  {
-                    if (tmpString.indexOf("<") > -1 || tmpString.indexOf(">") > -1)
-                    {
-                      //The description does not specify html is to
-                      //be used, so we must remove < > symbols
-                      tmpString = tmpString.replaceAll("<", "&lt;");
-                      tmpString = tmpString.replaceAll(">", "&gt;");
-
-                      tooltipText.append("; ");
-                      tooltipText.append(tmpString);
-
-                    }
-                    else
-                      tooltipText.append("; " + tmpString);
-                  }
+                  //The description does not specify html is to
+                  //be used, so we must remove < > symbols
+                  tmpString = tmpString.replaceAll("<", "&lt;");
+                  tmpString = tmpString.replaceAll(">", "&gt;");
+
+                  tooltipText.append("; ");
+                  tooltipText.append(tmpString);
+
                 }
-                if (features[i].getValue("status") != null)
+                else
                 {
-                  String status = features[i].getValue("status").toString();
-                  if (status.length() > 0)
-                    tooltipText.append("; (" + features[i].getValue("status") + ")");
+                  tooltipText.append("; " + tmpString);
                 }
-
-                if (features[i].links != null)
-                  tooltipText.append(" <img src=\"" + linkImageURL + "\">");
-
               }
             }
-          }
-        }
+            if (features[i].getValue("status") != null)
+            {
+              String status = features[i].getValue("status").toString();
+              if (status.length() > 0)
+              {
+                tooltipText.append("; (" + features[i].getValue("status") + ")");
+              }
+            }
 
-        if (tooltipText.length() == 6) // <html></html>
-        {
-          setToolTipText(null);
-        }
-        else
-        {
-          tooltipText.append("</html>");
-          setToolTipText(tooltipText.toString());
+            if (features[i].links != null)
+            {
+              tooltipText.append(" <img src=\"" + linkImageURL + "\">");
+            }
+
+          }
         }
-       // else
-        //  setToolTipText(null);
+      }
     }
 
-    void setStatusMessage(SequenceI sequence, int res, int seq)
+    if (tooltipText.length() == 6) // <html></html>
+    {
+      setToolTipText(null);
+    }
+    else
     {
-      StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
-                                           sequence.getName());
+      tooltipText.append("</html>");
+      setToolTipText(tooltipText.toString());
+    }
+    // else
+    //  setToolTipText(null);
+  }
 
-      Object obj = null;
-      if (av.alignment.isNucleotide())
+  void setStatusMessage(SequenceI sequence, int res, int seq)
+  {
+    StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
+                                         sequence.getName());
+
+    Object obj = null;
+    if (av.alignment.isNucleotide())
+    {
+      obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
+                                                 "");
+      if (obj != null)
       {
-        obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
-                                                   "");
-        if (obj != null)
-          text.append(" Nucleotide: ");
+        text.append(" Nucleotide: ");
       }
-      else
+    }
+    else
+    {
+      obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
+      if (obj != null)
       {
-        obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
-        if (obj != null)
-          text.append("  Residue: ");
+        text.append("  Residue: ");
       }
+    }
 
-      if (obj != null)
+    if (obj != null)
+    {
+
+      if (obj != "")
       {
+        text.append(obj + " (" + sequence.findPosition(res) +
+                    ")");
+      }
+    }
+    ap.alignFrame.statusBar.setText(text.toString());
 
-        if (obj != "")
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void mouseDragged(MouseEvent evt)
+  {
+    if (mouseWheelPressed)
+    {
+      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()))
+      {
+        int fontSize = av.font.getSize();
+
+        if (evt.getY() < lastMousePress.getY())
         {
-          text.append(obj + " (" + sequence.findPosition(res) +
-                      ")");
+          fontSize--;
         }
+        else if (evt.getY() > lastMousePress.getY())
+        {
+          fontSize++;
+        }
+
+        if (fontSize < 1)
+        {
+          fontSize = 1;
+        }
+
+        av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
+        av.charWidth = oldWidth;
+        ap.fontChanged();
       }
-      ap.alignFrame.statusBar.setText(text.toString());
+      else
+      {
+        if (evt.getX() < lastMousePress.getX() && av.charWidth > 1)
+        {
+          av.charWidth--;
+        }
+        else if (evt.getX() > lastMousePress.getX())
+        {
+          av.charWidth++;
+        }
+
+        ap.repaint();
+      }
+
+      FontMetrics fm = getFontMetrics(av.getFont());
+      av.validCharWidth = fm.charWidth('M') <= av.charWidth;
 
+      lastMousePress = evt.getPoint();
+
+      return;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mouseDragged(MouseEvent evt)
+    if (!editingSeqs)
     {
-      if (mouseWheelPressed)
-      {
-        int oldWidth = av.charWidth;
+      doMouseDraggedDefineMode(evt);
+      return;
+    }
 
-        //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();
+    int res = findRes(evt);
 
-          if (evt.getY() < lastMousePress.getY())
-          {
-            fontSize--;
-          }
-          else if (evt.getY() > lastMousePress.getY())
-          {
-            fontSize++;
-          }
+    if (res < 0)
+    {
+      res = 0;
+    }
 
-          if(fontSize<1)
-            fontSize = 1;
+    if ( (lastres == -1) || (lastres == res))
+    {
+      return;
+    }
 
-          av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
-          av.charWidth = oldWidth;
-          ap.fontChanged();
-        }
-        else
-        {
-          if (evt.getX() < lastMousePress.getX() && av.charWidth > 1)
-          {
-            av.charWidth--;
-          }
-          else if (evt.getX() > lastMousePress.getX())
-          {
-            av.charWidth++;
-          }
+    if ( (res < av.getAlignment().getWidth()) && (res < lastres))
+    {
+      // dragLeft, delete gap
+      editSequence(false, res);
+    }
+    else
+    {
+      editSequence(true, res);
+    }
 
-          ap.repaint();
-        }
+    mouseDragging = true;
+    if (scrollThread != null)
+    {
+      scrollThread.setEvent(evt);
+    }
 
-        FontMetrics fm = getFontMetrics(av.getFont());
-        av.validCharWidth = fm.charWidth('M') <= av.charWidth;
+  }
 
-        lastMousePress = evt.getPoint();
+  synchronized void editSequence(boolean insertGap, int startres)
+  {
+    int fixedLeft = -1;
+    int fixedRight = -1;
+    boolean fixedColumns = false;
+    SequenceGroup sg = av.getSelectionGroup();
 
-        return;
+    SequenceI seq = av.alignment.getSequenceAt(startseq);
+
+    //No group, but the sequence may represent a group
+    if (!groupEditing && av.hasHiddenRows)
+    {
+      if (av.hiddenRepSequences != null
+          && av.hiddenRepSequences.containsKey(seq))
+      {
+        sg = (SequenceGroup) av.hiddenRepSequences.get(seq);
+        groupEditing = true;
       }
+    }
 
-      if (!editingSeqs)
+    StringBuffer message = new StringBuffer();
+    if (groupEditing)
+    {
+      message.append("Edit group:");
+      if (editCommand == null)
       {
-        doMouseDraggedDefineMode(evt);
-        return;
+        editCommand = new EditCommand("Edit Group");
       }
+    }
+    else
+    {
+      message.append("Edit sequence: " + seq.getName());
+      String label = seq.getName();
+      if (label.length() > 10)
+      {
+        label = label.substring(0, 10);
+      }
+      if (editCommand == null)
+      {
+        editCommand = new EditCommand("Edit " + label);
+      }
+    }
 
-        int res = findRes(evt);
+    if (insertGap)
+    {
+      message.append(" insert ");
+    }
+    else
+    {
+      message.append(" delete ");
+    }
 
-        if (res < 0)
-        {
-            res = 0;
-        }
+    message.append(Math.abs(startres - lastres) + " gaps.");
+    ap.alignFrame.statusBar.setText(message.toString());
 
-        if ((lastres == -1) || (lastres == res))
-        {
-            return;
-        }
+    //Are we editing within a selection group?
+    if (groupEditing
+        || (sg != null && sg.getSequences(av.hiddenRepSequences).contains(seq)))
+    {
+      fixedColumns = true;
 
-        if ( (res < av.getAlignment().getWidth()) && (res < lastres))
+      //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))
         {
-          // dragLeft, delete gap
-          editSequence(false, res);
+          endEditing();
+          return;
         }
-        else
-          editSequence(true, res);
+        sg = (SequenceGroup) av.hiddenRepSequences.get(seq);
+      }
+
+      fixedLeft = sg.getStartRes();
+      fixedRight = sg.getEndRes();
 
-        mouseDragging = true;
-        if(scrollThread!=null)
-          scrollThread.setEvent(evt);
+      if ( (startres < fixedLeft && lastres >= fixedLeft)
+          || (startres >= fixedLeft && lastres < fixedLeft)
+          || (startres > fixedRight && lastres <= fixedRight)
+          || (startres <= fixedRight && lastres > fixedRight))
+      {
+        endEditing();
+        return;
+      }
 
+      if (fixedLeft > startres)
+      {
+        fixedRight = fixedLeft - 1;
+        fixedLeft = 0;
+      }
+      else if (fixedRight < startres)
+      {
+        fixedLeft = fixedRight;
+        fixedRight = -1;
+      }
     }
 
-    synchronized void editSequence(boolean insertGap, int startres)
+    if (av.hasHiddenColumns)
     {
-      int fixedLeft = -1;
-      int fixedRight = -1;
-      boolean fixedColumns = false;
-      SequenceGroup sg = av.getSelectionGroup();
+      fixedColumns = true;
+      int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
+      int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
 
-      SequenceI seq = av.alignment.getSequenceAt(startseq);
+      if ( (insertGap && startres > y1 && lastres < y1)
+          || (!insertGap && startres < y2 && lastres > y2))
+      {
+        endEditing();
+        return;
+      }
 
-      //No group, but the sequence may represent a group
-        if (!groupEditing && av.hasHiddenRows)
+      //System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
+      //Selection spans a hidden region
+      if (fixedLeft < y1 && (fixedRight > y2 || fixedRight == -1))
+      {
+        if (startres >= y2)
         {
-          if (av.hiddenRepSequences!=null
-              && av.hiddenRepSequences.containsKey(seq))
-          {
-            sg = (SequenceGroup)av.hiddenRepSequences.get(seq);
-            groupEditing = true;
-          }
+          fixedLeft = y2;
+        }
+        else
+        {
+          fixedRight = y2 - 1;
         }
+      }
+    }
 
+    if (groupEditing)
+    {
+      Vector vseqs = sg.getSequences(av.hiddenRepSequences);
+      int g, groupSize = vseqs.size();
+      SequenceI[] groupSeqs = new SequenceI[groupSize];
+      for (g = 0; g < groupSeqs.length; g++)
+      {
+        groupSeqs[g] = (SequenceI) vseqs.elementAt(g);
+      }
 
-        StringBuffer message = new StringBuffer();
-        if (groupEditing)
+      // drag to right
+      if (insertGap)
+      {
+        //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
+            )
         {
-          message.append("Edit group:");
-          if (editCommand == null)
-            editCommand = new EditCommand("Edit Group");
+          sg.setEndRes(av.alignment.getWidth() + startres - lastres);
+          fixedRight = sg.getEndRes();
         }
-        else
-         {
-           message.append("Edit sequence: " + seq.getName());
-           String label = seq.getName();
-           if(label.length()>10)
-             label = label.substring(0,10);
-           if(editCommand==null)
-             editCommand = new EditCommand("Edit "+label);
-         }
-
-       if(insertGap)
-         message.append(" insert ");
-       else
-         message.append(" delete ");
-
-       message.append(Math.abs(startres-lastres)+" gaps.");
-       ap.alignFrame.statusBar.setText(message.toString());
-
-
-        //Are we editing within a selection group?
-        if (groupEditing
-            || (sg != null && sg.getSequences(av.hiddenRepSequences).contains(seq)))
+
+        // Is it valid with fixed columns??
+        // Find the next gap before the end
+        // of the visible region boundary
+        boolean blank = false;
+        for (fixedRight = fixedRight;
+             fixedRight > lastres;
+             fixedRight--)
         {
-          fixedColumns = true;
+          blank = true;
 
-          //sg might be null as the user may only see 1 sequence,
-          //but the sequence represents a group
-          if (sg == null)
+          for (g = 0; g < groupSize; g++)
           {
-            if(av.hiddenRepSequences==null
-               || !av.hiddenRepSequences.containsKey(seq))
+            for (int j = 0; j < startres - lastres; j++)
             {
-              endEditing();
-              return;
+              if (!jalview.util.Comparison.isGap(
+                  groupSeqs[g].getCharAt(fixedRight - j)))
+              {
+                blank = false;
+                break;
+              }
             }
-            sg = (SequenceGroup) av.hiddenRepSequences.get(seq);
           }
-
-          fixedLeft = sg.getStartRes();
-          fixedRight = sg.getEndRes();
-
-          if (   (startres < fixedLeft && lastres >= fixedLeft)
-              || (startres >= fixedLeft && lastres < fixedLeft)
-              || (startres > fixedRight && lastres <=fixedRight)
-              || (startres <= fixedRight && lastres > fixedRight))
+          if (blank)
           {
-            endEditing();
-            return;
-          }
-
-          if (fixedLeft > startres)
-          {
-            fixedRight = fixedLeft - 1;
-            fixedLeft = 0;
-          }
-          else if (fixedRight < startres)
-          {
-            fixedLeft = fixedRight;
-            fixedRight = -1;
+            break;
           }
         }
 
-
-        if(av.hasHiddenColumns )
+        if (!blank)
         {
-            fixedColumns = true;
-            int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
-            int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
-
-            if ( (insertGap && startres > y1 && lastres < y1)
-                || (!insertGap && startres < y2 && lastres > y2))
+          if (sg.getSize() == av.alignment.getHeight())
+          {
+            if ( (av.hasHiddenColumns
+                  &&
+                  startres < av.getColumnSelection().getHiddenBoundaryRight(startres)))
             {
               endEditing();
               return;
             }
 
-            //System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
-            //Selection spans a hidden region
-            if(fixedLeft<y1 && (fixedRight>y2 || fixedRight==-1))
+            int alWidth = av.alignment.getWidth();
+            if (av.hasHiddenRows)
             {
-              if(startres>=y2)
+              int hwidth = av.alignment.getHiddenSequences().getWidth();
+              if (hwidth > alWidth)
               {
-                fixedLeft = y2;
+                alWidth = hwidth;
               }
-              else
-              {
-               fixedRight = y2 - 1;
-             }
             }
+            //We can still insert gaps if the selectionGroup
+            //contains all the sequences
+            sg.setEndRes(sg.getEndRes() + startres - lastres);
+            fixedRight = alWidth + startres - lastres;
+          }
+          else
+          {
+            endEditing();
+            return;
+          }
         }
+      }
 
+      // drag to left
+      else if (!insertGap)
+      {
+        /// Are we able to delete?
+        // ie are all columns blank?
 
-        if (groupEditing)
+        for (g = 0; g < groupSize; g++)
         {
-          Vector vseqs = sg.getSequences(av.hiddenRepSequences);
-          int g, groupSize = vseqs.size();
-          SequenceI[] groupSeqs = new SequenceI[groupSize];
-          for (g = 0; g < groupSeqs.length; g++)
-            groupSeqs[g] = (SequenceI) vseqs.elementAt(g);
-
-          // drag to right
-          if (insertGap)
+          for (int j = startres; j < lastres; j++)
           {
-              //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
-                 )
-              {
-                sg.setEndRes(av.alignment.getWidth() + startres - lastres);
-                fixedRight = sg.getEndRes();
-              }
-
-            // Is it valid with fixed columns??
-            // Find the next gap before the end
-            // of the visible region boundary
-            boolean blank = false;
-            for (fixedRight = fixedRight;
-                 fixedRight > lastres;
-                 fixedRight--)
+            if (groupSeqs[g].getLength() <= j)
             {
-              blank = true;
-
-              for (g = 0; g < groupSize; g++)
-              {
-                for (int j = 0; j < startres - lastres; j++)
-                {
-                  if (!jalview.util.Comparison.isGap(
-                      groupSeqs[g].getCharAt(fixedRight - j)))
-                  {
-                    blank = false;
-                    break;
-                  }
-                }
-              }
-              if (blank)
-                break;
+              continue;
             }
 
-            if (!blank)
+            if (!jalview.util.Comparison.isGap(
+                groupSeqs[g].getCharAt(j)))
             {
-              if(sg.getSize() == av.alignment.getHeight()  )
-              {
-                if((av.hasHiddenColumns
-                    && startres<av.getColumnSelection().getHiddenBoundaryRight(startres)))
-                {
-                  endEditing();
-                  return;
-                }
-
-                int alWidth = av.alignment.getWidth();
-                if(av.hasHiddenRows)
-                {
-                  int hwidth = av.alignment.getHiddenSequences().getWidth();
-                  if(hwidth>alWidth)
-                    alWidth = hwidth;
-                }
-                //We can still insert gaps if the selectionGroup
-                //contains all the sequences
-                sg.setEndRes(sg.getEndRes()+startres-lastres);
-                fixedRight = alWidth+startres-lastres;
-              }
-              else
-              {
-                endEditing();
-                return;
-              }
+              // Not a gap, block edit not valid
+              endEditing();
+              return;
             }
           }
+        }
+      }
 
-
-          // drag to left
-          else if(!insertGap)
+      if (insertGap)
+      {
+        // dragging to the right
+        if (fixedColumns && fixedRight != -1)
+        {
+          for (int j = lastres; j < startres; j++)
           {
-            /// Are we able to delete?
-            // ie are all columns blank?
-
-            for (g = 0; g < groupSize; g++)
-            {
-              for (int j = startres; j < lastres; j++)
-              {
-                if (groupSeqs[g].getLength() <= j)
-                {
-                  continue;
-                }
-
-                if (!jalview.util.Comparison.isGap(
-                    groupSeqs[g].getCharAt(j)))
-                {
-                  // Not a gap, block edit not valid
-                  endEditing();
-                  return;
-                }
-              }
-            }
+            insertChar(j, groupSeqs, fixedRight);
           }
+        }
+        else
+        {
+          editCommand.appendEdit(EditCommand.INSERT_GAP,
+                                 groupSeqs,
+                                 startres, startres - lastres,
+                                 av.alignment,
+                                 true);
+        }
+      }
+      else
+      {
+        // dragging to the left
+        if (fixedColumns && fixedRight != -1)
+        {
+          for (int j = lastres; j > startres; j--)
+          {
+            deleteChar(startres, groupSeqs, fixedRight);
+          }
+        }
+        else
+        {
+          editCommand.appendEdit(EditCommand.DELETE_GAP,
+                                 groupSeqs,
+                                 startres, lastres - startres,
+                                 av.alignment,
+                                 true);
+        }
 
-            if (insertGap)
-            {
-              // dragging to the right
-              if (fixedColumns && fixedRight != -1)
-              {
-                for (int j = lastres; j < startres; j++)
-                {
-                    insertChar(j, groupSeqs, fixedRight);
-                }
-              }
-              else
-              {
-                editCommand.appendEdit(EditCommand.INSERT_GAP,
-                                       groupSeqs,
-                                       startres, startres-lastres,
-                                       av.alignment,
-                                       true);
-              }
-            }
-            else
-            {
-              // dragging to the left
-              if (fixedColumns && fixedRight != -1)
-              {
-                for (int j = lastres; j > startres; j--)
-                {
-                  deleteChar(startres, groupSeqs, fixedRight);
-                }
-              }
-              else
-                editCommand.appendEdit(EditCommand.DELETE_GAP,
-                                       groupSeqs,
-                                       startres, lastres - startres,
-                                       av.alignment,
-                                       true);
-
-            }
+      }
+    }
+    else /////Editing a single sequence///////////
+    {
+      if (insertGap)
+      {
+        // dragging to the right
+        if (fixedColumns && fixedRight != -1)
+        {
+          for (int j = lastres; j < startres; j++)
+          {
+            insertChar(j, new SequenceI[]
+                       {seq}, fixedRight);
+          }
         }
-        else /////Editing a single sequence///////////
+        else
         {
-          if (insertGap)
+          editCommand.appendEdit(EditCommand.INSERT_GAP,
+                                 new SequenceI[]
+                                 {seq},
+                                 lastres, startres - lastres,
+                                 av.alignment,
+                                 true);
+        }
+      }
+      else
+      {
+        // dragging to the left
+        if (fixedColumns && fixedRight != -1)
+        {
+          for (int j = lastres; j > startres; j--)
           {
-            // dragging to the right
-            if (fixedColumns && fixedRight != -1)
-            {
-              for (int j = lastres; j < startres; j++)
-              {
-                insertChar(j, new SequenceI[]{seq}, fixedRight);
-              }
-            }
-            else
+            if (!jalview.util.Comparison.isGap(seq.getCharAt(startres)))
             {
-              editCommand.appendEdit(EditCommand.INSERT_GAP,
-                                     new SequenceI[]
-                                     {seq},
-                                     lastres, startres-lastres,
-                                     av.alignment,
-                                     true);
+              endEditing();
+              break;
             }
+            deleteChar(startres, new SequenceI[]
+                       {seq}, fixedRight);
           }
-          else
+        }
+        else
+        {
+          //could be a keyboard edit trying to delete none gaps
+          int max = 0;
+          for (int m = startres; m < lastres; m++)
           {
-            // dragging to the left
-            if (fixedColumns && fixedRight != -1)
+            if (!jalview.util.Comparison.isGap(seq.getCharAt(m)))
             {
-              for (int j = lastres; j > startres; j--)
-              {
-                if (!jalview.util.Comparison.isGap(seq.getCharAt(startres)))
-                {
-                  endEditing();
-                  break;
-                }
-                deleteChar(startres, new SequenceI[]{seq}, fixedRight);
-              }
+              break;
             }
-            else
-            {
-              //could be a keyboard edit trying to delete none gaps
-              int max=0;
-              for(int m = startres; m<lastres; m++)
-              {
-                if(!jalview.util.Comparison.isGap(seq.getCharAt(m)))
-                  break;
-                max++;
-              }
+            max++;
+          }
 
-              if (max>0)
-              {
-                editCommand.appendEdit(EditCommand.DELETE_GAP,
-                                       new SequenceI[]
-                                       {seq},
-                                       startres, max,
-                                       av.alignment,
-                                       true);
-              }
-            }
+          if (max > 0)
+          {
+            editCommand.appendEdit(EditCommand.DELETE_GAP,
+                                   new SequenceI[]
+                                   {seq},
+                                   startres, max,
+                                   av.alignment,
+                                   true);
           }
         }
+      }
+    }
+
+    lastres = startres;
+    seqCanvas.repaint();
+  }
+
+  void insertChar(int j, SequenceI[] seq, int fixedColumn)
+  {
+    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
+
+      for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
+      {
+        if (jalview.util.Comparison.isGap(seq[s].getCharAt(blankColumn)))
+        {
+          //Theres a space, so break and insert the gap
+          break;
+        }
+      }
 
-        lastres = startres;
-        seqCanvas.repaint();
+      if (blankColumn <= j)
+      {
+        blankColumn = fixedColumn;
+        endEditing();
+        return;
+      }
+    }
+
+    editCommand.appendEdit(EditCommand.DELETE_GAP,
+                           seq,
+                           blankColumn, 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.INSERT_GAP,
+                           seq,
+                           fixedColumn, 1, av.alignment, true);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void mouseEntered(MouseEvent e)
+  {
+    if (oldSeq < 0)
+    {
+      oldSeq = 0;
+    }
+
+    if (scrollThread != null)
+    {
+      scrollThread.running = false;
+      scrollThread = null;
     }
+  }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void mouseExited(MouseEvent e)
+  {
+    if (av.getWrapAlignment())
+    {
+      return;
+    }
 
+    if (mouseDragging)
+    {
+      scrollThread = new ScrollThread();
+    }
+  }
 
-    void insertChar(int j, SequenceI [] seq, int fixedColumn)
+  public void mouseClicked(MouseEvent evt)
+  {
+    SequenceI sequence = av.alignment.getSequenceAt(findSeq(evt));
+    if (evt.getClickCount() > 1)
     {
-      int blankColumn = fixedColumn;
-      for(int s=0; s<seq.length; s++)
+      if (av.getSelectionGroup().getSize() == 1
+          && av.getSelectionGroup().getEndRes()
+          - av.getSelectionGroup().getStartRes() < 2)
       {
-        //Find the next gap before the end of the visible region boundary
-        //If lastCol > j, theres a boundary after the gap insertion
+        av.setSelectionGroup(null);
+      }
 
-        for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
-        {
-          if (jalview.util.Comparison.isGap(seq[s].getCharAt(blankColumn)))
-          {
-            //Theres a space, so break and insert the gap
-            break;
-          }
-        }
+      SequenceFeature[] features = findFeaturesAtRes(
+          sequence.getDatasetSequence(),
+          sequence.findPosition(findRes(evt))
+          );
 
-        if (blankColumn <= j)
-        {
-          blankColumn = fixedColumn;
-          endEditing();
-          return;
-        }
+      if (features != null && features.length > 0)
+      {
+        SearchResults highlight = new SearchResults();
+        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.highlightSearchResults(null);
+      }
+    }
+  }
+
+  public void mouseWheelMoved(MouseWheelEvent e)
+  {
+    e.consume();
+    /* if (mouseWheelPressed)
+     {
+       Font font = av.getFont();
+       int fontSize = font.getSize();
+       if (e.getWheelRotation() > 0 && fontSize < 51)
+         fontSize++;
+       else if (fontSize > 1)
+         fontSize--;
+
+
+
+       av.setFont(new Font(font.getName(), font.getStyle(), fontSize));
+
+       ap.fontChanged();
+     }
+     else*/
+    {
+      if (e.getWheelRotation() > 0)
+      {
+        ap.scrollUp(false);
+      }
+      else
+      {
+        ap.scrollUp(true);
+      }
+    }
+
+  }
 
-      editCommand.appendEdit(EditCommand.DELETE_GAP,
-                             seq,
-                             blankColumn, 1, av.alignment, true);
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void doMousePressedDefineMode(MouseEvent evt)
+  {
+    int res = findRes(evt);
+    int seq = findSeq(evt);
+    oldSeq = seq;
 
-      editCommand.appendEdit(EditCommand.INSERT_GAP,
-                             seq,
-                             j, 1, av.alignment,
-                             true);
+    startWrapBlock = wrappedBlock;
 
+    if (av.wrapAlignment && seq > av.alignment.getHeight())
+    {
+      JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                                            "Cannot edit annotations in wrapped view.",
+                                            "Wrapped view - no edit",
+                                            JOptionPane.WARNING_MESSAGE);
+      return;
     }
 
-    void deleteChar(int j, SequenceI [] seq, int fixedColumn)
+    if (seq < 0 || res < 0)
     {
+      return;
+    }
 
-      editCommand.appendEdit(EditCommand.DELETE_GAP,
-                             seq,
-                             j, 1, av.alignment, true);
+    SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
 
-      editCommand.appendEdit(EditCommand.INSERT_GAP,
-                             seq,
-                             fixedColumn, 1, av.alignment, true);
+    if ( (sequence == null) || (res > sequence.getLength()))
+    {
+      return;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void mouseEntered(MouseEvent e)
+    stretchGroup = av.getSelectionGroup();
+
+    if (stretchGroup == null)
     {
-        if(oldSeq < 0)
-          oldSeq = 0;
+      stretchGroup = av.alignment.findGroup(sequence);
 
-        if (scrollThread != null)
-        {
-            scrollThread.running = false;
-            scrollThread = null;
-        }
+      if ( (stretchGroup != null) && (res > stretchGroup.getStartRes()) &&
+          (res < stretchGroup.getEndRes()))
+      {
+        av.setSelectionGroup(stretchGroup);
+      }
+      else
+      {
+        stretchGroup = null;
+      }
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void mouseExited(MouseEvent e)
+    else if (!stretchGroup.getSequences(null).contains(sequence) ||
+             (stretchGroup.getStartRes() > res) ||
+             (stretchGroup.getEndRes() < res))
     {
-        if (av.getWrapAlignment())
-        {
-            return;
-        }
+      stretchGroup = null;
 
-        if (mouseDragging)
+      SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
+
+      if (allGroups != null)
+      {
+        for (int i = 0; i < allGroups.length; i++)
         {
-            scrollThread = new ScrollThread();
+          if ( (allGroups[i].getStartRes() <= res) &&
+              (allGroups[i].getEndRes() >= res))
+          {
+            stretchGroup = allGroups[i];
+            break;
+          }
         }
+      }
+
+      av.setSelectionGroup(stretchGroup);
+
     }
 
-    public void mouseClicked(MouseEvent evt)
+    if (javax.swing.SwingUtilities.isRightMouseButton(evt))
     {
-      SequenceI sequence = av.alignment.getSequenceAt( findSeq(evt) );
-      if(evt.getClickCount()>1)
+      Vector allFeatures = getAllFeaturesAtRes(sequence.getDatasetSequence(),
+                                               sequence.findPosition(res));
+      Vector links = new Vector();
+      for (int i = 0; i < allFeatures.size(); i++)
       {
-        if (av.getSelectionGroup().getSize() == 1
-            && av.getSelectionGroup().getEndRes()
-            - av.getSelectionGroup().getStartRes() < 2)
-          av.setSelectionGroup(null);
-
-        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());
-          seqCanvas.highlightSearchResults(highlight);
-        }
-        if(features!=null && features.length>0)
+        SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(i);
+        if (sf.links != null)
         {
-          seqCanvas.getFeatureRenderer().amendFeatures(
-              new SequenceI[]
-              {sequence}, features, false, ap);
-
-          seqCanvas.highlightSearchResults(null);
+          for (int j = 0; j < sf.links.size(); j++)
+          {
+            links.addElement(sf.links.elementAt(j));
+          }
         }
       }
+
+      jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null, links);
+      pop.show(this, evt.getX(), evt.getY());
+      return;
     }
 
-    public void mouseWheelMoved(MouseWheelEvent e)
+    if (av.cursorMode)
     {
-      e.consume();
-     /* if (mouseWheelPressed)
-      {
-        Font font = av.getFont();
-        int fontSize = font.getSize();
-        if (e.getWheelRotation() > 0 && fontSize < 51)
-          fontSize++;
-        else if (fontSize > 1)
-          fontSize--;
+      seqCanvas.cursorX = findRes(evt);
+      seqCanvas.cursorY = findSeq(evt);
+      seqCanvas.repaint();
+      return;
+    }
 
+    if (stretchGroup == null)
+    {
+      //Only if left mouse button do we want to change group sizes
 
+      // define a new group here
+      SequenceGroup sg = new SequenceGroup();
+      sg.setStartRes(res);
+      sg.setEndRes(res);
+      sg.addSequence(sequence, false);
+      av.setSelectionGroup(sg);
+      stretchGroup = sg;
 
-        av.setFont(new Font(font.getName(), font.getStyle(), fontSize));
+      if (av.getConservationSelected())
+      {
+        SliderPanel.setConservationSlider(ap,
+                                          av.getGlobalColourScheme(),
+                                          "Background");
+      }
 
-        ap.fontChanged();
+      if (av.getAbovePIDThreshold())
+      {
+        SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
+                                       "Background");
       }
-      else*/
+      if ( (stretchGroup != null) && (stretchGroup.getEndRes() == res))
       {
-        if (e.getWheelRotation() > 0)
-          ap.scrollUp(false);
-        else
-          ap.scrollUp(true);
+        // Edit end res position of selected group
+        changeEndRes = true;
       }
-
+      else if ( (stretchGroup != null) &&
+               (stretchGroup.getStartRes() == res))
+      {
+        // Edit end res position of selected group
+        changeStartRes = true;
+      }
+      stretchGroup.getWidth();
     }
 
+    seqCanvas.repaint();
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void doMousePressedDefineMode(MouseEvent evt)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void doMouseReleasedDefineMode(MouseEvent evt)
+  {
+    if (stretchGroup == null)
     {
-      int res = findRes(evt);
-      int seq = findSeq(evt);
-      oldSeq = seq;
-
-      startWrapBlock=wrappedBlock;
+      return;
+    }
 
-      if(av.wrapAlignment && seq>av.alignment.getHeight())
+    if (stretchGroup.cs != null)
+    {
+      if (stretchGroup.cs instanceof ClustalxColourScheme)
       {
-          JOptionPane.showInternalMessageDialog(Desktop.desktop,
-              "Cannot edit annotations in wrapped view.",
-              "Wrapped view - no edit",
-              JOptionPane.WARNING_MESSAGE);
-          return;
+        ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(
+            stretchGroup.getSequences(av.hiddenRepSequences),
+            stretchGroup.getWidth());
       }
 
-      if(seq<0 || res<0)
-            return;
-
-        SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
-
-        if ((sequence == null) || (res > sequence.getLength()))
-        {
-            return;
-        }
-
-        stretchGroup = av.getSelectionGroup();
-
-        if (stretchGroup == null)
-        {
-            stretchGroup = av.alignment.findGroup(sequence);
-
-            if ((stretchGroup != null) && (res > stretchGroup.getStartRes()) &&
-                    (res < stretchGroup.getEndRes()))
-            {
-                av.setSelectionGroup(stretchGroup);
-            }
-            else
-            {
-                stretchGroup = null;
-            }
-        }
-        else if (!stretchGroup.getSequences(null).contains(sequence) ||
-                (stretchGroup.getStartRes() > res) ||
-                (stretchGroup.getEndRes() < res))
-        {
-            stretchGroup = null;
-
-            SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
-
-            if (allGroups != null)
-            {
-                for (int i = 0; i < allGroups.length; i++)
-                {
-                    if ((allGroups[i].getStartRes() <= res) &&
-                            (allGroups[i].getEndRes() >= res))
-                    {
-                        stretchGroup = allGroups[i];
-                        break;
-                    }
-                }
-            }
-
-            av.setSelectionGroup(stretchGroup);
-
-        }
-
-
-        if (javax.swing.SwingUtilities.isRightMouseButton(evt))
-        {
-          Vector allFeatures = getAllFeaturesAtRes(sequence.getDatasetSequence(),
-                                                  sequence.findPosition(res));
-          Vector links = new Vector();
-            for (int i = 0; i < allFeatures.size(); i++)
-            {
-              SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(i);
-              if (sf.links != null)
-              {
-                for (int j = 0; j < sf.links.size(); j++)
-                {
-                  links.addElement(sf.links.elementAt(j));
-                }
-              }
-            }
-
-            jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null, links);
-            pop.show(this, evt.getX(), evt.getY());
-            return;
-        }
-
-        if (av.cursorMode)
-        {
-          seqCanvas.cursorX = findRes(evt);
-          seqCanvas.cursorY = findSeq(evt);
-          seqCanvas.repaint();
-          return;
-        }
-
-        if (stretchGroup == null)
-        {
-          //Only if left mouse button do we want to change group sizes
+      if (stretchGroup.cs instanceof Blosum62ColourScheme
+          || stretchGroup.cs instanceof PIDColourScheme
+          || stretchGroup.cs.conservationApplied()
+          || stretchGroup.cs.getThreshold() > 0)
+      {
+        stretchGroup.recalcConservation();
+      }
 
-          // define a new group here
-          SequenceGroup sg = new SequenceGroup();
-          sg.setStartRes(res);
-          sg.setEndRes(res);
-          sg.addSequence(sequence, false);
-          av.setSelectionGroup(sg);
-          stretchGroup = sg;
+      if (stretchGroup.cs.conservationApplied())
+      {
+        SliderPanel.setConservationSlider(ap, stretchGroup.cs,
+                                          stretchGroup.getName());
+      }
+      else
+      {
+        SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
+                                       stretchGroup.getName());
+      }
+    }
+    changeEndRes = false;
+    changeStartRes = false;
+    stretchGroup = null;
 
-          if (av.getConservationSelected())
-          {
-            SliderPanel.setConservationSlider(ap,
-                                              av.getGlobalColourScheme(),
-                                              "Background");
-          }
+    PaintRefresher.Refresh(this, av.getSequenceSetId());
+  }
 
-          if (av.getAbovePIDThreshold())
-          {
-            SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
-                                           "Background");
-          }
-          if ( (stretchGroup != null) && (stretchGroup.getEndRes() == res))
-          {
-            // Edit end res position of selected group
-            changeEndRes = true;
-          }
-          else if ( (stretchGroup != null) &&
-                   (stretchGroup.getStartRes() == res))
-          {
-            // Edit end res position of selected group
-            changeStartRes = true;
-          }
-          stretchGroup.getWidth();
-        }
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void doMouseDraggedDefineMode(MouseEvent evt)
+  {
+    int res = findRes(evt);
+    int y = findSeq(evt);
 
-        seqCanvas.repaint();
+    if (wrappedBlock != startWrapBlock)
+    {
+      return;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void doMouseReleasedDefineMode(MouseEvent evt)
+    if (stretchGroup == null)
     {
-        if (stretchGroup == null)
-        {
-            return;
-        }
-
-
-        if(stretchGroup.cs!=null)
-        {
-          if (stretchGroup.cs instanceof ClustalxColourScheme)
-          {
-            ( (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.recalcConservation();
+      return;
+    }
 
-          if (stretchGroup.cs.conservationApplied())
-          {
-            SliderPanel.setConservationSlider(ap, stretchGroup.cs,
-                                              stretchGroup.getName());
-          }
-          else
-          {
-            SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
-                                           stretchGroup.getName());
-          }
-        }
-        changeEndRes = false;
-        changeStartRes = false;
-        stretchGroup = null;
+    if (res >= av.alignment.getWidth())
+    {
+      res = av.alignment.getWidth() - 1;
+    }
 
-        PaintRefresher.Refresh(this, av.getSequenceSetId());
+    if (stretchGroup.getEndRes() == res)
+    {
+      // Edit end res position of selected group
+      changeEndRes = true;
+    }
+    else if (stretchGroup.getStartRes() == res)
+    {
+      // Edit start res position of selected group
+      changeStartRes = true;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void doMouseDraggedDefineMode(MouseEvent evt)
+    if (res < av.getStartRes())
     {
-      int res = findRes(evt);
-      int y = findSeq(evt);
+      res = av.getStartRes();
+    }
 
-      if(wrappedBlock!=startWrapBlock)
-        return;
+    if (changeEndRes)
+    {
+      if (res > (stretchGroup.getStartRes() - 1))
+      {
+        stretchGroup.setEndRes(res);
+      }
+    }
+    else if (changeStartRes)
+    {
+      if (res < (stretchGroup.getEndRes() + 1))
+      {
+        stretchGroup.setStartRes(res);
+      }
+    }
 
-       if (stretchGroup == null)
-       {
-            return;
-       }
+    int dragDirection = 0;
 
-        if(res>= av.alignment.getWidth())
-        {
-          res = av.alignment.getWidth()-1;
-        }
+    if (y > oldSeq)
+    {
+      dragDirection = 1;
+    }
+    else if (y < oldSeq)
+    {
+      dragDirection = -1;
+    }
 
-        if (stretchGroup.getEndRes() == res)
-        {
-            // Edit end res position of selected group
-            changeEndRes = true;
-        }
-        else if (stretchGroup.getStartRes() == res)
-        {
-            // Edit start res position of selected group
-            changeStartRes = true;
-        }
+    while ( (y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))
+    {
+      // This routine ensures we don't skip any sequences, as the
+      // selection is quite slow.
+      Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
 
-        if (res < av.getStartRes())
-        {
-            res = av.getStartRes();
-        }
+      oldSeq += dragDirection;
 
-        if (changeEndRes)
-        {
-            if (res > (stretchGroup.getStartRes() - 1))
-            {
-                stretchGroup.setEndRes(res);
-            }
-        }
-        else if (changeStartRes)
-        {
-            if (res < (stretchGroup.getEndRes() + 1))
-            {
-                stretchGroup.setStartRes(res);
-            }
-        }
+      if (oldSeq < 0)
+      {
+        break;
+      }
 
-        int dragDirection = 0;
+      Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
 
-        if (y > oldSeq)
-        {
-            dragDirection = 1;
-        }
-        else if (y < oldSeq)
+      if (stretchGroup.getSequences(null).contains(nextSeq))
+      {
+        stretchGroup.deleteSequence(seq, false);
+      }
+      else
+      {
+        if (seq != null)
         {
-            dragDirection = -1;
+          stretchGroup.addSequence(seq, false);
         }
 
+        stretchGroup.addSequence(nextSeq, false);
+      }
+    }
 
-        while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))
-        {
-            // This routine ensures we don't skip any sequences, as the
-            // selection is quite slow.
-            Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
-
-            oldSeq += dragDirection;
+    if (oldSeq < 0)
+    {
+      oldSeq = -1;
+    }
 
-            if(oldSeq<0)
-              break;
+    mouseDragging = true;
 
-            Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
+    if (scrollThread != null)
+    {
+      scrollThread.setEvent(evt);
+    }
 
-            if (stretchGroup.getSequences(null).contains(nextSeq))
-            {
-                stretchGroup.deleteSequence(seq, false);
-            }
-            else
-            {
-                if (seq != null)
-                {
-                    stretchGroup.addSequence(seq, false);
-                }
+    seqCanvas.repaint();
+  }
 
-                stretchGroup.addSequence(nextSeq, false);
-            }
-        }
+  void scrollCanvas(MouseEvent evt)
+  {
+    if (evt == null)
+    {
+      if (scrollThread != null)
+      {
+        scrollThread.running = false;
+        scrollThread = null;
+      }
+      mouseDragging = false;
+    }
+    else
+    {
+      if (scrollThread == null)
+      {
+        scrollThread = new ScrollThread();
+      }
 
-        if(oldSeq < 0)
-          oldSeq = -1;
+      mouseDragging = true;
+      scrollThread.setEvent(evt);
+    }
 
-        mouseDragging = true;
+  }
 
-        if (scrollThread != null)
-        {
-            scrollThread.setEvent(evt);
-        }
+  // this class allows scrolling off the bottom of the visible alignment
+  class ScrollThread
+      extends Thread
+  {
+    MouseEvent evt;
+    boolean running = false;
 
-        seqCanvas.repaint();
+    public ScrollThread()
+    {
+      start();
     }
 
-    void scrollCanvas(MouseEvent evt)
+    public void setEvent(MouseEvent e)
     {
-      if(evt==null)
-      {
-        if(scrollThread!=null)
-        {
-          scrollThread.running = false;
-          scrollThread = null;
-        }
-        mouseDragging = false;
-      }
-      else
-      {
-        if (scrollThread == null)
-          scrollThread = new ScrollThread();
-
-        mouseDragging = true;
-        scrollThread.setEvent(evt);
-      }
-
+      evt = e;
     }
 
+    public void stopScrolling()
+    {
+      running = false;
+    }
 
-    // this class allows scrolling off the bottom of the visible alignment
-    class ScrollThread extends Thread
+    public void run()
     {
-        MouseEvent evt;
-        boolean running = false;
+      running = true;
 
-        public ScrollThread()
+      while (running)
+      {
+        if (evt != null)
         {
-            start();
-        }
+          if (mouseDragging && (evt.getY() < 0) &&
+              (av.getStartSeq() > 0))
+          {
+            running = ap.scrollUp(true);
+          }
 
-        public void setEvent(MouseEvent e)
-        {
-            evt = e;
+          if (mouseDragging && (evt.getY() >= getHeight()) &&
+              (av.alignment.getHeight() > av.getEndSeq()))
+          {
+            running = ap.scrollUp(false);
+          }
+
+          if (mouseDragging && (evt.getX() < 0))
+          {
+            running = ap.scrollRight(false);
+          }
+          else if (mouseDragging && (evt.getX() >= getWidth()))
+          {
+            running = ap.scrollRight(true);
+          }
         }
 
-        public void stopScrolling()
+        try
         {
-            running = false;
+          Thread.sleep(20);
         }
-
-        public void run()
+        catch (Exception ex)
         {
-            running = true;
-
-            while (running)
-            {
-                if (evt != null)
-                {
-                    if (mouseDragging && (evt.getY() < 0) &&
-                            (av.getStartSeq() > 0))
-                    {
-                        running = ap.scrollUp(true);
-                    }
-
-                    if (mouseDragging && (evt.getY() >= getHeight()) &&
-                            (av.alignment.getHeight() > av.getEndSeq()))
-                    {
-                        running = ap.scrollUp(false);
-                    }
-
-                    if (mouseDragging && (evt.getX() < 0))
-                    {
-                        running = ap.scrollRight(false);
-                    }
-                    else if (mouseDragging && (evt.getX() >= getWidth()))
-                    {
-                        running = ap.scrollRight(true);
-                    }
-                }
-
-                try
-                {
-                    Thread.sleep(20);
-                }
-                catch (Exception ex)
-                {
-                }
-            }
         }
+      }
     }
+  }
 }
diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index b4370b7..ce366c8 100755
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,16 +18,16 @@
  */
 package jalview.gui;
 
-import javax.swing.*;
+import java.io.*;
+import java.util.*;
+
 import java.awt.*;
 import java.awt.event.*;
-import jalview.io.EBIFetchClient;
+import javax.swing.*;
+
 import MCview.*;
 import jalview.datamodel.*;
-import jalview.analysis.AlignSeq;
-import java.io.File;
 import jalview.io.*;
-import java.util.*;
 
 public class SequenceFetcher
     extends JPanel implements Runnable
@@ -58,14 +58,19 @@ public class SequenceFetcher
     frame = new JInternalFrame();
     frame.setContentPane(this);
     if (System.getProperty("os.name").startsWith("Mac"))
+    {
       Desktop.addInternalFrame(frame, getFrameTitle(), 400, 140);
+    }
     else
+    {
       Desktop.addInternalFrame(frame, getFrameTitle(), 400, 125);
+    }
   }
 
   private String getFrameTitle()
   {
-    return ( (alignFrame == null) ? "New " : "Additional ") + "Sequence Fetcher";
+    return ( (alignFrame == null) ? "New " : "Additional ") +
+        "Sequence Fetcher";
   }
 
   private void jbInit()
@@ -163,11 +168,15 @@ public class SequenceFetcher
   {
     String error = "";
     if (database.getSelectedItem().equals(noDbSelected))
+    {
       error += "Please select the source database\n";
+    }
     com.stevesoft.pat.Regex empty = new com.stevesoft.pat.Regex("\\s+", "");
     textfield.setText(empty.replaceAll(textfield.getText()));
     if (textfield.getText().length() == 0)
+    {
       error += "Please enter a (semi-colon separated list of) database id(s)";
+    }
     if (error.length() > 0)
     {
       showErrorMessage(error);
@@ -184,7 +193,7 @@ public class SequenceFetcher
              || database.getSelectedItem().equals("EMBLCDS"))
     {
       StringTokenizer st = new StringTokenizer(textfield.getText(), ";");
-      while(st.hasMoreTokens())
+      while (st.hasMoreTokens())
       {
         EBIFetchClient dbFetch = new EBIFetchClient();
 
@@ -196,11 +205,13 @@ public class SequenceFetcher
         if (reply != null)
         {
           for (int i = 0; i < reply.length; i++)
+          {
             result.append(reply[i] + "\n");
+          }
         }
       }
 
-      if(result!=null && result.length()>1) // arbitrary minimum length for a seuqence file
+      if (result != null && result.length() > 1) // arbitrary minimum length for a seuqence file
       {
         System.out.println(result.toString());
 
@@ -212,49 +223,68 @@ public class SequenceFetcher
       StringTokenizer qset = new StringTokenizer(textfield.getText(), ";");
       String query;
       SequenceI[] seqs = null;
-      while (qset.hasMoreTokens() && ((query = qset.nextToken())!=null))
+      while (qset.hasMoreTokens() && ( (query = qset.nextToken()) != null))
       {
         SequenceI[] seqparts = getPDBFile(query.toUpperCase());
-          if (seqparts!=null) {
-              if (seqs==null) {
-                  seqs = seqparts;
-              } else {
-                  SequenceI[] newseqs = new SequenceI[seqs.length+seqparts.length];
-                  int i=0;
-                  for (;i<seqs.length; i++) {
-                      newseqs[i] = seqs[i];
-                      seqs[i] = null;
-                  }
-                  for (int j=0;j<seqparts.length; i++, j++)
-                      newseqs[i] = seqparts[j];
-                  seqs=newseqs;
-              }
-              result.append("# Success for "+query.toUpperCase()+"\n");
+        if (seqparts != null)
+        {
+          if (seqs == null)
+          {
+            seqs = seqparts;
           }
+          else
+          {
+            SequenceI[] newseqs = new SequenceI[seqs.length + seqparts.length];
+            int i = 0;
+            for (; i < seqs.length; i++)
+            {
+              newseqs[i] = seqs[i];
+              seqs[i] = null;
+            }
+            for (int j = 0; j < seqparts.length; i++, j++)
+            {
+              newseqs[i] = seqparts[j];
+            }
+            seqs = newseqs;
+          }
+          result.append("# Success for " + query.toUpperCase() + "\n");
+        }
       }
-      if (seqs!=null && seqs.length>0) {
-          if (parseResult(new Alignment(seqs), null, null)!=null)
-              result.append("# Successfully parsed the PDB File Queries into an Alignment");
+      if (seqs != null && seqs.length > 0)
+      {
+        if (parseResult(new Alignment(seqs), null, null) != null)
+        {
+          result.append(
+              "# Successfully parsed the PDB File Queries into an Alignment");
+        }
       }
     }
-    else if( database.getSelectedItem().equals("PFAM"))
+    else if (database.getSelectedItem().equals("PFAM"))
     {
-      try{
+      try
+      {
         result.append(new FastaFile(
-           "http://www.sanger.ac.uk/cgi-bin/Pfam/getalignment.pl?format=fal&acc="
-           +  textfield.getText().toUpperCase(), "URL").print()
-           );
+            "http://www.sanger.ac.uk/cgi-bin/Pfam/getalignment.pl?format=fal&acc="
+            + textfield.getText().toUpperCase(), "URL").print()
+            );
 
-         if(result.length()>0)
-           parseResult( result.toString(), textfield.getText().toUpperCase() );
+        if (result.length() > 0)
+        {
+          parseResult(result.toString(), textfield.getText().toUpperCase());
+        }
 
-      }catch(java.io.IOException ex)
-      {   result = null;    }
+      }
+      catch (java.io.IOException ex)
+      {
+        result = null;
+      }
     }
 
     if (result == null || result.length() == 0)
+    {
       showErrorMessage("Error retrieving " + textfield.getText()
                        + " from " + database.getSelectedItem());
+    }
 
     resetDialog();
     return;
@@ -292,7 +322,7 @@ public class SequenceFetcher
 
         if (entry.getProtein() != null)
         {
-           name.append(" " + entry.getProtein().getName().elementAt(0));
+          name.append(" " + entry.getProtein().getName().elementAt(0));
         }
 
         result.append(name + "\n" + entry.getUniprotSequence().getContent() +
@@ -311,7 +341,9 @@ public class SequenceFetcher
         {
           PDBEntry pdb = (PDBEntry) e.nextElement();
           if (!pdb.getType().equals("PDB"))
+          {
             continue;
+          }
 
           onlyPdbEntries.addElement(pdb);
         }
@@ -319,14 +351,12 @@ public class SequenceFetcher
         Enumeration en2 = entry.getAccession().elements();
         while (en2.hasMoreElements())
         {
-          al.getSequenceAt(i).getDatasetSequence().addDBRef(new DBRefEntry(DBRefSource.UNIPROT,
-                    "0",
-                    en2.nextElement().toString()));
+          al.getSequenceAt(i).getDatasetSequence().addDBRef(new DBRefEntry(
+              DBRefSource.UNIPROT,
+              "0",
+              en2.nextElement().toString()));
         }
 
-
-
-
         al.getSequenceAt(i).getDatasetSequence().setPDBId(onlyPdbEntries);
         if (entry.getFeature() != null)
         {
@@ -335,7 +365,7 @@ public class SequenceFetcher
           {
             SequenceFeature sf = (SequenceFeature) e.nextElement();
             sf.setFeatureGroup("Uniprot");
-            al.getSequenceAt(i).getDatasetSequence().addSequenceFeature( sf );
+            al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
           }
         }
       }
@@ -353,9 +383,12 @@ public class SequenceFetcher
     }
 
     EBIFetchClient ebi = new EBIFetchClient();
-    String file = ebi.fetchDataAsFile("pdb:" + id, "pdb", "raw").getAbsolutePath();
+    String file = ebi.fetchDataAsFile("pdb:" + id, "pdb", "raw").
+        getAbsolutePath();
     if (file == null)
+    {
       return null;
+    }
     try
     {
       PDBfile pdbfile = new PDBfile(file, jalview.io.AppletFormatAdapter.FILE);
@@ -363,33 +396,35 @@ public class SequenceFetcher
       {
         if (chain == null ||
             ( (PDBChain) pdbfile.chains.elementAt(i)).id.
-            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
-            SequenceI sq = pdbchain.sequence;
-            // Specially formatted name for the PDB chain sequences retrieved from the PDB
-            sq.setName("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);
-            */
-            // 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());
+            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
+          SequenceI sq = pdbchain.sequence;
+          // Specially formatted name for the PDB chain sequences retrieved from the PDB
+          sq.setName("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);
+           */
+          // 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());
         }
       }
     }
@@ -401,75 +436,91 @@ public class SequenceFetcher
       return null;
     }
     SequenceI[] results = new SequenceI[result.size()];
-    for (int i=0,j=result.size();i<j; i++) {
-        results[i] = (SequenceI) result.elementAt(i);
-        result.setElementAt(null,i);
+    for (int i = 0, j = result.size(); i < j; i++)
+    {
+      results[i] = (SequenceI) result.elementAt(i);
+      result.setElementAt(null, i);
     }
     return results;
   }
+
   Alignment parseResult(String result, String title)
   {
-      String format = new IdentifyFile().Identify(result, "Paste");
-      Alignment sequences = null;
-      if (FormatAdapter.isValidFormat(format))
+    String format = new IdentifyFile().Identify(result, "Paste");
+    Alignment sequences = null;
+    if (FormatAdapter.isValidFormat(format))
+    {
+      sequences = null;
+      try
       {
-        sequences = null;
-        try{ sequences = new FormatAdapter().readFile(result.toString(), "Paste",
-                                                 format);}
-        catch(Exception ex){}
-
-        if (sequences!=null)
-            return parseResult(sequences, title, format);
-      } else {
-              showErrorMessage("Error retrieving " + textfield.getText()
-                      + " from " + database.getSelectedItem());
+        sequences = new FormatAdapter().readFile(result.toString(), "Paste",
+                                                 format);
       }
+      catch (Exception ex)
+      {}
 
-      return null;
+      if (sequences != null)
+      {
+        return parseResult(sequences, title, format);
+      }
+    }
+    else
+    {
+      showErrorMessage("Error retrieving " + textfield.getText()
+                       + " from " + database.getSelectedItem());
+    }
+
+    return null;
   }
-  Alignment parseResult(Alignment al, String title, String currentFileFormat) {
-    
-      if (al != null && al.getHeight() > 0)
+
+  Alignment parseResult(Alignment al, String title, String currentFileFormat)
+  {
+
+    if (al != null && al.getHeight() > 0)
+    {
+      if (alignFrame == null)
       {
-        if (alignFrame == null)
+        AlignFrame af = new AlignFrame(al,
+                                       AlignFrame.DEFAULT_WIDTH,
+                                       AlignFrame.DEFAULT_HEIGHT);
+        if (currentFileFormat != null)
         {
-          AlignFrame af = new AlignFrame(al,
-                                           AlignFrame.DEFAULT_WIDTH,
-                                           AlignFrame.DEFAULT_HEIGHT);
-          if (currentFileFormat!=null)
-              af.currentFileFormat = currentFileFormat; // WHAT IS THE DEFAULT FORMAT FOR NON-FormatAdapter Sourced Alignments?
-          
-          if(title==null)
-            title = "Retrieved from " + database.getSelectedItem();
-          
-          Desktop.addInternalFrame(af,
-                                   title,
-                                   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)
-          {}
+          af.currentFileFormat = currentFileFormat; // WHAT IS THE DEFAULT FORMAT FOR NON-FormatAdapter Sourced Alignments?
         }
-        else
+
+        if (title == null)
         {
-          for (int i = 0; i < al.getHeight(); i++)
-          {
-            alignFrame.viewport.alignment.addSequence(al.getSequenceAt(i)); // this also creates dataset sequence entries
-          }
-          alignFrame.viewport.setEndSeq(alignFrame.viewport.alignment.
-                                        getHeight());
-          alignFrame.viewport.alignment.getWidth();
-          alignFrame.viewport.firePropertyChange("alignment", null,
-                                                 alignFrame.viewport.
-                                                 getAlignment().getSequences());
+          title = "Retrieved from " + database.getSelectedItem();
+        }
+
+        Desktop.addInternalFrame(af,
+                                 title,
+                                 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)
+        {}
       }
+      else
+      {
+        for (int i = 0; i < al.getHeight(); i++)
+        {
+          alignFrame.viewport.alignment.addSequence(al.getSequenceAt(i)); // this also creates dataset sequence entries
+        }
+        alignFrame.viewport.setEndSeq(alignFrame.viewport.alignment.
+                                      getHeight());
+        alignFrame.viewport.alignment.getWidth();
+        alignFrame.viewport.firePropertyChange("alignment", null,
+                                               alignFrame.viewport.
+                                               getAlignment().getSequences());
+      }
+    }
     return al;
   }
 
@@ -482,9 +533,8 @@ public class SequenceFetcher
       {
         JOptionPane.showInternalMessageDialog(Desktop.desktop,
                                               error, "Error Retrieving Data",
-                                          JOptionPane.WARNING_MESSAGE);
+                                              JOptionPane.WARNING_MESSAGE);
       }
     });
   }
 }
-
diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 6c7fb37..70f67d7 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,12 +18,11 @@
  */
 package jalview.gui;
 
-import jalview.datamodel.*;
+import java.awt.*;
 
+import jalview.datamodel.*;
 import jalview.schemes.*;
 
-import java.awt.*;
-
 /**
  * DOCUMENT ME!
  *
@@ -32,390 +31,404 @@ import java.awt.*;
  */
 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)
+  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))
     {
-        this.av = av;
+      if (currentSequenceGroup.getDisplayBoxes())
+      {
+        getBoxColour(currentSequenceGroup.cs, seq, i);
+      }
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param b DOCUMENT ME!
-     */
-    public void prepare(Graphics g, boolean renderGaps)
+    else if (av.getShowBoxes())
     {
-        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);
+      getBoxColour(av.globalColourScheme, seq, i);
+    }
 
-        this.renderGaps = renderGaps;
+    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);
+        }
 
-    public Color getResidueBoxColour(SequenceI seq, int i)
-    {
-      allGroups = av.alignment.findAllGroups(seq);
+      }
 
-      if (inCurrentSequenceGroup(i))
+      if (resBoxColour != tempColour)
       {
-        if (currentSequenceGroup.getDisplayBoxes())
+        if (tempColour != null)
         {
-          getBoxColour(currentSequenceGroup.cs, seq, i);
+          graphics.fillRect(av.charWidth * (curStart - start), y1,
+                            curWidth, av.charHeight);
         }
+
+        graphics.setColor(resBoxColour);
+
+        curStart = i;
+        curWidth = av.charWidth;
+        tempColour = resBoxColour;
       }
-      else if (av.getShowBoxes())
+      else
       {
-          getBoxColour(av.globalColourScheme, seq, i);
+        curWidth += av.charWidth;
       }
 
-      return resBoxColour;
+      i++;
     }
 
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param cs DOCUMENT ME!
-     * @param seq DOCUMENT ME!
-     * @param i DOCUMENT ME!
-     */
-    void getBoxColour(ColourSchemeI cs, SequenceI seq, int 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())
     {
-        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;
-        }
+      end = seq.getLength() - 1;
     }
+    graphics.setColor(av.textColour);
 
-    /**
-     * 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)
+    if (monospacedFont
+        && av.showText
+        && allGroups.length == 0
+        && !av.getColourText()
+        && av.thresholdTextColour == 0)
     {
-        allGroups = sg;
-
-        drawBoxes(seq, start, end, y1);
-
-        if (av.validCharWidth)
-          drawText(seq, start, end, y1);
+      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);
+      }
     }
-
-    /**
-     * 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)
+    else
     {
-      int i = start;
-      int length = seq.getLength();
-
-      int curStart = -1;
-      int curWidth = av.charWidth;
-
-      Color tempColour = null;
-
-      while (i <= end)
+      boolean getboxColour = false;
+      for (int i = start; i <= end; i++)
       {
-        resBoxColour = Color.white;
+        graphics.setColor(av.textColour);
+        getboxColour = false;
+        s = seq.getCharAt(i);
+        if (!renderGaps && jalview.util.Comparison.isGap(s))
+        {
+          continue;
+        }
 
-        if (i < length)
+        if (inCurrentSequenceGroup(i))
         {
-          if (inCurrentSequenceGroup(i))
+          if (!currentSequenceGroup.getDisplayText())
           {
-            if (currentSequenceGroup.getDisplayBoxes())
-            {
-              getBoxColour(currentSequenceGroup.cs, seq, i);
-            }
+            continue;
           }
-          else if (av.getShowBoxes())
+
+          if (currentSequenceGroup.thresholdTextColour > 0
+              || currentSequenceGroup.getColourText())
           {
-            getBoxColour(av.globalColourScheme, seq, i);
-          }
+            getboxColour = true;
+            getBoxColour(currentSequenceGroup.cs, seq, i);
 
-        }
+            if (currentSequenceGroup.getColourText())
+            {
+              graphics.setColor(resBoxColour.darker());
+            }
 
-          if (resBoxColour != tempColour)
-          {
-              if (tempColour != null)
+            if (currentSequenceGroup.thresholdTextColour > 0)
+            {
+              if (resBoxColour.getRed() +
+                  resBoxColour.getBlue() +
+                  resBoxColour.getGreen() <
+                  currentSequenceGroup.thresholdTextColour)
               {
-                  graphics.fillRect( av.charWidth * (curStart - start), y1,
-                      curWidth, av.charHeight);
+                graphics.setColor(currentSequenceGroup.textColour2);
               }
-
-              graphics.setColor(resBoxColour);
-
-              curStart = i;
-              curWidth = av.charWidth;
-              tempColour = resBoxColour;
+            }
           }
           else
           {
-              curWidth += av.charWidth;
+            graphics.setColor(currentSequenceGroup.textColour);
           }
 
-          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++)
+          if (!av.getShowText())
           {
-            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;
-              }
+            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);
+          if (av.getColourText())
+          {
+            getboxColour = true;
+            getBoxColour(av.globalColourScheme, seq, i);
 
+            if (av.getShowBoxes())
+            {
+              graphics.setColor(resBoxColour.darker());
             }
             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);
-              }
-
+              graphics.setColor(resBoxColour);
             }
-
-
-
-          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))
+          if (av.thresholdTextColour > 0)
+          {
+            if (!getboxColour)
             {
-                currentSequenceGroup = allGroups[i];
+              getBoxColour(av.globalColourScheme, seq, i);
+            }
 
-                return true;
+            if (resBoxColour.getRed() +
+                resBoxColour.getBlue() +
+                resBoxColour.getGreen() < av.thresholdTextColour)
+            {
+              graphics.setColor(av.textColour2);
             }
+          }
+
         }
 
-        return false;
-    }
+        charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+        graphics.drawString(String.valueOf(s),
+                            charOffset + av.charWidth * (i - start),
+                            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 void drawHighlightedText(SequenceI seq, int start, int end, int x1, int y1)
+      }
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param res DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  boolean inCurrentSequenceGroup(int res)
+  {
+    if (allGroups == null)
     {
-        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 = '~';
+      return false;
+    }
 
-        // 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);
-            }
+    for (int i = 0; i < allGroups.length; i++)
+    {
+      if ( (allGroups[i].getStartRes() <= res) &&
+          (allGroups[i].getEndRes() >= res))
+      {
+        currentSequenceGroup = allGroups[i];
 
-            charOffset = (av.charWidth - fm.charWidth(s)) / 2;
-            graphics.drawString(String.valueOf(s),
-                                charOffset + x1 + (av.charWidth * (i - start)),
-                                (y1 + av.charHeight) - pady);
-          }
-        }
+        return true;
+      }
     }
 
-    public void drawCursor(SequenceI seq, int res, int x1, int y1)
+    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)
     {
-      int pady = av.charHeight / 5;
-      int charOffset = 0;
-      graphics.setColor(Color.black);
-      graphics.fillRect(x1, y1, av.charWidth, av.charHeight);
-
-      if(av.validCharWidth)
+      for (int i = start; i <= end; i++)
       {
-        graphics.setColor(Color.white);
-
-        char s = seq.getCharAt(res);
+        if (i < seq.getLength())
+        {
+          s = seq.getCharAt(i);
+        }
 
         charOffset = (av.charWidth - fm.charWidth(s)) / 2;
         graphics.drawString(String.valueOf(s),
-                            charOffset + x1,
+                            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 647c70d..98579eb 100755
--- a/src/jalview/gui/SliderPanel.java
+++ b/src/jalview/gui/SliderPanel.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,19 +18,15 @@
  */
 package jalview.gui;
 
-import jalview.datamodel.*;
-
-import jalview.jbgui.*;
-
-import jalview.schemes.*;
-
-import java.awt.event.*;
-
 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!
@@ -38,315 +34,318 @@ import javax.swing.event.*;
  * @author $author$
  * @version $Revision$
  */
-public class SliderPanel extends GSliderPanel
+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(AlignmentPanel ap, int value, boolean forConserve,
-        ColourSchemeI cs)
+  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(AlignmentPanel ap, int value, boolean forConserve,
+                     ColourSchemeI cs)
+  {
+    this.ap = ap;
+    this.cs = cs;
+    forConservation = forConserve;
+    undoButton.setVisible(false);
+    applyButton.setVisible(false);
+
+    if (forConservation)
     {
-        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.setValue(value);
-        valueField.setText(value + "");
+      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);
     }
 
-
-    /**
-     * 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)
+    slider.addChangeListener(new ChangeListener()
+    {
+      public void stateChanged(ChangeEvent evt)
+      {
+        valueField.setText(slider.getValue() + "");
+        valueChanged(slider.getValue());
+      }
+    });
+
+    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
     {
-        SliderPanel sp = null;
+      sp = (SliderPanel) conservationSlider.getContentPane();
+      sp.cs = cs;
+    }
 
-        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 + ")");
 
-        conservationSlider.setTitle("Conservation Colour Increment  (" +
-            source + ")");
+    if (ap.av.alignment.getGroups() != null)
+    {
+      sp.setAllGroupsCheckEnabled(true);
+    }
+    else
+    {
+      sp.setAllGroupsCheckEnabled(false);
+    }
 
-        if (ap.av.alignment.getGroups() != null)
-        {
-            sp.setAllGroupsCheckEnabled(true);
-        }
-        else
-        {
-            sp.setAllGroupsCheckEnabled(false);
-        }
+    return sp.getValue();
+  }
 
-        return sp.getValue();
+  /**
+   * DOCUMENT ME!
+   */
+  public static void showConservationSlider()
+  {
+    try
+    {
+      PIDSlider.setClosed(true);
+      PIDSlider = null;
     }
-
-    /**
-     * DOCUMENT ME!
-     */
-    public static void showConservationSlider()
+    catch (Exception ex)
     {
-        try
-        {
-            PIDSlider.setClosed(true);
-            PIDSlider = null;
-        }
-        catch (Exception ex)
-        {
-        }
+    }
 
-        if (!conservationSlider.isVisible())
+    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)
         {
-            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);
+          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)
+  }
+
+  /**
+   * 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)
     {
-        SliderPanel pid = 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;
+    }
 
-        int threshold = cs.getThreshold();
+    PIDSlider.setTitle("Percentage Identity Threshold (" + source + ")");
 
-        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;
-        }
+    if (ap.av.alignment.getGroups() != null)
+    {
+      pid.setAllGroupsCheckEnabled(true);
+    }
+    else
+    {
+      pid.setAllGroupsCheckEnabled(false);
+    }
 
-        PIDSlider.setTitle("Percentage Identity Threshold (" + source + ")");
+    return pid.getValue();
+  }
 
-        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;
     }
-
-    /**
-     * DOCUMENT ME!
-     */
-    public static void showPIDSlider()
+    catch (Exception ex)
     {
-        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 (!PIDSlider.isVisible())
     {
-        if (cs == null)
-        {
-            return;
-        }
-
-        ColourSchemeI toChange = null;
-        Vector allGroups = null;
-        int groupIndex = 0;
-
-        if (allGroupsCheck.isSelected())
+      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)
         {
-            allGroups = ap.av.alignment.getGroups();
-            groupIndex = allGroups.size() - 1;
+          PIDSlider = null;
         }
-        else
-        {
-            toChange = cs;
-        }
-
+      });
+      PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param i DOCUMENT ME!
+   */
+  public void valueChanged(int i)
+  {
+    if (cs == null)
+    {
+      return;
+    }
 
-        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--;
-        }
+    ColourSchemeI toChange = null;
+    Vector allGroups = null;
+    int groupIndex = 0;
 
-        ap.seqPanel.seqCanvas.repaint();
+    if (allGroupsCheck.isSelected())
+    {
+      allGroups = ap.av.alignment.getGroups();
+      groupIndex = allGroups.size() - 1;
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param b DOCUMENT ME!
-     */
-    public void setAllGroupsCheckEnabled(boolean b)
+    else
     {
-        allGroupsCheck.setEnabled(b);
+      toChange = cs;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void valueField_actionPerformed(ActionEvent e)
+    while (groupIndex > -1)
     {
-        try
+      if (allGroups != null)
+      {
+        toChange = ( (SequenceGroup) allGroups.get(groupIndex)).cs;
+
+        if (toChange == null)
         {
-            int i = Integer.parseInt(valueField.getText());
-            slider.setValue(i);
+          groupIndex--;
+
+          continue;
         }
-        catch (NumberFormatException ex)
+      }
+
+      if (forConservation)
+      {
+        if (toChange.conservationApplied())
         {
-            valueField.setText(slider.getValue() + "");
+          toChange.setConservationInc(i);
         }
+      }
+      else
+      {
+        toChange.setThreshold(i, ap.av.getIgnoreGapsConsensus());
+      }
+
+      groupIndex--;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param value DOCUMENT ME!
-     */
-    public void setValue(int value)
+    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
     {
-        slider.setValue(value);
+      int i = Integer.parseInt(valueField.getText());
+      slider.setValue(i);
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getValue()
+    catch (NumberFormatException ex)
     {
-        return Integer.parseInt(valueField.getText());
+      valueField.setText(slider.getValue() + "");
     }
-
-    public void slider_mouseReleased(MouseEvent e)
+  }
+
+  /**
+   * 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)
     {
-      if (ap.overviewPanel != null)
-        ap.overviewPanel.updateOverviewImage();
+      ap.overviewPanel.updateOverviewImage();
     }
+  }
 
 }
diff --git a/src/jalview/gui/SplashScreen.java b/src/jalview/gui/SplashScreen.java
index 063a11c..9f4429a 100755
--- a/src/jalview/gui/SplashScreen.java
+++ b/src/jalview/gui/SplashScreen.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -20,150 +20,155 @@ package jalview.gui;
 
 import java.awt.*;
 import java.awt.event.*;
-
 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;
-
-    /**
-     * Creates a new SplashScreen object.
-     *
-     * @param iframe DOCUMENT ME!
-     * @param i DOCUMENT ME!
-     */
-    public SplashScreen(JInternalFrame iframe, Image i)
-    {
-        this.iframe = iframe;
-        image = i;
-
-        Thread t = new Thread(this);
-        t.start();
-        addMouseListener(new MouseAdapter()
-            {
-                public void mousePressed(MouseEvent evt)
-                {
-                    try
-                    {
-                        closeSplash();
-                    }
-                    catch (Exception ex)
-                    {
-                    }
-                }
-            });
-    }
-
-    /**
-     * DOCUMENT ME!
-     */
-    public void run()
-    {
-        long startTime = System.currentTimeMillis() / 1000;
-
-        while (visible)
-        {
-            if (((System.currentTimeMillis() / 1000) - startTime) > 5)
-            {
-                visible = false;
-            }
-
-            try
-            {
-                Thread.sleep(1000);
-                repaint();
-            }
-            catch (Exception ex)
-            {
-            }
-        }
-
-        closeSplash();
-    }
-
-    /**
-     * DOCUMENT ME!
-     */
-    public void closeSplash()
+  boolean visible = true;
+  JInternalFrame iframe;
+  Image image;
+  int fontSize = 11;
+  int yoffset = 30;
+
+  /**
+   * Creates a new SplashScreen object.
+   *
+   * @param iframe DOCUMENT ME!
+   * @param i DOCUMENT ME!
+   */
+  public SplashScreen(JInternalFrame iframe, Image i)
+  {
+    this.iframe = iframe;
+    image = i;
+
+    Thread t = new Thread(this);
+    t.start();
+    addMouseListener(new MouseAdapter()
     {
+      public void mousePressed(MouseEvent evt)
+      {
         try
         {
-            iframe.setClosed(true);
+          closeSplash();
         }
         catch (Exception ex)
         {
-          ex.printStackTrace();
         }
+      }
+    });
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void run()
+  {
+    long startTime = System.currentTimeMillis() / 1000;
+
+    while (visible)
+    {
+      if ( ( (System.currentTimeMillis() / 1000) - startTime) > 5)
+      {
+        visible = false;
+      }
+
+      try
+      {
+        Thread.sleep(1000);
+        repaint();
+      }
+      catch (Exception ex)
+      {
+      }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param g DOCUMENT ME!
-     */
-    public void paintComponent(Graphics g)
-    {
-        g.setColor(Color.white);
-        g.fillRect(0, 0, getWidth(), getHeight());
-        g.setColor(Color.black);
-        g.setFont(new Font("Verdana", Font.BOLD, fontSize + 6));
+    closeSplash();
+  }
 
-        if (image != null)
-        {
-            g.drawImage(image, 5, yoffset + 12, this);
-        }
+  /**
+   * DOCUMENT ME!
+   */
+  public void closeSplash()
+  {
+    try
+    {
+      iframe.setClosed(true);
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param g DOCUMENT ME!
+   */
+  public void paintComponent(Graphics g)
+  {
+    g.setColor(Color.white);
+    g.fillRect(0, 0, getWidth(), getHeight());
+    g.setColor(Color.black);
+    g.setFont(new Font("Verdana", Font.BOLD, fontSize + 6));
+
+    if (image != null)
+    {
+      g.drawImage(image, 5, yoffset + 12, this);
+    }
 
-        int y = yoffset;
+    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"));
-        g.setFont(new Font("Verdana", Font.BOLD, fontSize + 2));
-        g.drawString("Last updated: " + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"),
-                     50 + vwidth +5, y);
+    FontMetrics fm = g.getFontMetrics();
+    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"))
-        {
-          // Displayed when code version and jnlp version do not match
-          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")))
-        {
-          // Displayed when code version and jnlp version do not match
-          g.setColor(Color.red);
-          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("Current development managed by Andrew Waterhouse; 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);
+    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);
+      y += 5;
+      g.setColor(Color.black);
     }
+    else if (!jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking").equals(
+        jalview.bin.Cache.getProperty("VERSION")))
+    {
+      // Displayed when code version and jnlp version do not match
+      g.setColor(Color.red);
+      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("Current development managed by Andrew Waterhouse; 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 c9840d8..504e1d5 100644
--- a/src/jalview/gui/TextColourChooser.java
+++ b/src/jalview/gui/TextColourChooser.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -19,34 +19,27 @@
 
 package jalview.gui;
 
-import java.awt.BorderLayout;
-import java.awt.event.MouseAdapter;
-import javax.swing.JOptionPane;
-import jalview.datamodel.SequenceGroup;
-import javax.swing.BorderFactory;
-import javax.swing.JColorChooser;
-import javax.swing.JPanel;
-import javax.swing.event.ChangeEvent;
-import java.awt.Color;
-import java.awt.event.MouseEvent;
-import java.awt.Dimension;
-import javax.swing.JSlider;
-import javax.swing.event.ChangeListener;
-import javax.swing.JLabel;
-import java.util.Vector;
+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 )
+  public void chooseColour(AlignmentPanel ap, SequenceGroup sg)
   {
     this.ap = ap;
     this.sg = sg;
 
-    int original1,original2, originalThreshold;
-    if(sg==null)
+    int original1, original2, originalThreshold;
+    if (sg == null)
     {
       original1 = ap.av.textColour.getRGB();
       original2 = ap.av.textColour2.getRGB();
@@ -130,7 +123,7 @@ public class TextColourChooser
 
     if (reply == JOptionPane.CANCEL_OPTION)
     {
-      if(sg==null)
+      if (sg == null)
       {
         ap.av.textColour = new Color(original1);
         ap.av.textColour2 = new Color(original2);
@@ -147,52 +140,64 @@ public class TextColourChooser
 
   void colour1Changed(Color col)
   {
-    if(sg==null)
+    if (sg == null)
     {
       ap.av.textColour = col;
       if (ap.av.colourAppliesToAllGroups)
+      {
         setGroupTextColour();
+      }
     }
     else
+    {
       sg.textColour = col;
+    }
 
     ap.repaint();
   }
 
   void colour2Changed(Color col)
   {
-    if(sg==null)
+    if (sg == null)
     {
       ap.av.textColour2 = col;
       if (ap.av.colourAppliesToAllGroups)
+      {
         setGroupTextColour();
+      }
     }
     else
+    {
       sg.textColour2 = col;
+    }
 
     ap.repaint();
   }
 
   void thresholdChanged(int value)
   {
-    if(sg==null)
+    if (sg == null)
     {
       ap.av.thresholdTextColour = value;
       if (ap.av.colourAppliesToAllGroups)
+      {
         setGroupTextColour();
+      }
     }
     else
+    {
       sg.thresholdTextColour = value;
+    }
 
     ap.repaint();
   }
 
-
-
   void setGroupTextColour()
   {
     if (ap.av.alignment.getGroups() == null)
+    {
       return;
+    }
 
     Vector groups = ap.av.alignment.getGroups();
 
diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index db5de1c..58ca6f6 100755
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,22 +18,17 @@
  */
 package jalview.gui;
 
-import jalview.analysis.*;
-
-import jalview.datamodel.*;
-
-import jalview.schemes.*;
-
-import jalview.util.*;
+import java.util.*;
 
 import java.awt.*;
 import java.awt.event.*;
 import java.awt.print.*;
-
-import java.util.*;
-
 import javax.swing.*;
 
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.schemes.*;
+import jalview.util.*;
 
 /**
  * DOCUMENT ME!
@@ -41,7 +36,8 @@ import javax.swing.*;
  * @author $author$
  * @version $Revision$
  */
-public class TreeCanvas extends JPanel implements MouseListener, Runnable,
+public class TreeCanvas
+    extends JPanel implements MouseListener, Runnable,
     Printable, MouseMotionListener
 {
   /** DOCUMENT ME!! */
@@ -269,9 +265,13 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
       // Draw horizontal line
       g.drawLine(xstart, ypos, xend, ypos);
       if (node == highlightNode)
+      {
         g.fillRect(xend - 3, ypos - 3, 6, 6);
+      }
       else
+      {
         g.fillRect(xend - 2, ypos - 2, 4, 4);
+      }
 
       int ystart = (int) ( ( (SequenceNode) node.left()).ycount * chunk) +
           offy;
@@ -827,11 +827,13 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
 
         }
         else
+        {
           cs = ColourSchemeProperty.getColour(sequences,
                                               av.alignment.getWidth(),
                                               ColourSchemeProperty.
                                               getColourName(
                                                   av.getGlobalColourScheme()));
+        }
 
         cs.setThreshold(av.getGlobalColourScheme().getThreshold(),
                         av.getIgnoreGapsConsensus());
@@ -842,7 +844,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
                                            0,
                                            av.alignment.getWidth() - 1);
 
-      sg.setName("JTreeGroup:"+sg.hashCode());
+      sg.setName("JTreeGroup:" + sg.hashCode());
 
       AlignmentPanel[] aps = getAssociatedPanels();
       for (int a = 0; a < aps.length; a++)
@@ -906,6 +908,10 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
       return PaintRefresher.getAssociatedPanels(av.getSequenceSetId());
     }
     else
-      return new AlignmentPanel[]{ap};
+    {
+      return new AlignmentPanel[]
+          {
+          ap};
+    }
   }
 }
diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index f4543ed..72bdbf1 100755
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,29 +18,21 @@
  */
 package jalview.gui;
 
-import jalview.analysis.*;
-
-import jalview.datamodel.*;
-
-import jalview.io.*;
-
-import jalview.jbgui.*;
-
-import org.jibble.epsgraphics.*;
+import java.beans.*;
+import java.io.*;
+import java.util.*;
+import javax.imageio.*;
 
 import java.awt.*;
 import java.awt.event.*;
 import java.awt.image.*;
-
-import java.io.*;
-
-import java.util.*;
-
 import javax.swing.*;
-import javax.imageio.*;
-
-import java.beans.PropertyChangeEvent;
 
+import org.jibble.epsgraphics.*;
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.io.*;
+import jalview.jbgui.*;
 
 /**
  * DOCUMENT ME!
@@ -48,584 +40,605 @@ import java.beans.PropertyChangeEvent;
  * @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!
-     */
-    public TreePanel(AlignmentPanel ap, String type, String pwtype)
+  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!
+   */
+  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
+    // 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!
+   */
+  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)
+  {
+    super();
+    initTreePanel(av, type, pwtype, newtree, inputData);
+  }
+
+  public AlignmentI getAlignment()
+  {
+    return treeCanvas.av.getAlignment();
+  }
+
+  public AlignViewport getViewPort()
+  {
+    return treeCanvas.av;
+  }
+
+  void initTreePanel(AlignmentPanel ap, String type, String pwtype,
+                     NewickFile newTree, AlignmentView inputData)
+  {
+
+    av = ap.av;
+    this.type = type;
+    this.pwtype = pwtype;
+
+    treeCanvas = new TreeCanvas(this, ap, scrollPane);
+    scrollPane.setViewportView(treeCanvas);
+
+    PaintRefresher.Register(this, ap.av.getSequenceSetId());
+
+    buildAssociatedViewMenu();
+
+    av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
     {
-      super();
-      initTreePanel(ap, type, pwtype, null, null);
+      public void propertyChange(PropertyChangeEvent evt)
+      {
+        if (evt.getPropertyName().equals("alignment"))
+        {
+          if (tree == null)
+          {
+            System.out.println("tree is null");
+          }
+          if (evt.getNewValue() == null)
+          {
+            System.out.println("new alignment sequences vector value is null");
+          }
 
-      // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default
-      // showDistances(true);
-    }
+          tree.UpdatePlaceHolders( (Vector) evt.getNewValue());
+          treeCanvas.nameHash.clear(); // reset the mapping between canvas rectangles and leafnodes
+          repaint();
+        }
+      }
+    });
 
-    /**
-     * 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!
-     */
-    public TreePanel(AlignmentPanel ap,
-                     String type,
-                     String pwtype,
-                     NewickFile newtree)
+    TreeLoader tl = new TreeLoader(newTree);
+    if (inputData != null)
     {
-      super();
-      initTreePanel(ap, type, pwtype, newtree, null);
+      tl.odata = inputData;
     }
+    tl.start();
 
-    public TreePanel(AlignmentPanel av,
-        String type,
-        String pwtype,
-        NewickFile newtree, AlignmentView inputData) {
-     super();
-     initTreePanel(av,type,pwtype,newtree,inputData);
-    }
+  }
 
-    public AlignmentI getAlignment()
-    {
-      return treeCanvas.av.getAlignment();
-    }
-    public AlignViewport getViewPort() {
-      return treeCanvas.av;
-    }
+  public void viewMenu_menuSelected()
+  {
+    buildAssociatedViewMenu();
+  }
 
-    void initTreePanel(AlignmentPanel ap, String type,  String pwtype,
-                       NewickFile newTree, AlignmentView inputData)
+  void buildAssociatedViewMenu()
+  {
+    AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av.
+        getSequenceSetId());
+    if (aps.length == 1 && treeCanvas.ap == aps[0])
     {
+      associateLeavesMenu.setVisible(false);
+      return;
+    }
 
-      av = ap.av;
-      this.type = type;
-      this.pwtype = pwtype;
-
-      treeCanvas = new TreeCanvas(this, ap, scrollPane);
-      scrollPane.setViewportView(treeCanvas);
+    associateLeavesMenu.setVisible(true);
 
-      PaintRefresher.Register(this, ap.av.getSequenceSetId());
+    if ( (viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
+    {
+      viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
+    }
 
-      buildAssociatedViewMenu();
+    associateLeavesMenu.removeAll();
 
-      av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
+    JRadioButtonMenuItem item;
+    ButtonGroup buttonGroup = new ButtonGroup();
+    int i, iSize = aps.length;
+    final TreePanel thisTreePanel = this;
+    for (i = 0; i < iSize; i++)
+    {
+      final AlignmentPanel ap = aps[i];
+      item = new JRadioButtonMenuItem(ap.av.viewName, ap == treeCanvas.ap);
+      buttonGroup.add(item);
+      item.addActionListener(new ActionListener()
       {
-        public void propertyChange(PropertyChangeEvent evt)
+        public void actionPerformed(ActionEvent evt)
         {
-          if (evt.getPropertyName().equals("alignment"))
-          {
-            if(tree==null)
-              System.out.println("tree is null");
-            if(evt.getNewValue()==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
-            repaint();
-          }
+          treeCanvas.applyToAllViews = false;
+          treeCanvas.ap = ap;
+          treeCanvas.av = ap.av;
+          PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
         }
       });
 
-      TreeLoader tl = new TreeLoader(newTree);
-      if (inputData!=null) {
-        tl.odata=inputData;
-      }
-      tl.start();
-
+      associateLeavesMenu.add(item);
     }
 
-    public void viewMenu_menuSelected()
+    final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem("All Views");
+    buttonGroup.add(itemf);
+    itemf.setSelected(treeCanvas.applyToAllViews);
+    itemf.addActionListener(new ActionListener()
     {
-      buildAssociatedViewMenu();
-    }
-
-
-    void buildAssociatedViewMenu()
-    {
-      AlignmentPanel [] aps = PaintRefresher.getAssociatedPanels(av.getSequenceSetId());
-      if(aps.length==1 && treeCanvas.ap==aps[0])
+      public void actionPerformed(ActionEvent evt)
       {
-        associateLeavesMenu.setVisible(false);
-        return;
+        treeCanvas.applyToAllViews = itemf.isSelected();
       }
+    });
+    associateLeavesMenu.add(itemf);
 
-      associateLeavesMenu.setVisible(true);
+  }
 
-      if( (viewMenu.getItem(viewMenu.getItemCount()-2) instanceof JMenuItem))
+  class TreeLoader
+      extends Thread
+  {
+    NewickFile newtree;
+    jalview.datamodel.AlignmentView odata = null;
+    public TreeLoader(NewickFile newtree)
+    {
+      this.newtree = newtree;
+      if (newtree != null)
       {
-        viewMenu.insertSeparator(viewMenu.getItemCount()-1);
+        // Must be outside run(), as Jalview2XML tries to
+        // update distance/bootstrap visibility at the same time
+        showBootstrap(newtree.HasBootstrap());
+        showDistances(newtree.HasDistances());
       }
+    }
 
-      associateLeavesMenu.removeAll();
-
-
-      JRadioButtonMenuItem item;
-      ButtonGroup buttonGroup = new ButtonGroup();
-      int i, iSize = aps.length;
-      final TreePanel thisTreePanel = this;
-      for(i=0; i<iSize; i++)
-      {
-          final AlignmentPanel ap = aps[i];
-          item = new JRadioButtonMenuItem(ap.av.viewName, ap==treeCanvas.ap );
-          buttonGroup.add(item);
-          item.addActionListener(new ActionListener()
-              {
-                public void actionPerformed(ActionEvent evt)
-                {
-                  treeCanvas.applyToAllViews = false;
-                  treeCanvas.ap = ap;
-                  treeCanvas.av = ap.av;
-                  PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
-                }
-              });
-
-          associateLeavesMenu.add(item);
-      }
+    public void run()
+    {
 
-      final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem("All Views");
-      buttonGroup.add(itemf);
-      itemf.setSelected(treeCanvas.applyToAllViews);
-      itemf.addActionListener(new ActionListener()
+      if (newtree != null)
       {
-        public void actionPerformed(ActionEvent evt)
+        if (odata == null)
         {
-          treeCanvas.applyToAllViews = itemf.isSelected();
+          tree = new NJTree(av.alignment.getSequencesArray(),
+                            newtree);
         }
-      });
-      associateLeavesMenu.add(itemf);
-
-    }
-
-    class TreeLoader extends Thread
-    {
-      NewickFile newtree;
-      jalview.datamodel.AlignmentView odata=null;
-      public TreeLoader(NewickFile newtree)
-      {
-        this.newtree = newtree;
-        if (newtree != null)
+        else
+        {
+          tree = new NJTree(av.alignment.getSequencesArray(), odata, newtree);
+        }
+        if (!tree.hasOriginalSequenceData())
         {
-          // Must be outside run(), as Jalview2XML tries to
-          // update distance/bootstrap visibility at the same time
-          showBootstrap(newtree.HasBootstrap());
-          showDistances(newtree.HasDistances());
+          allowOriginalSeqData(false);
         }
       }
-
-      public void run()
+      else
       {
-
-        if(newtree!=null)
+        int start, end;
+        SequenceI[] seqs;
+        AlignmentView seqStrings = av.getAlignmentView(av.getSelectionGroup() != null);
+        if (av.getSelectionGroup() == null)
         {
-          if (odata==null) {
-            tree = new NJTree(av.alignment.getSequencesArray(),
-                              newtree);
-          } else {
-            tree = new NJTree(av.alignment.getSequencesArray(), odata, newtree);
-          }
-          if (!tree.hasOriginalSequenceData())
-            allowOriginalSeqData(false);
+          start = 0;
+          end = av.alignment.getWidth();
+          seqs = av.alignment.getSequencesArray();
         }
         else
         {
-          int start, end;
-          SequenceI [] seqs;
-          AlignmentView seqStrings = av.getAlignmentView(av.getSelectionGroup()!=null);
-          if(av.getSelectionGroup()==null)
-          {
-            start = 0;
-            end = av.alignment.getWidth();
-            seqs = av.alignment.getSequencesArray();
-          }
-          else
-          {
-            start = av.getSelectionGroup().getStartRes();
-            end = av.getSelectionGroup().getEndRes()+1;
-            seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
-          }
-
-          tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
-          showDistances(true);
+          start = av.getSelectionGroup().getStartRes();
+          end = av.getSelectionGroup().getEndRes() + 1;
+          seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
         }
 
+        tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
+        showDistances(true);
+      }
 
-        tree.reCount(tree.getTopNode());
-        tree.findHeight(tree.getTopNode());
-        treeCanvas.setTree(tree);
-        treeCanvas.repaint();
-        av.setCurrentTree(tree);
+      tree.reCount(tree.getTopNode());
+      tree.findHeight(tree.getTopNode());
+      treeCanvas.setTree(tree);
+      treeCanvas.repaint();
+      av.setCurrentTree(tree);
 
-      }
     }
-
-    public void showDistances(boolean b)
+  }
+
+  public void showDistances(boolean b)
+  {
+    treeCanvas.setShowDistances(b);
+    distanceMenu.setSelected(b);
+  }
+
+  public void showBootstrap(boolean b)
+  {
+    treeCanvas.setShowBootstrap(b);
+    bootstrapMenu.setSelected(b);
+  }
+
+  public void showPlaceholders(boolean b)
+  {
+    placeholdersMenu.setState(b);
+    treeCanvas.setMarkPlaceholders(b);
+  }
+
+  private void allowOriginalSeqData(boolean b)
+  {
+    originalSeqData.setVisible(b);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public NJTree getTree()
+  {
+    return tree;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void textbox_actionPerformed(ActionEvent e)
+  {
+    CutAndPasteTransfer cap = new CutAndPasteTransfer();
+
+    StringBuffer buffer = new StringBuffer();
+
+    if (type.equals("AV"))
     {
-      treeCanvas.setShowDistances(b);
-      distanceMenu.setSelected(b);
+      buffer.append("Average distance tree using ");
     }
-
-    public void showBootstrap(boolean b)
+    else
     {
-      treeCanvas.setShowBootstrap(b);
-      bootstrapMenu.setSelected(b);
+      buffer.append("Neighbour joining tree using ");
     }
 
-    public void showPlaceholders(boolean b)
+    if (pwtype.equals("BL"))
     {
-      placeholdersMenu.setState(b);
-      treeCanvas.setMarkPlaceholders(b);
+      buffer.append("BLOSUM62");
     }
-
-    private void allowOriginalSeqData(boolean b) {
-      originalSeqData.setVisible(b);
-    }
-
-
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public NJTree getTree()
+    else
     {
-        return tree;
+      buffer.append("PID");
     }
 
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void textbox_actionPerformed(ActionEvent e)
+    Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
+
+    jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
+    cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(),
+                           tree.isHasRootDistance()));
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void saveAsNewick_actionPerformed(ActionEvent e)
+  {
+    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+        getProperty(
+            "LAST_DIRECTORY"));
+    chooser.setFileView(new JalviewFileView());
+    chooser.setDialogTitle("Save tree as newick file");
+    chooser.setToolTipText("Save");
+
+    int value = chooser.showSaveDialog(null);
+
+    if (value == JalviewFileChooser.APPROVE_OPTION)
     {
-        CutAndPasteTransfer cap = new CutAndPasteTransfer();
-
-        StringBuffer buffer = new StringBuffer();
-
-        if (type.equals("AV"))
-        {
-            buffer.append("Average distance tree using ");
-        }
-        else
-        {
-            buffer.append("Neighbour joining tree using ");
-        }
-
-        if (pwtype.equals("BL"))
-        {
-            buffer.append("BLOSUM62");
-        }
-        else
-        {
-            buffer.append("PID");
-        }
-
-        Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
+      String choice = chooser.getSelectedFile().getPath();
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+                                    chooser.getSelectedFile().getParent());
 
+      try
+      {
         jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
-        cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance()));
+        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)
+      {
+        ex.printStackTrace();
+      }
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void saveAsNewick_actionPerformed(ActionEvent e)
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void printMenu_actionPerformed(ActionEvent e)
+  {
+    //Putting in a thread avoids Swing painting problems
+    treeCanvas.startPrinting();
+  }
+
+  public void originalSeqData_actionPerformed(ActionEvent e)
+  {
+    if (!tree.hasOriginalSequenceData())
     {
-        JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
-                    "LAST_DIRECTORY"));
-        chooser.setFileView(new JalviewFileView());
-        chooser.setDialogTitle("Save tree as newick file");
-        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
-            {
-                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)
-            {
-                ex.printStackTrace();
-            }
-        }
+      jalview.bin.Cache.log.info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
+      return;
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void printMenu_actionPerformed(ActionEvent e)
+    // 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[])
+    Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(av.
+        getGapCharacter());
+
+    if (alAndColsel != null && alAndColsel[0] != null)
     {
-        //Putting in a thread avoids Swing painting problems
-        treeCanvas.startPrinting();
-    }
-
+      // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
 
-    public void originalSeqData_actionPerformed(ActionEvent e)
-    {
-      if (!tree.hasOriginalSequenceData())
+      Alignment al = new Alignment( (SequenceI[]) alAndColsel[0]);
+      Alignment dataset = av.getAlignment().getDataset();
+      if (dataset != null)
       {
-        jalview.bin.Cache.log.info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
-        return;
+        al.setDataset(dataset);
       }
-      // 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[])
-      Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(av.
-          getGapCharacter());
-
-
-      if (alAndColsel != null && alAndColsel[0]!=null)
-       {
-         // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
-
-         Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
-         Alignment dataset = av.getAlignment().getDataset();
-         if (dataset != null)
-         {
-           al.setDataset(dataset);
-         }
-
-         if (true)
-         {
-           // make a new frame!
-           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!!<<<
-           // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
-
-       //           af.addSortByOrderMenuItem(ServiceName + " Ordering",
-       //                                     msaorder);
-
-           Desktop.addInternalFrame(af, "Original Data for " + this.title,
-                                    AlignFrame.DEFAULT_WIDTH,
-                                    AlignFrame.DEFAULT_HEIGHT);
-         }
-       }
-    }
 
+      if (true)
+      {
+        // make a new frame!
+        AlignFrame af = new AlignFrame(al, (ColumnSelection) alAndColsel[1],
+                                       AlignFrame.DEFAULT_WIDTH,
+                                       AlignFrame.DEFAULT_HEIGHT
+            );
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void fitToWindow_actionPerformed(ActionEvent e)
-    {
-        treeCanvas.fitToWindow = fitToWindow.isSelected();
-        repaint();
-    }
+        //>>>This is a fix for the moment, until a better solution is found!!<<<
+        // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void font_actionPerformed(ActionEvent e)
-    {
-        if (treeCanvas == null)
-        {
-            return;
-        }
+        //           af.addSortByOrderMenuItem(ServiceName + " Ordering",
+        //                                     msaorder);
 
-        new FontChooser(this);
+        Desktop.addInternalFrame(af, "Original Data for " + this.title,
+                                 AlignFrame.DEFAULT_WIDTH,
+                                 AlignFrame.DEFAULT_HEIGHT);
+      }
     }
-
-    public Font getTreeFont()
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void fitToWindow_actionPerformed(ActionEvent e)
+  {
+    treeCanvas.fitToWindow = fitToWindow.isSelected();
+    repaint();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void font_actionPerformed(ActionEvent e)
+  {
+    if (treeCanvas == null)
     {
-        return treeCanvas.font;
+      return;
     }
 
-    public void setTreeFont(Font font)
-    {
-      if(treeCanvas!=null)
-      treeCanvas.setFont(font);
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void distanceMenu_actionPerformed(ActionEvent e)
-    {
-        treeCanvas.setShowDistances(distanceMenu.isSelected());
-    }
+    new FontChooser(this);
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void bootstrapMenu_actionPerformed(ActionEvent e)
-    {
-        treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
-    }
+  public Font getTreeFont()
+  {
+    return treeCanvas.font;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void placeholdersMenu_actionPerformed(ActionEvent e)
+  public void setTreeFont(Font font)
+  {
+    if (treeCanvas != null)
     {
-        treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
+      treeCanvas.setFont(font);
     }
-
-    /**
-     * 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");
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void distanceMenu_actionPerformed(ActionEvent e)
+  {
+    treeCanvas.setShowDistances(distanceMenu.isSelected());
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void bootstrapMenu_actionPerformed(ActionEvent e)
+  {
+    treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void placeholdersMenu_actionPerformed(ActionEvent e)
+  {
+    treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
+  }
+
+  /**
+   * 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");
 
     // 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("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.equalsIgnoreCase("text"))
+      if (renderStyle == null || eps.cancelled)
       {
-        accurateText = false;
+        return;
       }
 
-        int width = treeCanvas.getWidth();
-        int height = treeCanvas.getHeight();
+    }
 
-        try
-        {
-            jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(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");
+    if (renderStyle.equalsIgnoreCase("text"))
+    {
+      accurateText = false;
+    }
 
-            int value = chooser.showSaveDialog(this);
+    int width = treeCanvas.getWidth();
+    int height = treeCanvas.getHeight();
 
-            if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
-            {
-                return;
-            }
+    try
+    {
+      jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
+          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");
+
+      int value = chooser.showSaveDialog(this);
+
+      if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
+      {
+        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);
+      FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
+      EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
+                                           height);
 
-            pg.setAccurateTextMode(accurateText);
+      pg.setAccurateTextMode(accurateText);
 
-            treeCanvas.draw(pg, width, height);
+      treeCanvas.draw(pg, width, height);
 
-            pg.flush();
-            pg.close();
-        }
-        catch (Exception ex)
-        {
-            ex.printStackTrace();
-        }
+      pg.flush();
+      pg.close();
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void pngTree_actionPerformed(ActionEvent e)
+    catch (Exception ex)
     {
-        int width = treeCanvas.getWidth();
-        int height = treeCanvas.getHeight();
-
-        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");
+      ex.printStackTrace();
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void pngTree_actionPerformed(ActionEvent e)
+  {
+    int width = treeCanvas.getWidth();
+    int height = treeCanvas.getHeight();
+
+    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");
 
-            chooser.setFileView(new jalview.io.JalviewFileView());
-            chooser.setDialogTitle("Create PNG image from tree");
-            chooser.setToolTipText("Save");
+      chooser.setFileView(new jalview.io.JalviewFileView());
+      chooser.setDialogTitle("Create PNG image from tree");
+      chooser.setToolTipText("Save");
 
-            int value = chooser.showSaveDialog(this);
+      int value = chooser.showSaveDialog(this);
 
-            if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
-            {
-                return;
-            }
+      if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
+      {
+        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());
+      FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
 
-            BufferedImage bi = new BufferedImage(width, height,
-                    BufferedImage.TYPE_INT_RGB);
-            Graphics png = bi.getGraphics();
+      BufferedImage bi = new BufferedImage(width, height,
+                                           BufferedImage.TYPE_INT_RGB);
+      Graphics png = bi.getGraphics();
 
-            treeCanvas.draw(png, width, height);
+      treeCanvas.draw(png, width, height);
 
-            ImageIO.write(bi, "png", out);
-            out.close();
-        }
-        catch (Exception ex)
-        {
-            ex.printStackTrace();
-        }
+      ImageIO.write(bi, "png", out);
+      out.close();
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
     }
+  }
 }
diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java
index a39f4ca..001b232 100755
--- a/src/jalview/gui/UserDefinedColours.java
+++ b/src/jalview/gui/UserDefinedColours.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,25 +18,18 @@
  */
 package jalview.gui;
 
-import jalview.datamodel.*;
-
-import jalview.io.*;
-
-import jalview.jbgui.*;
-
-import jalview.schemes.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
 import java.io.*;
-
 import java.util.*;
 
+import java.awt.*;
+import java.awt.event.*;
 import javax.swing.*;
 import javax.swing.event.*;
 
-
+import jalview.datamodel.*;
+import jalview.io.*;
+import jalview.jbgui.*;
+import jalview.schemes.*;
 
 /**
  * DOCUMENT ME!
@@ -44,819 +37,893 @@ import javax.swing.event.*;
  * @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;
-    MCview.PDBCanvas pdbcanvas;
-    Vector upperCaseButtons;
-    Vector lowerCaseButtons;
-
-
-    /**
-     * Creates a new UserDefinedColours object.
-     *
-     * @param ap DOCUMENT ME!
-     * @param sg DOCUMENT ME!
-     */
-    public UserDefinedColours(AlignmentPanel ap, SequenceGroup sg)
-    {
-        super();
+  AlignmentPanel ap;
+  SequenceGroup seqGroup;
+  Vector selectedButtons;
+  ColourSchemeI oldColourScheme;
+  JInternalFrame frame;
+  MCview.PDBCanvas pdbcanvas;
+  Vector upperCaseButtons;
+  Vector lowerCaseButtons;
+
+  /**
+   * Creates a new UserDefinedColours object.
+   *
+   * @param ap DOCUMENT ME!
+   * @param sg DOCUMENT ME!
+   */
+  public UserDefinedColours(AlignmentPanel ap, SequenceGroup sg)
+  {
+    super();
+
+    lcaseColour.setEnabled(false);
+
+    this.ap = ap;
+    seqGroup = sg;
+
+    if (seqGroup != null)
+    {
+      oldColourScheme = seqGroup.cs;
+    }
+    else
+    {
+      oldColourScheme = ap.av.getGlobalColourScheme();
+    }
 
-        lcaseColour.setEnabled(false);
+    if (oldColourScheme instanceof UserColourScheme)
+    {
+      schemeName.setText( ( (UserColourScheme) oldColourScheme).getName());
+      if ( ( (UserColourScheme) oldColourScheme).getLowerCaseColours() != null)
+      {
+        caseSensitive.setSelected(true);
+        lcaseColour.setEnabled(true);
+        resetButtonPanel(true);
+      }
+      else
+      {
+        resetButtonPanel(false);
+      }
+    }
+    else
+    {
+      resetButtonPanel(false);
+    }
 
-        this.ap = ap;
-        seqGroup = sg;
+    showFrame();
+  }
 
-        if (seqGroup != null)
-            oldColourScheme = seqGroup.cs;
-        else
-            oldColourScheme = ap.av.getGlobalColourScheme();
+  public UserDefinedColours(MCview.PDBCanvas pdb, ColourSchemeI oldcs)
+  {
+    super();
+    pdbcanvas = pdb;
 
-        if (oldColourScheme instanceof UserColourScheme)
-        {
-          schemeName.setText( ( (UserColourScheme) oldColourScheme).getName());
-          if(( (UserColourScheme) oldColourScheme).getLowerCaseColours()!=null)
-          {
-            caseSensitive.setSelected(true);
-            lcaseColour.setEnabled(true);
-            resetButtonPanel(true);
-          }
-          else
-            resetButtonPanel(false);
-        }
-        else
-           resetButtonPanel(false);
+    colorChooser.getSelectionModel().addChangeListener(this);
 
-        showFrame();
-    }
+    oldColourScheme = oldcs;
 
-    public UserDefinedColours(MCview.PDBCanvas pdb, ColourSchemeI oldcs)
+    if (oldColourScheme instanceof UserColourScheme)
     {
-        super();
-        pdbcanvas = pdb;
-
-        colorChooser.getSelectionModel().addChangeListener(this);
+      schemeName.setText( ( (UserColourScheme) oldColourScheme).getName());
+    }
 
-        oldColourScheme = oldcs;
+    resetButtonPanel(false);
 
-        if (oldColourScheme instanceof UserColourScheme)
-        {
-              schemeName.setText( ( (UserColourScheme) oldColourScheme).getName());
-        }
+    showFrame();
 
-        resetButtonPanel(false);
+  }
 
-        showFrame();
+  void showFrame()
+  {
+    colorChooser.getSelectionModel().addChangeListener(this);
+    frame = new JInternalFrame();
+    frame.setContentPane(this);
+    Desktop.addInternalFrame(frame, "User Defined Colours", 720, 370, true);
 
+    if (seqGroup != null)
+    {
+      frame.setTitle(frame.getTitle() + " (" + seqGroup.getName() + ")");
     }
 
-    void showFrame()
+    if (System.getProperty("os.name").startsWith("Mac"))
     {
-      colorChooser.getSelectionModel().addChangeListener(this);
-      frame = new JInternalFrame();
-      frame.setContentPane(this);
-      Desktop.addInternalFrame(frame, "User Defined Colours", 720, 370, true);
+      frame.setSize(760, 370);
+    }
+  }
 
-      if (seqGroup != null)
-            frame.setTitle(frame.getTitle() + " (" + seqGroup.getName() + ")");
+  void resetButtonPanel(boolean caseSensitive)
+  {
+    buttonPanel.removeAll();
 
-      if (System.getProperty("os.name").startsWith("Mac"))
-      {
-        frame.setSize(760, 370);
-      }
+    if (upperCaseButtons == null)
+    {
+      upperCaseButtons = new Vector();
     }
 
-    void resetButtonPanel(boolean caseSensitive)
+    JButton button;
+    String label;
+    for (int i = 0; i < 20; i++)
     {
-      buttonPanel.removeAll();
-
-
-      if(upperCaseButtons==null)
-        upperCaseButtons = new Vector();
-
-      JButton button;
-      String label;
-      for (int i = 0; i < 20; i++)
+      if (caseSensitive)
       {
-        if(caseSensitive)
-          label = ResidueProperties.aa[i];
-        else
-          label = ResidueProperties.aa2Triplet.get
-              (ResidueProperties.aa[i]).toString();
-
-        button = makeButton(label,
-                              ResidueProperties.aa[i],
-                              upperCaseButtons, i);
-
-        buttonPanel.add(button);
-      }
-
-        buttonPanel.add(makeButton("B", "B", upperCaseButtons, 20));
-        buttonPanel.add(makeButton("Z", "Z", upperCaseButtons, 21));
-        buttonPanel.add(makeButton("X", "X", upperCaseButtons, 22));
-        buttonPanel.add(makeButton("Gap", "-", upperCaseButtons, 23));
-
-      if(!caseSensitive)
-      {
-        gridLayout.setRows(6);
-        gridLayout.setColumns(4);
+        label = ResidueProperties.aa[i];
       }
       else
       {
-        gridLayout.setRows(7);
-        int cols = 7;
-        gridLayout.setColumns(cols+1);
+        label = ResidueProperties.aa2Triplet.get
+            (ResidueProperties.aa[i]).toString();
+      }
 
-        if(lowerCaseButtons==null)
-          lowerCaseButtons = new Vector();
+      button = makeButton(label,
+                          ResidueProperties.aa[i],
+                          upperCaseButtons, i);
 
+      buttonPanel.add(button);
+    }
 
-          for (int i = 0; i < 20; i++)
-          {
-            int row = i / cols + 1;
-            int index = (row * cols) + i;
-            button = makeButton(
-                ResidueProperties.aa[i].toLowerCase(),
-                ResidueProperties.aa[i].toLowerCase(),
-                lowerCaseButtons,
-                i);
-
-            buttonPanel.add(button, index);
-          }
-      }
+    buttonPanel.add(makeButton("B", "B", upperCaseButtons, 20));
+    buttonPanel.add(makeButton("Z", "Z", upperCaseButtons, 21));
+    buttonPanel.add(makeButton("X", "X", upperCaseButtons, 22));
+    buttonPanel.add(makeButton("Gap", "-", upperCaseButtons, 23));
 
+    if (!caseSensitive)
+    {
+      gridLayout.setRows(6);
+      gridLayout.setColumns(4);
+    }
+    else
+    {
+      gridLayout.setRows(7);
+      int cols = 7;
+      gridLayout.setColumns(cols + 1);
 
-      if(caseSensitive)
+      if (lowerCaseButtons == null)
       {
-        buttonPanel.add(makeButton("b", "b", lowerCaseButtons, 20));
-        buttonPanel.add(makeButton("z", "z", lowerCaseButtons, 21));
-        buttonPanel.add(makeButton("x", "x", lowerCaseButtons, 22));
+        lowerCaseButtons = new Vector();
       }
 
-      buttonPanel.validate();
-      validate();
+      for (int i = 0; i < 20; i++)
+      {
+        int row = i / cols + 1;
+        int index = (row * cols) + i;
+        button = makeButton(
+            ResidueProperties.aa[i].toLowerCase(),
+            ResidueProperties.aa[i].toLowerCase(),
+            lowerCaseButtons,
+            i);
+
+        buttonPanel.add(button, index);
+      }
     }
 
+    if (caseSensitive)
+    {
+      buttonPanel.add(makeButton("b", "b", lowerCaseButtons, 20));
+      buttonPanel.add(makeButton("z", "z", lowerCaseButtons, 21));
+      buttonPanel.add(makeButton("x", "x", lowerCaseButtons, 22));
+    }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void stateChanged(ChangeEvent evt)
+    buttonPanel.validate();
+    validate();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void stateChanged(ChangeEvent evt)
+  {
+    if (selectedButtons != null)
     {
-        if (selectedButtons != null)
+      JButton button = null;
+      for (int i = 0; i < selectedButtons.size(); i++)
+      {
+        button = (JButton) selectedButtons.elementAt(i);
+        button.setBackground(colorChooser.getColor());
+        button.setForeground(button.getBackground().brighter().brighter().
+                             brighter());
+      }
+      if (button == lcaseColour)
+      {
+        for (int i = 0; i < lowerCaseButtons.size(); i++)
         {
-          JButton button=null;
-          for(int i=0; i<selectedButtons.size(); i++)
-          {
-            button = (JButton)selectedButtons.elementAt(i);
-            button.setBackground(colorChooser.getColor());
-            button.setForeground( button.getBackground().brighter().brighter().brighter());
-          }
-          if(button==lcaseColour)
-          {
-            for(int i=0; i<lowerCaseButtons.size(); i++)
-            {
-              button = (JButton)lowerCaseButtons.elementAt(i);
-              button.setBackground(colorChooser.getColor());
-              button.setForeground( button.getBackground().brighter().brighter().brighter());
-            }
-          }
+          button = (JButton) lowerCaseButtons.elementAt(i);
+          button.setBackground(colorChooser.getColor());
+          button.setForeground(button.getBackground().brighter().brighter().
+                               brighter());
         }
+      }
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void colourButtonPressed(MouseEvent e)
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void colourButtonPressed(MouseEvent e)
+  {
+    if (selectedButtons == null)
     {
-      if(selectedButtons == null)
-        selectedButtons = new Vector();
+      selectedButtons = new Vector();
+    }
 
-      JButton pressed = (JButton) e.getSource();
+    JButton pressed = (JButton) e.getSource();
 
-      if(e.isShiftDown())
+    if (e.isShiftDown())
+    {
+      JButton start, end = (JButton) e.getSource();
+      if (selectedButtons.size() > 0)
       {
-        JButton start, end = (JButton) e.getSource();
-        if(selectedButtons.size()>0)
-          start = (JButton)selectedButtons.elementAt(selectedButtons.size()-1);
-        else
-          start = (JButton) e.getSource();
+        start = (JButton) selectedButtons.elementAt(selectedButtons.size() - 1);
+      }
+      else
+      {
+        start = (JButton) e.getSource();
+      }
 
-        int startIndex=0, endIndex=0;
-        for(int b=0; b<buttonPanel.getComponentCount(); b++)
+      int startIndex = 0, endIndex = 0;
+      for (int b = 0; b < buttonPanel.getComponentCount(); b++)
+      {
+        if (buttonPanel.getComponent(b) == start)
         {
-          if(buttonPanel.getComponent(b)==start)
-            startIndex = b;
-          if(buttonPanel.getComponent(b)==end)
-            endIndex = b;
+          startIndex = b;
         }
-
-        if(startIndex > endIndex)
+        if (buttonPanel.getComponent(b) == end)
         {
-          int temp = startIndex;
-          startIndex = endIndex;
-          endIndex = temp;
+          endIndex = b;
         }
+      }
 
-        for(int b=startIndex; b<=endIndex; b++)
-        {
-          JButton button = (JButton)buttonPanel.getComponent(b);
-          if(!selectedButtons.contains(button))
-          {
-            button.setForeground(button.getBackground().brighter().brighter());
-            selectedButtons.add(button);
-          }
-        }
+      if (startIndex > endIndex)
+      {
+        int temp = startIndex;
+        startIndex = endIndex;
+        endIndex = temp;
       }
-      else if(!e.isControlDown())
+
+      for (int b = startIndex; b <= endIndex; b++)
       {
-        for(int b=0; b<selectedButtons.size(); b++)
+        JButton button = (JButton) buttonPanel.getComponent(b);
+        if (!selectedButtons.contains(button))
         {
-          JButton button = (JButton)selectedButtons.elementAt(b);
-          button.setForeground(button.getBackground().darker().darker());
+          button.setForeground(button.getBackground().brighter().brighter());
+          selectedButtons.add(button);
         }
-        selectedButtons.clear();
-        pressed.setForeground( pressed.getBackground().brighter().brighter());
-        selectedButtons.addElement(pressed);
-
       }
-      else if(e.isControlDown())
+    }
+    else if (!e.isControlDown())
+    {
+      for (int b = 0; b < selectedButtons.size(); b++)
       {
-        if(selectedButtons.contains(pressed))
-        {
-          pressed.setForeground(pressed.getBackground().darker().darker());
-          selectedButtons.remove(pressed);
-        }
-        else
-        {
-          pressed.setForeground( pressed.getBackground().brighter().brighter());
-          selectedButtons.addElement(pressed);
-        }
+        JButton button = (JButton) selectedButtons.elementAt(b);
+        button.setForeground(button.getBackground().darker().darker());
       }
+      selectedButtons.clear();
+      pressed.setForeground(pressed.getBackground().brighter().brighter());
+      selectedButtons.addElement(pressed);
 
-      if(selectedButtons.size()>0)
-      colorChooser.setColor( ((JButton)selectedButtons.elementAt(0)).getBackground());
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param label DOCUMENT ME!
-     * @param aa DOCUMENT ME!
-     */
-    JButton makeButton(String label,
-                       String aa,
-                       Vector caseSensitiveButtons,
-                       int buttonIndex)
+    else if (e.isControlDown())
     {
-        final JButton button;
-        Color col;
+      if (selectedButtons.contains(pressed))
+      {
+        pressed.setForeground(pressed.getBackground().darker().darker());
+        selectedButtons.remove(pressed);
+      }
+      else
+      {
+        pressed.setForeground(pressed.getBackground().brighter().brighter());
+        selectedButtons.addElement(pressed);
+      }
+    }
 
-        if(buttonIndex<caseSensitiveButtons.size())
+    if (selectedButtons.size() > 0)
+    {
+      colorChooser.setColor( ( (JButton) selectedButtons.elementAt(0)).
+                            getBackground());
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param label DOCUMENT ME!
+   * @param aa DOCUMENT ME!
+   */
+  JButton makeButton(String label,
+                     String aa,
+                     Vector caseSensitiveButtons,
+                     int buttonIndex)
+  {
+    final JButton button;
+    Color col;
+
+    if (buttonIndex < caseSensitiveButtons.size())
+    {
+      button = (JButton) caseSensitiveButtons.elementAt(buttonIndex);
+      col = button.getBackground();
+    }
+    else
+    {
+      button = new JButton();
+      button.addMouseListener(new java.awt.event.MouseAdapter()
+      {
+        public void mouseClicked(MouseEvent e)
         {
-          button = (JButton) caseSensitiveButtons.elementAt(buttonIndex);
-          col = button.getBackground();
+          colourButtonPressed(e);
         }
-        else
-        {
-          button = new JButton();
-          button.addMouseListener(new java.awt.event.MouseAdapter()
-          {
-            public void mouseClicked(MouseEvent e)
-            {
-              colourButtonPressed(e);
-            }
-          });
+      });
 
-          caseSensitiveButtons.addElement(button);
+      caseSensitiveButtons.addElement(button);
 
-          col = Color.white;
+      col = Color.white;
 
-          try
-          {
-            col = oldColourScheme.findColour(aa.charAt(0), -1);
-          }
-          catch (Exception ex)
-          {    }
-        }
+      try
+      {
+        col = oldColourScheme.findColour(aa.charAt(0), -1);
+      }
+      catch (Exception ex)
+      {}
+    }
 
-        if(caseSensitive.isSelected())
-          button.setMargin(new java.awt.Insets(2,2,2,2));
-        else
-         button.setMargin(new java.awt.Insets(2,14,2,14));
+    if (caseSensitive.isSelected())
+    {
+      button.setMargin(new java.awt.Insets(2, 2, 2, 2));
+    }
+    else
+    {
+      button.setMargin(new java.awt.Insets(2, 14, 2, 14));
+    }
 
-        button.setBackground(col);
-        button.setText(label);
-        button.setForeground(col.darker().darker().darker());
-        button.setFont(new java.awt.Font("Verdana", Font.BOLD, 10));
+    button.setBackground(col);
+    button.setText(label);
+    button.setForeground(col.darker().darker().darker());
+    button.setFont(new java.awt.Font("Verdana", Font.BOLD, 10));
 
-        return button;
-    }
+    return button;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void okButton_actionPerformed(ActionEvent e)
-    {
-        applyButton_actionPerformed(null);
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void okButton_actionPerformed(ActionEvent e)
+  {
+    applyButton_actionPerformed(null);
 
-        try
-        {
-            frame.setClosed(true);
-        }
-        catch (Exception ex)
-        {
-        }
+    try
+    {
+      frame.setClosed(true);
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void applyButton_actionPerformed(ActionEvent e)
+    catch (Exception ex)
     {
-        UserColourScheme ucs = getSchemeFromButtons();
-        ucs.setName(schemeName.getText());
-
-        if (seqGroup != null)
-        {
-            seqGroup.cs = ucs;
-            ap.repaint();
-        }
-        else if(ap!=null)
-        {
-            ap.alignFrame.changeColour(ucs);
-        }
-        else if(pdbcanvas!=null)
-        {
-          pdbcanvas.pdb.setColours(ucs);
-          pdbcanvas.updateSeqColours();
-        }
     }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void applyButton_actionPerformed(ActionEvent e)
+  {
+    UserColourScheme ucs = getSchemeFromButtons();
+    ucs.setName(schemeName.getText());
+
+    if (seqGroup != null)
+    {
+      seqGroup.cs = ucs;
+      ap.repaint();
+    }
+    else if (ap != null)
+    {
+      ap.alignFrame.changeColour(ucs);
+    }
+    else if (pdbcanvas != null)
+    {
+      pdbcanvas.pdb.setColours(ucs);
+      pdbcanvas.updateSeqColours();
+    }
+  }
+
+  UserColourScheme getSchemeFromButtons()
+  {
 
-    UserColourScheme getSchemeFromButtons()
+    Color[] newColours = new Color[24];
+
+    for (int i = 0; i < 24; i++)
     {
+      JButton button = (JButton) upperCaseButtons.elementAt(i);
+      newColours[i] = button.getBackground();
+    }
 
-      Color[] newColours = new Color[24];
+    UserColourScheme ucs = new UserColourScheme(newColours);
 
-      for (int i = 0; i < 24; i++)
+    if (caseSensitive.isSelected())
+    {
+      newColours = new Color[23];
+      for (int i = 0; i < 23; i++)
       {
-        JButton button = (JButton) upperCaseButtons.elementAt(i);
+        JButton button = (JButton) lowerCaseButtons.elementAt(i);
         newColours[i] = button.getBackground();
       }
+      ucs.setLowerCaseColours(newColours);
+    }
+
+    if (ap != null)
+    {
+      ucs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
+    }
+
+    return ucs;
+  }
+
+  /**
+   * 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");
+    chooser.setFileView(new jalview.io.JalviewFileView());
+    chooser.setDialogTitle("Load colour scheme");
+    chooser.setToolTipText("Load");
+
+    int value = chooser.showOpenDialog(this);
+
+    if (value == JalviewFileChooser.APPROVE_OPTION)
+    {
+      File choice = chooser.getSelectedFile();
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
+      String defaultColours = jalview.bin.Cache.getDefault(
+          "USER_DEFINED_COLOURS",
+          choice.getPath());
+      if (defaultColours.indexOf(choice.getPath()) == -1)
+      {
+        defaultColours = defaultColours.concat("|").concat(choice.getPath());
+      }
 
-      UserColourScheme ucs = new UserColourScheme(newColours);
+      jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);
 
+      UserColourScheme ucs = loadColours(choice.getAbsolutePath());
+      Color[] colors = ucs.getColours();
+      schemeName.setText(ucs.getName());
 
-      if(caseSensitive.isSelected())
+      if (ucs.getLowerCaseColours() != null)
       {
-        newColours = new Color[23];
-        for (int i = 0; i < 23; i++)
+        caseSensitive.setSelected(true);
+        lcaseColour.setEnabled(true);
+        resetButtonPanel(true);
+        for (int i = 0; i < lowerCaseButtons.size(); i++)
         {
           JButton button = (JButton) lowerCaseButtons.elementAt(i);
-          newColours[i] = button.getBackground();
+          button.setBackground(ucs.getLowerCaseColours()[i]);
         }
-        ucs.setLowerCaseColours(newColours);
-      }
 
-      if(ap!=null)
-        ucs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
+      }
+      else
+      {
+        caseSensitive.setSelected(false);
+        lcaseColour.setEnabled(false);
+        resetButtonPanel(false);
+      }
 
+      for (int i = 0; i < upperCaseButtons.size(); i++)
+      {
+        JButton button = (JButton) upperCaseButtons.elementAt(i);
+        button.setBackground(colors[i]);
+      }
 
-      return ucs;
     }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public static UserColourScheme loadDefaultColours()
+  {
+    UserColourScheme ret = null;
+
+    String colours = jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS");
+    if (colours != null)
+    {
+      if (colours.indexOf("|") > -1)
+      {
+        colours = colours.substring(0, colours.indexOf("|"));
+      }
 
+      ret = loadColours(colours);
+    }
 
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void loadbutton_actionPerformed(ActionEvent e)
+    if (ret == null)
     {
-      upperCaseButtons = new Vector();
-      lowerCaseButtons = new Vector();
+      Color[] newColours = new Color[24];
+      for (int i = 0; i < 24; i++)
+      {
+        newColours[i] = Color.white;
+      }
+      ret = new UserColourScheme(newColours);
+    }
 
-        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");
+    return ret;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param file DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  static UserColourScheme loadColours(String file)
+  {
+    UserColourScheme ucs = null;
+    Color[] newColours = null;
+    try
+    {
+      InputStreamReader in = new InputStreamReader(new FileInputStream(
+          file), "UTF-8");
 
-        int value = chooser.showOpenDialog(this);
+      jalview.schemabinding.version2.JalviewUserColours jucs
+          = new jalview.schemabinding.version2.JalviewUserColours();
 
-        if (value == JalviewFileChooser.APPROVE_OPTION)
-        {
-            File choice = chooser.getSelectedFile();
-            jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
-            String defaultColours = jalview.bin.Cache.getDefault("USER_DEFINED_COLOURS",
-                choice.getPath());
-            if (defaultColours.indexOf(choice.getPath()) == -1)
-              defaultColours = defaultColours.concat("|").concat(choice.getPath());
-
-            jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);
-
-
-            UserColourScheme ucs = loadColours(choice.getAbsolutePath());
-            Color[] colors = ucs.getColours();
-            schemeName.setText(ucs.getName());
-
-            if(ucs.getLowerCaseColours()!=null)
-            {
-              caseSensitive.setSelected(true);
-              lcaseColour.setEnabled(true);
-              resetButtonPanel(true);
-              for (int i = 0; i < lowerCaseButtons.size(); i++)
-              {
-                JButton button = (JButton) lowerCaseButtons.elementAt(i);
-                button.setBackground(ucs.getLowerCaseColours()[i]);
-              }
-
-            }
-            else
-            {
-              caseSensitive.setSelected(false);
-              lcaseColour.setEnabled(false);
-              resetButtonPanel(false);
-            }
-
-            for (int i = 0; i < upperCaseButtons.size(); i++)
-            {
-                JButton button = (JButton) upperCaseButtons.elementAt(i);
-                button.setBackground(colors[i]);
-            }
+      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];
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public static UserColourScheme loadDefaultColours()
-    {
-        UserColourScheme ret = null;
+      Color[] lowerCase = null;
+      boolean caseSensitive = false;
 
-        String colours = jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS");
-        if ( colours != null )
+      String name;
+      int index;
+      for (int i = 0; i < jucs.getColourCount(); i++)
+      {
+        name = jucs.getColour(i).getName();
+        if (ResidueProperties.aa3Hash.containsKey(name))
         {
-          if(colours.indexOf("|")>-1)
-            colours = colours.substring(0, colours.indexOf("|"));
-
-          ret = loadColours(colours);
+          index = ( (Integer) ResidueProperties.aa3Hash.get(name)).intValue();
+        }
+        else
+        {
+          index = ResidueProperties.aaIndex[name.charAt(0)];
+        }
+        if (index == -1)
+        {
+          continue;
         }
 
-        if(ret == null)
+        if (name.toLowerCase().equals(name))
         {
-          Color[] newColours = new Color[24];
-          for (int i = 0; i < 24; i++)
+          if (lowerCase == null)
           {
-            newColours[i] = Color.white;
+            lowerCase = new Color[23];
           }
-          ret =  new UserColourScheme(newColours);
+          caseSensitive = true;
+          lowerCase[index] = new Color(Integer.parseInt(
+              jucs.getColour(i).getRGB(), 16));
         }
+        else
+        {
+          newColours[index] = new Color(Integer.parseInt(
+              jucs.getColour(i).getRGB(), 16));
+        }
+      }
 
-        return ret;
-    }
+      if (newColours != null)
+      {
+        ucs = new UserColourScheme(newColours);
+        ucs.setName(jucs.getSchemeName());
+        if (caseSensitive)
+        {
+          ucs.setLowerCaseColours(lowerCase);
+        }
+      }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param file DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    static UserColourScheme loadColours(String file)
+    }
+    catch (Exception ex)
     {
-         UserColourScheme ucs = null;
-         Color[]  newColours = null;
-        try
-        {
-            InputStreamReader in = new InputStreamReader(new FileInputStream(
-                        file), "UTF-8");
-
-              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 );
-
-              newColours = new Color[24];
-
-              Color [] lowerCase = null;
-              boolean caseSensitive = false;
-
-
-            String name;
-            int index;
-            for (int i = 0; i < jucs.getColourCount(); i++)
-            {
-              name =  jucs.getColour(i).getName();
-              if(ResidueProperties.aa3Hash.containsKey(name))
-              {
-                index = ((Integer)ResidueProperties.aa3Hash.get(name)).intValue();
-              }
-              else
-              {
-                index = ResidueProperties.aaIndex[name.charAt(0)];
-              }
-              if(index == -1)
-                continue;
-
-              if(name.toLowerCase().equals(name))
-              {
-                if(lowerCase==null)
-                   lowerCase = new Color[23];
-                caseSensitive = true;
-                lowerCase[index] = new Color(Integer.parseInt(
-                  jucs.getColour(i).getRGB(), 16));
-              }
-              else
-              {
-                newColours[index] = new Color(Integer.parseInt(
-                    jucs.getColour(i).getRGB(), 16));
-              }
-            }
-
-            if (newColours != null)
-            {
-              ucs = new UserColourScheme(newColours);
-              ucs.setName( jucs.getSchemeName() );
-              if(caseSensitive)
-              {
-                ucs.setLowerCaseColours(lowerCase);
-              }
-            }
+      //Could be Archive Jalview format
+      try
+      {
+        InputStreamReader in = new InputStreamReader(new FileInputStream(
+            file), "UTF-8");
+
+        jalview.binding.JalviewUserColours jucs
+            = new jalview.binding.JalviewUserColours();
+
+        jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in);
 
+        newColours = new Color[jucs.getColourCount()];
+
+        for (int i = 0; i < 24; i++)
+        {
+          newColours[i] = new Color(Integer.parseInt(
+              jucs.getColour(i).getRGB(), 16));
         }
-        catch (Exception ex)
+        if (newColours != null)
         {
-            //Could be Archive Jalview format
-            try{
-              InputStreamReader in = new InputStreamReader(new FileInputStream(
-                  file), "UTF-8");
-
-              jalview.binding.JalviewUserColours jucs
-                  = new jalview.binding.JalviewUserColours();
-
-              jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in);
-
-              newColours = new Color[jucs.getColourCount()];
-
-              for (int i = 0; i < 24; i++)
-              {
-                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)
-            { ex2.printStackTrace(); }
-
-            if(newColours==null)
-              System.out.println("Error loading User ColourFile\n"+ex);
+          ucs = new UserColourScheme(newColours);
+          ucs.setName(jucs.getSchemeName());
         }
+      }
+      catch (Exception ex2)
+      {
+        ex2.printStackTrace();
+      }
 
-       return ucs;
+      if (newColours == null)
+      {
+        System.out.println("Error loading User ColourFile\n" + ex);
+      }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void savebutton_actionPerformed(ActionEvent e)
+    return ucs;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void savebutton_actionPerformed(ActionEvent e)
+  {
+    if (schemeName.getText().trim().length() < 1)
     {
-      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);
-        return;
-      }
+      JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                                            "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);
+      if (reply != JOptionPane.YES_OPTION)
       {
-        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);
-        if(reply != JOptionPane.YES_OPTION)
-          return;
-
-         userColourSchemes.remove(schemeName.getText());
+        return;
       }
-        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");
-        chooser.setToolTipText("Save");
+      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");
 
-        int value = chooser.showSaveDialog(this);
+    chooser.setFileView(new jalview.io.JalviewFileView());
+    chooser.setDialogTitle("Save colour scheme");
+    chooser.setToolTipText("Save");
 
-        if (value == JalviewFileChooser.APPROVE_OPTION)
-        {
-            String choice = chooser.getSelectedFile().getPath();
-            String defaultColours = jalview.bin.Cache.getDefault("USER_DEFINED_COLOURS", choice);
-            if(defaultColours.indexOf(choice)==-1)
-            {
-              if(defaultColours.length()>0)
-                defaultColours = defaultColours.concat("|");
-              defaultColours = defaultColours.concat(choice);
-            }
-
-            userColourSchemes.put(schemeName.getText(), getSchemeFromButtons());
-
-            ap.alignFrame.updateUserColourMenu();
-
-            jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);
-
-            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"));
-
-                for (int i = 0; i < buttonPanel.getComponentCount(); i++)
-                {
-                    JButton button = (JButton) buttonPanel.getComponent(i);
-                    jalview.schemabinding.version2.Colour col
-                        = new jalview.schemabinding.version2.Colour();
-                    col.setName(button.getText());
-                    col.setRGB(jalview.util.Format.getHexString(
-                            button.getBackground()));
-                    ucs.addColour(col);
-                }
-
-                ucs.marshal(out);
-                out.close();
-            }
-            catch (Exception ex)
-            {
-                ex.printStackTrace();
-            }
-        }
-    }
+    int value = chooser.showSaveDialog(this);
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void cancelButton_actionPerformed(ActionEvent e)
+    if (value == JalviewFileChooser.APPROVE_OPTION)
     {
-      if (ap != null)
+      String choice = chooser.getSelectedFile().getPath();
+      String defaultColours = jalview.bin.Cache.getDefault(
+          "USER_DEFINED_COLOURS", choice);
+      if (defaultColours.indexOf(choice) == -1)
       {
-        if (seqGroup != null)
+        if (defaultColours.length() > 0)
         {
-          seqGroup.cs = oldColourScheme;
+          defaultColours = defaultColours.concat("|");
         }
-        else if (ap != null)
-        {
-          ap.av.setGlobalColourScheme(oldColourScheme);
-        }
-        ap.repaint();
+        defaultColours = defaultColours.concat(choice);
       }
 
-      if(pdbcanvas!=null)
+      userColourSchemes.put(schemeName.getText(), getSchemeFromButtons());
+
+      ap.alignFrame.updateUserColourMenu();
+
+      jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);
+
+      jalview.schemabinding.version2.JalviewUserColours ucs
+          = new jalview.schemabinding.version2.JalviewUserColours();
+
+      ucs.setSchemeName(schemeName.getText());
+      try
       {
-        pdbcanvas.pdb.setColours(oldColourScheme);
-      }
+        PrintWriter out = new PrintWriter(new OutputStreamWriter(
+            new FileOutputStream(choice), "UTF-8"));
 
-        try
+        for (int i = 0; i < buttonPanel.getComponentCount(); i++)
         {
-            frame.setClosed(true);
+          JButton button = (JButton) buttonPanel.getComponent(i);
+          jalview.schemabinding.version2.Colour col
+              = new jalview.schemabinding.version2.Colour();
+          col.setName(button.getText());
+          col.setRGB(jalview.util.Format.getHexString(
+              button.getBackground()));
+          ucs.addColour(col);
         }
-        catch (Exception ex)
-        {
-        }
-    }
 
+        ucs.marshal(out);
+        out.close();
+      }
+      catch (Exception ex)
+      {
+        ex.printStackTrace();
+      }
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void cancelButton_actionPerformed(ActionEvent e)
+  {
+    if (ap != null)
+    {
+      if (seqGroup != null)
+      {
+        seqGroup.cs = oldColourScheme;
+      }
+      else if (ap != null)
+      {
+        ap.av.setGlobalColourScheme(oldColourScheme);
+      }
+      ap.repaint();
+    }
 
-    static Hashtable userColourSchemes;
-
-    public static Hashtable getUserColourSchemes()
+    if (pdbcanvas != null)
     {
-      return userColourSchemes;
+      pdbcanvas.pdb.setColours(oldColourScheme);
     }
 
-    public static void initUserColourSchemes(String files)
+    try
+    {
+      frame.setClosed(true);
+    }
+    catch (Exception ex)
     {
-      userColourSchemes = new Hashtable();
+    }
+  }
 
-      if(files==null || files.length()==0)
-        return;
+  static Hashtable userColourSchemes;
+
+  public static Hashtable getUserColourSchemes()
+  {
+    return userColourSchemes;
+  }
 
+  public static void initUserColourSchemes(String files)
+  {
+    userColourSchemes = new Hashtable();
+
+    if (files == null || files.length() == 0)
+    {
+      return;
+    }
 
-      // In case colours can't be loaded, we'll remove them
-      // from the default list here.
-      StringBuffer coloursFound = new StringBuffer();
-      StringTokenizer st = new StringTokenizer(files, "|");
-      while (st.hasMoreElements())
+    // In case colours can't be loaded, we'll remove them
+    // from the default list here.
+    StringBuffer coloursFound = new StringBuffer();
+    StringTokenizer st = new StringTokenizer(files, "|");
+    while (st.hasMoreElements())
+    {
+      String file = st.nextToken();
+      try
       {
-        String file = st.nextToken();
-        try
+        UserColourScheme ucs = loadColours(file);
+        if (ucs != null)
         {
-          UserColourScheme ucs = loadColours(file);
-          if (ucs != null)
+          if (coloursFound.length() > 0)
           {
-            if (coloursFound.length() > 0)
-              coloursFound.append("|");
-            coloursFound.append(file);
-            userColourSchemes.put(ucs.getName(), ucs);
+            coloursFound.append("|");
           }
-        }
-        catch (Exception ex)
-        {
-          System.out.println("Error loading User ColourFile\n" + ex);
+          coloursFound.append(file);
+          userColourSchemes.put(ucs.getName(), ucs);
         }
       }
-      if (!files.equals(coloursFound.toString()))
+      catch (Exception ex)
       {
-        if (coloursFound.toString().length() > 1)
-          jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS",
-                                        coloursFound.toString());
-        else
-          jalview.bin.Cache.applicationProperties.remove("USER_DEFINED_COLOURS");
+        System.out.println("Error loading User ColourFile\n" + ex);
       }
     }
-
-    public static void removeColourFromDefaults(String target)
+    if (!files.equals(coloursFound.toString()))
     {
-      // The only way to find colours by name is to load them in
-      // In case colours can't be loaded, we'll remove them
-      // from the default list here.
+      if (coloursFound.toString().length() > 1)
+      {
+        jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS",
+                                      coloursFound.toString());
+      }
+      else
+      {
+        jalview.bin.Cache.applicationProperties.remove("USER_DEFINED_COLOURS");
+      }
+    }
+  }
 
-      userColourSchemes = new Hashtable();
+  public static void removeColourFromDefaults(String target)
+  {
+    // The only way to find colours by name is to load them in
+    // In case colours can't be loaded, we'll remove them
+    // from the default list here.
 
-      StringBuffer coloursFound = new StringBuffer();
-      StringTokenizer st = new StringTokenizer(
-           jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS"), "|");
+    userColourSchemes = new Hashtable();
 
-      while (st.hasMoreElements())
+    StringBuffer coloursFound = new StringBuffer();
+    StringTokenizer st = new StringTokenizer(
+        jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS"), "|");
+
+    while (st.hasMoreElements())
+    {
+      String file = st.nextToken();
+      try
       {
-        String file = st.nextToken();
-        try
+        UserColourScheme ucs = loadColours(file);
+        if (ucs != null && !ucs.getName().equals(target))
         {
-          UserColourScheme ucs = loadColours(file);
-          if (ucs != null && !ucs.getName().equals(target))
+          if (coloursFound.length() > 0)
           {
-            if (coloursFound.length() > 0)
-              coloursFound.append("|");
-            coloursFound.append(file);
-            userColourSchemes.put(ucs.getName(), ucs);
+            coloursFound.append("|");
           }
-        }
-        catch (Exception ex)
-        {
-          System.out.println("Error loading User ColourFile\n" + ex);
+          coloursFound.append(file);
+          userColourSchemes.put(ucs.getName(), ucs);
         }
       }
-
-      if (coloursFound.toString().length() > 1)
-        jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", coloursFound.toString());
-      else
-        jalview.bin.Cache.applicationProperties.remove("USER_DEFINED_COLOURS");
-
+      catch (Exception ex)
+      {
+        System.out.println("Error loading User ColourFile\n" + ex);
+      }
     }
 
-    public void caseSensitive_actionPerformed(ActionEvent e)
+    if (coloursFound.toString().length() > 1)
     {
-      resetButtonPanel(caseSensitive.isSelected());
-      lcaseColour.setEnabled(caseSensitive.isSelected());
+      jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS",
+                                    coloursFound.toString());
     }
+    else
+    {
+      jalview.bin.Cache.applicationProperties.remove("USER_DEFINED_COLOURS");
+    }
+
+  }
 
-    public void lcaseColour_actionPerformed(ActionEvent e)
+  public void caseSensitive_actionPerformed(ActionEvent e)
+  {
+    resetButtonPanel(caseSensitive.isSelected());
+    lcaseColour.setEnabled(caseSensitive.isSelected());
+  }
+
+  public void lcaseColour_actionPerformed(ActionEvent e)
+  {
+    if (selectedButtons == null)
     {
-      if(selectedButtons==null)
-        selectedButtons = new Vector();
-      else
-        selectedButtons.clear();
-      selectedButtons.add(lcaseColour);
+      selectedButtons = new Vector();
+    }
+    else
+    {
+      selectedButtons.clear();
     }
+    selectedButtons.add(lcaseColour);
+  }
 
 }
diff --git a/src/jalview/gui/UserQuestionnaireCheck.java b/src/jalview/gui/UserQuestionnaireCheck.java
index 902b2a5..f384c96 100644
--- a/src/jalview/gui/UserQuestionnaireCheck.java
+++ b/src/jalview/gui/UserQuestionnaireCheck.java
@@ -1,105 +1,144 @@
 package jalview.gui;
 
-import java.io.BufferedReader;
-import java.io.InputStreamReader;
-import java.net.URL;
+import java.io.*;
+import java.net.*;
 
-import javax.swing.JOptionPane;
+import javax.swing.*;
 
-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
-     */
-    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.");
-        } else {
-            this.url = url;
-        }
+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
+   */
+  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.");
+    }
+    else
+    {
+      this.url = url;
     }
-    String qid=null,rid=null;
-    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()));
-        String qresp;
-        while ((qresp=br.readLine())!=null) {
-            if (qresp.indexOf("NOTYET:")==0) {
-                prompt=true; // not yet responded under that ID
-            } else {
-                if (qresp.indexOf("QUESTIONNAIRE:")==0) {
-                    // QUESTIONNAIRE:qid:rid for the latest questionnaire.
-                    int p=qresp.indexOf(':',14);
-                    if (p>-1) {
-                        rid=null;
-                        qid=qresp.substring(14,p);
-                        if (p<(qresp.length()-1)) {
-                            rid = qresp.substring(p+1);
-                            prompt=true; // this is a new qid/rid pair
-                        }
-                    }
-                } else {
-                    prompt=false;
-                }
+  }
+
+  String qid = null, rid = null;
+  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()));
+    String qresp;
+    while ( (qresp = br.readLine()) != null)
+    {
+      if (qresp.indexOf("NOTYET:") == 0)
+      {
+        prompt = true; // not yet responded under that ID
+      }
+      else
+      {
+        if (qresp.indexOf("QUESTIONNAIRE:") == 0)
+        {
+          // QUESTIONNAIRE:qid:rid for the latest questionnaire.
+          int p = qresp.indexOf(':', 14);
+          if (p > -1)
+          {
+            rid = null;
+            qid = qresp.substring(14, p);
+            if (p < (qresp.length() - 1))
+            {
+              rid = qresp.substring(p + 1);
+              prompt = true; // this is a new qid/rid pair
             }
+          }
         }
-        return prompt;
+        else
+        {
+          prompt = false;
+        }
+      }
     }
-    public void run() {
-        if (url==null)
-            return;
-        boolean prompt=false;
-        try {
-            // First - check to see if wee have an old questionnaire/response id pair.
-            String lastq=jalview.bin.Cache.getProperty("QUESTIONNAIRE");
-            if (lastq==null) {
-                prompt = checkresponse(new URL(url+(url.indexOf('?')>-1 ? "&" : "?") +"checkresponse=1"));
-            } else {
-                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;
-                if (qqid!=null && qqid!="null" && qqid.length()>0) {
-                    qurl+="&qid="+qqid;
-                    qid=qqid;
-                    String qrid = lastq.substring(lastq.indexOf(':')+1); // retrieve old rid
-                    if (qrid!=null && !qrid.equals("null")) {
-                        rid=qrid;
-                        qurl+="&rid="+qrid;
-                    }
-                }
-                // see if we have already responsed to this questionnaire.
-                prompt = checkresponse(new URL(qurl));
-            }
-            if (qid!=null && rid!=null) {
-                // Update our local property cache with latest qid and rid
-                jalview.bin.Cache.setProperty("QUESTIONNAIRE",qid+":"+rid);
-            }
-            if (prompt) {
-                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);
+    return prompt;
+  }
 
-                if (reply == JOptionPane.YES_OPTION)
-                {
-                    jalview.bin.Cache.log.debug("Opening "+qurl);
-                    jalview.util.BrowserLauncher.openURL(qurl);
-                }
-            }
-        } catch (Exception e) {
-            jalview.bin.Cache.log.warn("When trying to access questionnaire URL "+url,e);
+  public void run()
+  {
+    if (url == null)
+    {
+      return;
+    }
+    boolean prompt = false;
+    try
+    {
+      // First - check to see if wee have an old questionnaire/response id pair.
+      String lastq = jalview.bin.Cache.getProperty("QUESTIONNAIRE");
+      if (lastq == null)
+      {
+        prompt = checkresponse(new URL(url + (url.indexOf('?') > -1 ? "&" : "?") +
+                                       "checkresponse=1"));
+      }
+      else
+      {
+        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;
+        if (qqid != null && qqid != "null" && qqid.length() > 0)
+        {
+          qurl += "&qid=" + qqid;
+          qid = qqid;
+          String qrid = lastq.substring(lastq.indexOf(':') + 1); // retrieve old rid
+          if (qrid != null && !qrid.equals("null"))
+          {
+            rid = qrid;
+            qurl += "&rid=" + qrid;
+          }
         }
+        // see if we have already responsed to this questionnaire.
+        prompt = checkresponse(new URL(qurl));
+      }
+      if (qid != null && rid != null)
+      {
+        // Update our local property cache with latest qid and rid
+        jalview.bin.Cache.setProperty("QUESTIONNAIRE", qid + ":" + rid);
+      }
+      if (prompt)
+      {
+        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);
+
+        if (reply == JOptionPane.YES_OPTION)
+        {
+          jalview.bin.Cache.log.debug("Opening " + qurl);
+          jalview.util.BrowserLauncher.openURL(qurl);
+        }
+      }
+    }
+    catch (Exception e)
+    {
+      jalview.bin.Cache.log.warn("When trying to access questionnaire URL " +
+                                 url, e);
     }
+  }
 
 }
diff --git a/src/jalview/gui/VamsasClient.java b/src/jalview/gui/VamsasClient.java
index 6d9e94d..7c37bd3 100755
--- a/src/jalview/gui/VamsasClient.java
+++ b/src/jalview/gui/VamsasClient.java
@@ -29,16 +29,22 @@ import org.vamsas.test.simpleclient.ClientDoc;
  * @author jimp
  *
  */
-public class VamsasClient extends ArchiveClient {
+public class VamsasClient
+    extends ArchiveClient
+{
   // Cache.preferences for vamsas client session arena
   // preferences for check for default session at startup.
   // user and organisation stuff.
   public VamsasClient(Desktop jdesktop,
-      File sessionPath) {
-    super(System.getProperty("user.name"),System.getProperty("host.name"), "jalview","2.7",
-        sessionPath);
+                      File sessionPath)
+  {
+    super(System.getProperty("user.name"), System.getProperty("host.name"),
+          "jalview", "2.7",
+          sessionPath);
   }
-  public void initial_update() {
+
+  public void initial_update()
+  {
     Cache.log.info("Jalview loading the Vamsas Session.");
     // load in the vamsas archive for the first time
     ClientDoc cdoc = this.getUpdateable();
@@ -61,18 +67,23 @@ public class VamsasClient extends ArchiveClient {
           af.alignPanel.alignmentChanged();
         }
       }
-    } catch (Exception e) {
-      Cache.log.warn("Exception whilst refreshing jalview windows after a vamsas document update.", e);
+    }
+    catch (Exception e)
+    {
+      Cache.log.warn(
+          "Exception whilst refreshing jalview windows after a vamsas document update.",
+          e);
     }
     doUpdate(cdoc);
     cdoc.closeDoc();
   }
+
   /**
    * this will close all windows currently in Jalview.
    *
 
-	protected void closeWindows() {
-		JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+    protected void closeWindows() {
+     JInternalFrame[] frames = Desktop.desktop.getAllFrames();
 
         if (frames == null)
         {
@@ -82,70 +93,91 @@ public class VamsasClient extends ArchiveClient {
         try
         {
             for (int i = frames.length - 1; i > -1; i--) {
-            	frames[i].dispose();
+             frames[i].dispose();
             }
         } catch (Exception e) {
-        	Cache.log.error("Whilst closing windows",e);
+         Cache.log.error("Whilst closing windows",e);
         }
 
-	}
+    }
 
-	public void get_update(VamsasArchive doc) {
-		// Close windows - load update.
-		Cache.log.info("Jalview updating from Vamsas Session.");
-	}
+    public void get_update(VamsasArchive doc) {
+     // Close windows - load update.
+     Cache.log.info("Jalview updating from Vamsas Session.");
+    }
    */
-  VamsasClientWatcher watcher=null;
-  public void push_update() {
-    watchForChange=false;
-    try {
+  VamsasClientWatcher watcher = null;
+  public void push_update()
+  {
+    watchForChange = false;
+    try
+    {
       Thread.sleep(WATCH_SLEEP);
-    } catch (Exception e) {
+    }
+    catch (Exception e)
+    {
 
-    };
+    }
+    ;
     ClientDoc cdoc = getUpdateable();
     updateVamsasDocument(cdoc);
     doUpdate(cdoc);
     cdoc.closeDoc();
-    cdoc=null;
-    watchForChange=true;
-    if (watcher!=null) {
+    cdoc = null;
+    watchForChange = true;
+    if (watcher != null)
+    {
       watcher.start();
     }
     // collect all uncached alignments and put them into the vamsas dataset.
     // store them.
     Cache.log.info("Jalview updating the Vamsas Session.");
   }
-  public void end_session() {
+
+  public void end_session()
+  {
     //   stop any update/watcher thread.
-    watchForChange=false; // this makes any watch(long) loops return.
+    watchForChange = false; // this makes any watch(long) loops return.
     // we should also wait arount for this.WATCH_SLEEP to really make sure the watcher thread has stopped.
-    try {
+    try
+    {
       Thread.sleep(WATCH_SLEEP);
-    } catch (Exception e) {
+    }
+    catch (Exception e)
+    {
 
-    };
+    }
+    ;
     Cache.log.info("Jalview disconnecting from the Vamsas Session.");
   }
-  public void updateJalview(ClientDoc cdoc) {
+
+  public void updateJalview(ClientDoc cdoc)
+  {
     ensureJvVamsas();
-    VamsasDatastore vds = new VamsasDatastore(cdoc, vobj2jv, jv2vobj, baseProvEntry());
+    VamsasDatastore vds = new VamsasDatastore(cdoc, vobj2jv, jv2vobj,
+                                              baseProvEntry());
     vds.updateToJalview();
   }
-  private void ensureJvVamsas() {
-    if (jv2vobj==null) {
+
+  private void ensureJvVamsas()
+  {
+    if (jv2vobj == null)
+    {
       jv2vobj = new IdentityHashMap();
       vobj2jv = new Hashtable();
     }
   }
+
   /**
    * jalview object binding to VorbaIds
    */
   IdentityHashMap jv2vobj = null;
   Hashtable vobj2jv = null;
-  public void updateVamsasDocument(ClientDoc doc) {
+  public void updateVamsasDocument(ClientDoc doc)
+  {
     ensureJvVamsas();
-    VamsasDatastore vds = new VamsasDatastore(doc, vobj2jv, jv2vobj, baseProvEntry());
+    VamsasDatastore vds = new VamsasDatastore(doc, vobj2jv, jv2vobj,
+                                              baseProvEntry());
     // wander through frames
     JInternalFrame[] frames = Desktop.desktop.getAllFrames();
 
@@ -168,11 +200,14 @@ public class VamsasClient extends ArchiveClient {
         }
       }
     }
-    catch (Exception e) {
-      Cache.log.error("Vamsas Document store exception",e);
+    catch (Exception e)
+    {
+      Cache.log.error("Vamsas Document store exception", e);
     }
   }
-  private Entry baseProvEntry() {
+
+  private Entry baseProvEntry()
+  {
     org.vamsas.objects.core.Entry pentry = new org.vamsas.objects.core.Entry();
     pentry.setUser(this.getProvenanceUser());
     pentry.setApp(this.getClientHandle().getClientName());
@@ -180,42 +215,58 @@ public class VamsasClient extends ArchiveClient {
     pentry.setAction("created");
     return pentry;
   }
-  protected class VamsasClientWatcher extends Thread {
+
+  protected class VamsasClientWatcher
+      extends Thread
+  {
     /* (non-Javadoc)
      * @see java.lang.Thread#run()
      */
-    VamsasClient client=null;
-    VamsasClientWatcher(VamsasClient client) {
+    VamsasClient client = null;
+    VamsasClientWatcher(VamsasClient client)
+    {
       this.client = client;
     }
-    boolean running=false;
-    public void run() {
-      running=true;
-      while (client.watchForChange) {
+
+    boolean running = false;
+    public void run()
+    {
+      running = true;
+      while (client.watchForChange)
+      {
         ClientDoc docio = client.watch(0);
-        if (docio!=null) {
+        if (docio != null)
+        {
           client.disableGui(true);
           Cache.log.debug("Updating jalview from changed vamsas document.");
           client.updateJalview(docio);
           Cache.log.debug("Finished updating from document change.");
           docio.closeDoc();
-          docio=null;
+          docio = null;
           client.disableGui(false);
         }
       }
-      running=false;
+      running = false;
 
     }
 
   }
-  public void disableGui(boolean b) {
+
+  public void disableGui(boolean b)
+  {
     Desktop.instance.setVamsasUpdate(b);
   }
-  public void startWatcher() {
-    if (watcher==null)
-      watcher=new VamsasClientWatcher(this);
-    Thread thr = new Thread() {
-      public void run() {
+
+  public void startWatcher()
+  {
+    if (watcher == null)
+    {
+      watcher = new VamsasClientWatcher(this);
+    }
+    Thread thr = new Thread()
+    {
+      public void run()
+      {
         watcher.start();
       }
     };
diff --git a/src/jalview/gui/WebserviceInfo.java b/src/jalview/gui/WebserviceInfo.java
index 4b4e885..df18a62 100755
--- a/src/jalview/gui/WebserviceInfo.java
+++ b/src/jalview/gui/WebserviceInfo.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -27,360 +27,399 @@ import javax.swing.*;
 
 import jalview.jbgui.*;
 
-
 /**
  * Base class for web service client thread and gui
  *
  * @author $author$
  * @version $Revision$
  */
-public class WebserviceInfo extends GWebserviceInfo
+public class WebserviceInfo
+    extends GWebserviceInfo
 {
 
-    /** Job is Queued */
-    public static final int STATE_QUEUING = 0;
-
-    /** Job is Running */
-    public static final int STATE_RUNNING = 1;
-
-    /** Job has finished with no errors */
-    public static final int STATE_STOPPED_OK = 2;
-
-    /** Job has been cancelled with no errors */
-    public static final int STATE_CANCELLED_OK = 3;
-
-    /** job has stopped because of some error */
-    public static final int STATE_STOPPED_ERROR = 4;
-
-    /** job has failed because of some unavoidable service interruption */
-    public static final int STATE_STOPPED_SERVERERROR = 5;
-    int currentStatus = STATE_QUEUING;
-    Image image;
-    int angle = 0;
-    String title = "";
-    jalview.ws.WSClientI thisService;
-    boolean serviceIsCancellable;
-    JInternalFrame frame;
-    JTabbedPane subjobs=null;
-    java.util.Vector jobPanes = null;
-    private boolean serviceCanMergeResults = false;
-    private boolean viewResultsImmediatly = true;
+  /** Job is Queued */
+  public static final int STATE_QUEUING = 0;
+
+  /** Job is Running */
+  public static final int STATE_RUNNING = 1;
+
+  /** Job has finished with no errors */
+  public static final int STATE_STOPPED_OK = 2;
+
+  /** Job has been cancelled with no errors */
+  public static final int STATE_CANCELLED_OK = 3;
+
+  /** job has stopped because of some error */
+  public static final int STATE_STOPPED_ERROR = 4;
+
+  /** job has failed because of some unavoidable service interruption */
+  public static final int STATE_STOPPED_SERVERERROR = 5;
+  int currentStatus = STATE_QUEUING;
+  Image image;
+  int angle = 0;
+  String title = "";
+  jalview.ws.WSClientI thisService;
+  boolean serviceIsCancellable;
+  JInternalFrame frame;
+  JTabbedPane subjobs = null;
+  java.util.Vector jobPanes = null;
+  private boolean serviceCanMergeResults = false;
+  private boolean viewResultsImmediatly = true;
   // tabbed or not
-    public synchronized int addJobPane() {
-      JScrollPane jobpane = new JScrollPane();
-      JTextArea progressText = new JTextArea();
-      progressText.setFont(new java.awt.Font("Verdana", 0, 10));
-      progressText.setBorder(null);
-      progressText.setEditable(false);
-      progressText.setText("WS Job");
-      progressText.setLineWrap(true);
-      progressText.setWrapStyleWord(true);
-      jobpane.setName("JobPane");
-      jobpane.getViewport().add(progressText, null);
-      jobpane.setBorder(null);
-      if (jobPanes==null) {
-        jobPanes = new Vector();
-      }
-      int newpane = jobPanes.size();
-      jobPanes.add(jobpane);
-
-      if (newpane==0) {
-        this.add(jobpane, BorderLayout.CENTER);
-      } else {
-        if (newpane==1) {
-        // revert to a tabbed pane.
-        JScrollPane firstpane;
-        this.remove(firstpane=(JScrollPane) jobPanes.get(0));
-        subjobs=new JTabbedPane();
-          this.add(subjobs, BorderLayout.CENTER);
-          subjobs.add(firstpane);
-          subjobs.setTitleAt(0, firstpane.getName());
-        }
-        subjobs.add(jobpane);
-      }
-      return newpane; // index for accessor methods below
-    }
-    /**
-     * Creates a new WebserviceInfo object.
-     *
-     * @param title short name and job type
-     * @param info reference or other human readable description
-     */
-    public WebserviceInfo(String title, String info)
+  public synchronized int addJobPane()
+  {
+    JScrollPane jobpane = new JScrollPane();
+    JTextArea progressText = new JTextArea();
+    progressText.setFont(new java.awt.Font("Verdana", 0, 10));
+    progressText.setBorder(null);
+    progressText.setEditable(false);
+    progressText.setText("WS Job");
+    progressText.setLineWrap(true);
+    progressText.setWrapStyleWord(true);
+    jobpane.setName("JobPane");
+    jobpane.getViewport().add(progressText, null);
+    jobpane.setBorder(null);
+    if (jobPanes == null)
     {
-        init(title, info, 520, 500);
+      jobPanes = new Vector();
     }
+    int newpane = jobPanes.size();
+    jobPanes.add(jobpane);
 
-    /**
-     * Creates a new WebserviceInfo object.
-     *
-     * @param title DOCUMENT ME!
-     * @param info DOCUMENT ME!
-     * @param width DOCUMENT ME!
-     * @param height DOCUMENT ME!
-     */
-    public WebserviceInfo(String title, String info, int width, int height)
+    if (newpane == 0)
     {
-        init(title, info, width, height);
+      this.add(jobpane, BorderLayout.CENTER);
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public jalview.ws.WSClientI getthisService()
+    else
     {
-        return thisService;
+      if (newpane == 1)
+      {
+        // revert to a tabbed pane.
+        JScrollPane firstpane;
+        this.remove(firstpane = (JScrollPane) jobPanes.get(0));
+        subjobs = new JTabbedPane();
+        this.add(subjobs, BorderLayout.CENTER);
+        subjobs.add(firstpane);
+        subjobs.setTitleAt(0, firstpane.getName());
+      }
+      subjobs.add(jobpane);
     }
+    return newpane; // index for accessor methods below
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param newservice DOCUMENT ME!
-     */
-    public void setthisService(jalview.ws.WSClientI newservice)
-    {
-        thisService = newservice;
-        serviceIsCancellable = newservice.isCancellable();
-        frame.setClosable(!serviceIsCancellable);
-        serviceCanMergeResults = newservice.canMergeResults();
-    }
+  /**
+   * Creates a new WebserviceInfo object.
+   *
+   * @param title short name and job type
+   * @param info reference or other human readable description
+   */
+  public WebserviceInfo(String title, String info)
+  {
+    init(title, info, 520, 500);
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param title DOCUMENT ME!
-     * @param info DOCUMENT ME!
-     * @param width DOCUMENT ME!
-     * @param height DOCUMENT ME!
-     */
-    void init(String title, String info, int width, int height)
-    {
-        frame = new JInternalFrame();
-        frame.setContentPane(this);
-        Desktop.addInternalFrame(frame, title, width, height);
-        frame.setClosable(false);
+  /**
+   * Creates a new WebserviceInfo object.
+   *
+   * @param title DOCUMENT ME!
+   * @param info DOCUMENT ME!
+   * @param width DOCUMENT ME!
+   * @param height DOCUMENT ME!
+   */
+  public WebserviceInfo(String title, String info, int width, int height)
+  {
+    init(title, info, width, height);
+  }
 
-        this.title = title;
-        setInfoText(info);
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public jalview.ws.WSClientI getthisService()
+  {
+    return thisService;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param newservice DOCUMENT ME!
+   */
+  public void setthisService(jalview.ws.WSClientI newservice)
+  {
+    thisService = newservice;
+    serviceIsCancellable = newservice.isCancellable();
+    frame.setClosable(!serviceIsCancellable);
+    serviceCanMergeResults = newservice.canMergeResults();
+  }
 
-        java.net.URL url = getClass().getResource("/images/logo.gif");
-        image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
+  /**
+   * DOCUMENT ME!
+   *
+   * @param title DOCUMENT ME!
+   * @param info DOCUMENT ME!
+   * @param width DOCUMENT ME!
+   * @param height DOCUMENT ME!
+   */
+  void init(String title, String info, int width, int height)
+  {
+    frame = new JInternalFrame();
+    frame.setContentPane(this);
+    Desktop.addInternalFrame(frame, title, width, height);
+    frame.setClosable(false);
 
-        MediaTracker mt = new MediaTracker(this);
-        mt.addImage(image, 0);
+    this.title = title;
+    setInfoText(info);
 
-        try
-        {
-            mt.waitForID(0);
-        }
-        catch (Exception ex)
-        {
-        }
+    java.net.URL url = getClass().getResource("/images/logo.gif");
+    image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
 
-        AnimatedPanel ap = new AnimatedPanel();
-        titlePanel.add(ap, BorderLayout.CENTER);
+    MediaTracker mt = new MediaTracker(this);
+    mt.addImage(image, 0);
 
-        Thread thread = new Thread(ap);
-        thread.start();
+    try
+    {
+      mt.waitForID(0);
+    }
+    catch (Exception ex)
+    {
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param status integer status from state constants
-     */
-    public void setStatus(int status)
+    AnimatedPanel ap = new AnimatedPanel();
+    titlePanel.add(ap, BorderLayout.CENTER);
+
+    Thread thread = new Thread(ap);
+    thread.start();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param status integer status from state constants
+   */
+  public void setStatus(int status)
+  {
+    currentStatus = status;
+  }
+
+  /**
+   * subjob status indicator
+   * @param jobpane
+   * @param status
+   */
+  public void setStatus(int jobpane, int status)
+  {
+    if (jobpane < 0 || jobpane >= jobPanes.size())
     {
-        currentStatus = status;
+      throw new Error("setStatus called for non-existent job pane." + jobpane);
     }
-    /**
-     * subjob status indicator
-     * @param jobpane
-     * @param status
-     */
-    public void setStatus(int jobpane, int status) {
-      if (jobpane<0 || jobpane>=jobPanes.size()) {
-        throw new Error("setStatus called for non-existent job pane."+jobpane);
-      }
-      switch (status) {
+    switch (status)
+    {
       case STATE_QUEUING:
-        setProgressName(jobpane+" - QUEUED", jobpane);
+        setProgressName(jobpane + " - QUEUED", jobpane);
         break;
       case STATE_RUNNING:
-        setProgressName(jobpane+" - RUNNING", jobpane);
+        setProgressName(jobpane + " - RUNNING", jobpane);
         break;
       case STATE_STOPPED_OK:
-        setProgressName(jobpane+" - FINISHED", jobpane);
-      break;
+        setProgressName(jobpane + " - FINISHED", jobpane);
+        break;
       case STATE_CANCELLED_OK:
-        setProgressName(jobpane+" - CANCELLED", jobpane);
+        setProgressName(jobpane + " - CANCELLED", jobpane);
         break;
       case STATE_STOPPED_ERROR:
-        setProgressName(jobpane+" - BROKEN",jobpane);
+        setProgressName(jobpane + " - BROKEN", jobpane);
         break;
       case STATE_STOPPED_SERVERERROR:
-        setProgressName(jobpane+" - ALERT", jobpane);
+        setProgressName(jobpane + " - ALERT", jobpane);
         break;
-        default:
-          setProgressName(jobpane+" - UNKNOWN STATE", jobpane);
-      }
+      default:
+        setProgressName(jobpane + " - UNKNOWN STATE", jobpane);
     }
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String getInfoText()
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public String getInfoText()
+  {
+    return infoText.getText();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param text DOCUMENT ME!
+   */
+  public void setInfoText(String text)
+  {
+    infoText.setText(text);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param text DOCUMENT ME!
+   */
+  public void appendInfoText(String text)
+  {
+    infoText.append(text);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public String getProgressText(int which)
+  {
+    if (jobPanes == null)
     {
-        return infoText.getText();
+      addJobPane();
     }
+    return ( (JTextArea) ( (JScrollPane) jobPanes.get(which)).getViewport().
+            getComponent(0)).getText();
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param text DOCUMENT ME!
-     */
-    public void setInfoText(String text)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param text DOCUMENT ME!
+   */
+  public void setProgressText(int which, String text)
+  {
+    if (jobPanes == null)
     {
-        infoText.setText(text);
+      addJobPane();
     }
+    ( (JTextArea) ( (JScrollPane) jobPanes.get(which)).getViewport().
+     getComponent(0)).setText(text);
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param text DOCUMENT ME!
-     */
-    public void appendInfoText(String text)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param text DOCUMENT ME!
+   */
+  public void appendProgressText(int which, String text)
+  {
+    if (jobPanes == null)
     {
-        infoText.append(text);
+      addJobPane();
     }
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String getProgressText(int which)
+    ( (JTextArea) ( (JScrollPane) jobPanes.get(which)).getViewport().
+     getComponent(0)).append(text);
+  }
+
+  /**
+   * setProgressText(0, text)
+   */
+  public void setProgressText(String text)
+  {
+    setProgressText(0, text);
+  }
+
+  /**
+   * appendProgressText(0, text)
+   */
+  public void appendProgressText(String text)
+  {
+    appendProgressText(0, text);
+  }
+
+  /**
+   * getProgressText(0)
+   */
+  public String getProgressText()
+  {
+    return getProgressText(0);
+  }
+
+  /**
+   * get the tab title for a subjob
+   * @param which int
+   * @return String
+   */
+  public String getProgressName(int which)
+  {
+    if (jobPanes == null)
     {
-      if (jobPanes == null)
-        addJobPane();
-      return ( (JTextArea) ( (JScrollPane) jobPanes.get(which)).getViewport().
-              getComponent(0)).getText();
+      addJobPane();
     }
-    /**
-     * DOCUMENT ME!
-     *
-     * @param text DOCUMENT ME!
-     */
-    public void setProgressText(int which, String text)
+    if (subjobs != null)
     {
-      if (jobPanes == null)
-        addJobPane();
-      ( (JTextArea) ( (JScrollPane) jobPanes.get(which)).getViewport().
-       getComponent(0)).setText(text);
+      return subjobs.getTitleAt(which);
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param text DOCUMENT ME!
-     */
-    public void appendProgressText(int which, String text)
+    else
     {
-      if (jobPanes == null)
-        addJobPane();
-      ( (JTextArea) ( (JScrollPane) jobPanes.get(which)).getViewport().
-       getComponent(0)).append(text);
+      return ( (JScrollPane) jobPanes.get(which)).getViewport().getComponent(0).
+          getName();
     }
-    /**
-     * setProgressText(0, text)
-     */
-    public void setProgressText(String text)
+  }
+
+  /**
+   * set the tab title for a subjob
+   * @param name String
+   * @param which int
+   */
+  public void setProgressName(String name, int which)
+  {
+    if (subjobs != null)
     {
-      setProgressText(0, text);
+      subjobs.setTitleAt(which, name);
+      subjobs.revalidate();
+      subjobs.repaint();
     }
-    /**
-     * appendProgressText(0, text)
-     */
-    public void appendProgressText(String text)
+    JScrollPane c = (JScrollPane) jobPanes.get(which);
+    c.getViewport().getComponent(0).setName(name);
+    c.repaint();
+  }
+
+  /**
+   * Gui action for cancelling the current job, if possible.
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void cancel_actionPerformed(ActionEvent e)
+  {
+    if (!serviceIsCancellable)
     {
-      appendProgressText(0, text);
+      JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                                            "This job cannot be cancelled.\nJust close the window.",
+                                            "Cancel job",
+                                            JOptionPane.WARNING_MESSAGE);
     }
-    /**
-     * getProgressText(0)
-     */
-    public String getProgressText()
+    else
     {
-      return getProgressText(0);
-    }
-    /**
-     * get the tab title for a subjob
-     * @param which int
-     * @return String
-     */
-    public String getProgressName(int which) {
-      if (jobPanes==null)
-        addJobPane();
-      if (subjobs!=null)
-        return subjobs.getTitleAt(which);
-      else
-        return ((JScrollPane) jobPanes.get(which)).getViewport().getComponent(0).getName();
-    }
-    /**
-     * set the tab title for a subjob
-     * @param name String
-     * @param which int
-     */
-    public void setProgressName(String name, int which) {
-      if (subjobs!=null) {
-        subjobs.setTitleAt(which, name);
-        subjobs.revalidate();
-        subjobs.repaint();
-      }
-      JScrollPane c=(JScrollPane) jobPanes.get(which);
-      c.getViewport().getComponent(0).setName(name);
-      c.repaint();
+      thisService.cancelJob();
     }
+    frame.setClosable(true);
+  }
 
-    /**
-     * Gui action for cancelling the current job, if possible.
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void cancel_actionPerformed(ActionEvent e)
+  /**
+   * Set up GUI for user to get at results - and possibly automatically display
+   * them if viewResultsImmediatly is set.
+   */
+  public void setResultsReady()
+  {
+    frame.setClosable(true);
+    buttonPanel.remove(cancel);
+    buttonPanel.add(showResultsNewFrame);
+    if (serviceCanMergeResults)
     {
-        if (!serviceIsCancellable)
-        {
-            JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                "This job cannot be cancelled.\nJust close the window.", "Cancel job",
-                JOptionPane.WARNING_MESSAGE);
-        }
-        else
-        {
-            thisService.cancelJob();
-        }
-        frame.setClosable(true);
+      buttonPanel.add(mergeResults);
+      buttonPanel.setLayout(new GridLayout(2, 1, 5, 5));
     }
-    /**
-     * Set up GUI for user to get at results - and possibly automatically display
-     * them if viewResultsImmediatly is set.
-     */
-    public void setResultsReady()
+    buttonPanel.validate();
+    validate();
+    if (viewResultsImmediatly)
     {
-      frame.setClosable(true);
-      buttonPanel.remove(cancel);
-      buttonPanel.add(showResultsNewFrame);
-      if (serviceCanMergeResults)
-      {
-        buttonPanel.add(mergeResults);
-        buttonPanel.setLayout(new GridLayout(2, 1, 5, 5));
-      }
-      buttonPanel.validate();
-      validate();
-      if (viewResultsImmediatly)
-        showResultsNewFrame.doClick();
+      showResultsNewFrame.doClick();
     }
+  }
 
   /**
    * called when job has finished but no result objects can be passed back to user
@@ -393,105 +432,108 @@ public class WebserviceInfo extends GWebserviceInfo
     validate();
   }
 
-  class AnimatedPanel extends JPanel implements Runnable
+  class AnimatedPanel
+      extends JPanel implements Runnable
+  {
+    long startTime = 0;
+    BufferedImage offscreen;
+
+    public void run()
     {
-        long startTime = 0;
-        BufferedImage offscreen;
+      startTime = System.currentTimeMillis();
 
-        public void run()
+      while (currentStatus < STATE_STOPPED_OK)
+      {
+        try
         {
-            startTime = System.currentTimeMillis();
-
-            while (currentStatus < STATE_STOPPED_OK)
-            {
-                try
-                {
-                    Thread.sleep(50);
-
-                    int units = (int) ( (System.currentTimeMillis() - startTime) /
-                                       10f);
-                    angle += units;
-                    angle %= 360;
-                    startTime = System.currentTimeMillis();
-
-                    if (currentStatus >= STATE_STOPPED_OK)
-                      angle = 0;
-
-                    repaint();
-                }
-                catch (Exception ex)
-                {
-                }
-            }
-
-            cancel.setEnabled(false);
-        }
+          Thread.sleep(50);
 
-        void drawPanel()
-        {
-          if (offscreen == null || offscreen.getWidth(this) != getWidth()
-              || offscreen.getHeight(this) != getHeight())
+          int units = (int) ( (System.currentTimeMillis() - startTime) /
+                             10f);
+          angle += units;
+          angle %= 360;
+          startTime = System.currentTimeMillis();
+
+          if (currentStatus >= STATE_STOPPED_OK)
           {
-            offscreen = new BufferedImage(getWidth(), getHeight(),
-                                          BufferedImage.TYPE_INT_ARGB);
-         }
+            angle = 0;
+          }
 
-          Graphics2D g = (Graphics2D)offscreen.getGraphics();
+          repaint();
+        }
+        catch (Exception ex)
+        {
+        }
+      }
 
-          g.setColor(Color.white);
-          g.fillRect(0, 0, getWidth(), getHeight());
+      cancel.setEnabled(false);
+    }
 
-          g.setFont(new Font("Arial", Font.BOLD, 12));
-          g.setColor(Color.black);
+    void drawPanel()
+    {
+      if (offscreen == null || offscreen.getWidth(this) != getWidth()
+          || offscreen.getHeight(this) != getHeight())
+      {
+        offscreen = new BufferedImage(getWidth(), getHeight(),
+                                      BufferedImage.TYPE_INT_ARGB);
+      }
 
-          switch (currentStatus)
-          {
-            case STATE_QUEUING:
-              g.drawString(title.concat(" - queuing"), 60, 30);
+      Graphics2D g = (Graphics2D) offscreen.getGraphics();
 
-              break;
+      g.setColor(Color.white);
+      g.fillRect(0, 0, getWidth(), getHeight());
 
-            case STATE_RUNNING:
-              g.drawString(title.concat(" - running"), 60, 30);
+      g.setFont(new Font("Arial", Font.BOLD, 12));
+      g.setColor(Color.black);
 
-              break;
+      switch (currentStatus)
+      {
+        case STATE_QUEUING:
+          g.drawString(title.concat(" - queuing"), 60, 30);
 
-            case STATE_STOPPED_OK:
-              g.drawString(title.concat(" - complete"), 60, 30);
+          break;
 
-              break;
+        case STATE_RUNNING:
+          g.drawString(title.concat(" - running"), 60, 30);
 
-            case STATE_CANCELLED_OK:
-              g.drawString(title.concat(" - job cancelled!"), 60, 30);
+          break;
 
-              break;
+        case STATE_STOPPED_OK:
+          g.drawString(title.concat(" - complete"), 60, 30);
 
-            case STATE_STOPPED_ERROR:
-              g.drawString(title.concat(" - job error!"), 60, 30);
+          break;
 
-              break;
+        case STATE_CANCELLED_OK:
+          g.drawString(title.concat(" - job cancelled!"), 60, 30);
 
-            case STATE_STOPPED_SERVERERROR:
-              g.drawString(title.concat(" - Server Error! (try later)"),
-                           60,
-                           30);
+          break;
 
-              break;
-          }
+        case STATE_STOPPED_ERROR:
+          g.drawString(title.concat(" - job error!"), 60, 30);
 
-          if (image != null)
-          {
-            g.rotate(Math.toRadians(angle), 28, 28);
-            g.drawImage(image, 10, 10, this);
-            g.rotate( -Math.toRadians(angle), 28, 28);
-          }
-        }
+          break;
 
-        public void paintComponent(Graphics g1)
-        {
-          drawPanel();
+        case STATE_STOPPED_SERVERERROR:
+          g.drawString(title.concat(" - Server Error! (try later)"),
+                       60,
+                       30);
 
-          g1.drawImage(offscreen, 0,0,this);
-        }
+          break;
+      }
+
+      if (image != null)
+      {
+        g.rotate(Math.toRadians(angle), 28, 28);
+        g.drawImage(image, 10, 10, this);
+        g.rotate( -Math.toRadians(angle), 28, 28);
+      }
     }
+
+    public void paintComponent(Graphics g1)
+    {
+      drawPanel();
+
+      g1.drawImage(offscreen, 0, 0, this);
+    }
+  }
 }
diff --git a/src/jalview/io/AMSAFile.java b/src/jalview/io/AMSAFile.java
index 4f21875..1f3fca0 100644
--- a/src/jalview/io/AMSAFile.java
+++ b/src/jalview/io/AMSAFile.java
@@ -1,85 +1,96 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 jalview.io;
 
 import jalview.datamodel.*;
 
-public class AMSAFile extends jalview.io.FastaFile
+public class AMSAFile
+    extends jalview.io.FastaFile
 {
 
-   AlignmentI al;
-    /**
-     * Creates a new AMSAFile object for output.
-     */
-    public AMSAFile(AlignmentI al)
-    {
-      this.al = al;
-    }
+  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());
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public String print()
+  {
+    super.print(getSeqsAsArray());
 
-      AlignmentAnnotation aa;
-      if (al.getAlignmentAnnotation() != null)
+    AlignmentAnnotation aa;
+    if (al.getAlignmentAnnotation() != null)
+    {
+      for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
       {
-        for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
+        aa = al.getAlignmentAnnotation()[i];
+        if (aa.autoCalculated || !aa.visible)
         {
-          aa = al.getAlignmentAnnotation()[i];
-          if (aa.autoCalculated || !aa.visible)
-            continue;
+          continue;
+        }
 
-          out.append(">#_" + aa.label);
-          if (aa.description != null)
-            out.append(" " + aa.description);
+        out.append(">#_" + aa.label);
+        if (aa.description != null)
+        {
+          out.append(" " + aa.description);
+        }
 
-          out.append("\n");
+        out.append("\n");
 
-          int nochunks = (aa.annotations.length / len) + 1;
+        int nochunks = (aa.annotations.length / len) + 1;
 
-          for (int j = 0; j < nochunks; j++)
+        for (int j = 0; j < nochunks; j++)
+        {
+          int start = j * len;
+          int end = start + len;
+          if (end > aa.annotations.length)
           {
-            int start = j * len;
-            int end = start + len;
-            if (end > aa.annotations.length)
-              end = aa.annotations.length;
+            end = aa.annotations.length;
+          }
 
-            String ch;
-            for (int k = start; k < end; k++)
+          String ch;
+          for (int k = start; k < end; k++)
+          {
+            if (aa.annotations[k] == null)
+            {
+              ch = " ";
+            }
+            else
             {
-              if (aa.annotations[k] == null)
-                ch = " ";
-              else
-                ch = aa.annotations[k].displayCharacter;
+              ch = aa.annotations[k].displayCharacter;
+            }
 
-              out.append(ch);
+            out.append(ch);
 
-            }
-            out.append("\n");
           }
+          out.append("\n");
         }
       }
-      return out.toString();
     }
+    return out.toString();
+  }
 }
diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index 3fa4ac2..f115361 100755
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -1,29 +1,27 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 jalview.io;
 
-import jalview.datamodel.*;
-
 import java.io.*;
-
 import java.util.*;
 
+import jalview.datamodel.*;
 
 /**
  * DOCUMENT ME!
@@ -31,146 +29,146 @@ import java.util.*;
  * @author $author$
  * @version $Revision$
  */
-public abstract class AlignFile extends FileParse
+public abstract class AlignFile
+    extends FileParse
 {
-    int noSeqs = 0;
-    int maxLength = 0;
-    Vector seqs;
-    Vector annotations;
-    long start;
-    long end;
-    boolean jvSuffix = true;
-
-    /**
-     * Creates a new AlignFile object.
-     */
-    public 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)
-     */
-    public AlignFile(String inFile, String type) throws IOException
-    {
-        super(inFile, type);
-
-        initData();
-
-        parse();
-    }
-
-    /**
-     * Return the seqs Vector
-     */
-    public Vector getSeqs()
+  int noSeqs = 0;
+  int maxLength = 0;
+  Vector seqs;
+  Vector annotations;
+  long start;
+  long end;
+  boolean jvSuffix = true;
+
+  /**
+   * Creates a new AlignFile object.
+   */
+  public 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)
+   */
+  public AlignFile(String inFile, String type)
+      throws IOException
+  {
+    super(inFile, type);
+
+    initData();
+
+    parse();
+  }
+
+  /**
+   * Return the seqs Vector
+   */
+  public Vector getSeqs()
+  {
+    return seqs;
+  }
+
+  /**
+   * Return the Sequences in the seqs Vector as an array of Sequences
+   */
+  public SequenceI[] getSeqsAsArray()
+  {
+    SequenceI[] s = new SequenceI[seqs.size()];
+
+    for (int i = 0; i < seqs.size(); i++)
     {
-        return seqs;
+      s[i] = (SequenceI) seqs.elementAt(i);
     }
 
-    /**
-     * Return the Sequences in the seqs Vector as an array of Sequences
-     */
-    public SequenceI[] getSeqsAsArray()
-    {
-        SequenceI[] s = new SequenceI[seqs.size()];
-
-        for (int i = 0; i < seqs.size(); i++)
-        {
-            s[i] = (SequenceI) seqs.elementAt(i);
-        }
+    return s;
+  }
 
-        return s;
-    }
-
-    public void addAnnotations(Alignment al)
+  public void addAnnotations(Alignment al)
+  {
+    for (int i = 0; i < annotations.size(); i++)
     {
-      for(int i=0; i<annotations.size(); i++)
-      {
-        al.addAnnotation(
-            (AlignmentAnnotation)annotations.elementAt(i)
-            );
-      }
-
+      al.addAnnotation(
+          (AlignmentAnnotation) annotations.elementAt(i)
+          );
     }
 
-    /**
-     * Initialise objects to store sequence data in.
-     */
-    protected void initData()
+  }
+
+  /**
+   * Initialise objects to store sequence data in.
+   */
+  protected void initData()
+  {
+    seqs = new Vector();
+    annotations = new Vector();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param s DOCUMENT ME!
+   */
+  protected void setSeqs(SequenceI[] s)
+  {
+    seqs = new Vector();
+
+    for (int i = 0; i < s.length; i++)
     {
-        seqs = new Vector();
-        annotations = new Vector();
+      seqs.addElement(s[i]);
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param s DOCUMENT ME!
-     */
-    protected void setSeqs(SequenceI[] s)
+  }
+
+  /**
+   * This method must be implemented to parse the contents of the file.
+   */
+  public abstract void parse()
+      throws IOException;
+
+  /**
+   * Print out in alignment file format the Sequences in the seqs Vector.
+   */
+  public abstract String print();
+
+  public void addJVSuffix(boolean b)
+  {
+    jvSuffix = b;
+  }
+
+  /**
+   * A general parser for ids.
+   *
+   * @String id Id to be parsed
+   */
+  Sequence parseId(String id)
+  {
+    Sequence seq = null;
+    id = id.trim();
+    int space = id.indexOf(" ");
+    if (space > -1)
     {
-        seqs = new Vector();
-
-        for (int i = 0; i < s.length; i++)
-        {
-            seqs.addElement(s[i]);
-        }
+      seq = new Sequence(id.substring(0, space), "");
+      seq.setDescription(id.substring(space + 1));
     }
-
-
-
-    /**
-     * This method must be implemented to parse the contents of the file.
-     */
-    public abstract void parse() throws IOException;
-
-    /**
-     * Print out in alignment file format the Sequences in the seqs Vector.
-     */
-    public abstract String print();
-
-    public void addJVSuffix(boolean b)
-    {
-      jvSuffix = b;
-    }
-
-    /**
-     * A general parser for ids.
-     *
-     * @String id Id to be parsed
-     */
-    Sequence parseId(String id)
+    else
     {
-      Sequence seq = null;
-      id = id.trim();
-      int space = id.indexOf(" ");
-      if(space>-1)
-      {
-        seq = new Sequence(id.substring(0, space),"");
-        seq.setDescription(id.substring(space+1));
-      }
-      else
-      {
-        seq = new Sequence(id, "");
-      }
-
-      return seq;
+      seq = new Sequence(id, "");
     }
 
-    /**
-     * 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);
-    }
+    return seq;
+  }
+
+  /**
+   * 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);
+  }
 
 }
diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 8ec234d..1b7b72a 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -20,24 +20,24 @@
 package jalview.io;
 
 import java.io.*;
-import jalview.datamodel.*;
+import java.net.*;
 import java.util.*;
-import java.net.URL;
-import jalview.schemes.*;
-import jalview.analysis.Conservation;
 
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.schemes.*;
 
 public class AnnotationFile
 {
   StringBuffer text = new StringBuffer(
-        "JALVIEW_ANNOTATION\n"
-        +"# Created: "
-      +new java.util.Date()+"\n\n");
+      "JALVIEW_ANNOTATION\n"
+      + "# Created: "
+      + new java.util.Date() + "\n\n");
 
-  public String printAnnotations(AlignmentAnnotation [] annotations,
-                                Vector groups)
+  public String printAnnotations(AlignmentAnnotation[] annotations,
+                                 Vector groups)
   {
-    if(annotations!=null)
+    if (annotations != null)
     {
       AlignmentAnnotation row;
       String comma;
@@ -55,14 +55,18 @@ public class AnnotationFile
         row = annotations[i];
 
         if (!row.visible)
+        {
           continue;
+        }
 
         color = null;
 
         if (row.sequenceRef == null)
         {
           if (seqref != null)
+          {
             text.append("\nSEQUENCE_REF\tALIGNMENT\n");
+          }
 
           seqref = null;
         }
@@ -80,11 +84,16 @@ public class AnnotationFile
         else
         {
           if (row.graph == AlignmentAnnotation.BAR_GRAPH)
+          {
             text.append("BAR_GRAPH\t");
+          }
           else if (row.graph == AlignmentAnnotation.LINE_GRAPH)
+          {
             text.append("LINE_GRAPH\t");
+          }
 
           if (row.getThreshold() != null)
+          {
             graphLine.append("GRAPHLINE\t"
                              + row.label + "\t"
                              + row.getThreshold().value + "\t"
@@ -92,27 +101,36 @@ public class AnnotationFile
                              + jalview.util.Format.getHexString(
                                  row.getThreshold().colour) + "\n"
                 );
+          }
 
           if (row.graphGroup > -1)
           {
             String key = String.valueOf(row.graphGroup);
             if (graphGroup.containsKey(key))
+            {
               graphGroup.put(key, graphGroup.get(key)
                              + "\t" + row.label);
+            }
             else
+            {
               graphGroup.put(key, row.label);
+            }
           }
         }
 
         text.append(row.label + "\t");
         if (row.description != null)
+        {
           text.append(row.description + "\t");
+        }
 
         for (int j = 0; j < row.annotations.length; j++)
         {
           if (seqref != null &&
               jalview.util.Comparison.isGap(seqref.getCharAt(j)))
+          {
             continue;
+          }
 
           if (row.annotations[j] != null)
           {
@@ -133,7 +151,9 @@ public class AnnotationFile
             {
               color = row.annotations[j].colour;
               if (row.annotations[j].value != 0f)
+              {
                 text.append(comma + row.annotations[j].value);
+              }
             }
           }
           text.append("|");
@@ -165,8 +185,7 @@ public class AnnotationFile
       }
     }
 
-
-    if(groups!=null)
+    if (groups != null)
     {
       printGroups(groups);
     }
@@ -174,7 +193,6 @@ public class AnnotationFile
     return text.toString();
   }
 
-
   public void printGroups(Vector sequenceGroups)
   {
     SequenceGroup sg;
@@ -183,47 +201,60 @@ public class AnnotationFile
       sg = (SequenceGroup) sequenceGroups.elementAt(i);
       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++)
+                  + (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");
+        text.append(sg.getSequenceAt(s).getName() + "\t");
       }
 
-      text.append("\nPROPERTIES\t"+sg.getName()+"\t");
+      text.append("\nPROPERTIES\t" + sg.getName() + "\t");
 
-      if(sg.getDescription()!=null)
-        text.append("description="+sg.getDescription()+"\t");
-      if(sg.cs!=null)
+      if (sg.getDescription() != null)
       {
-        text.append("colour="+ColourSchemeProperty.getColourName(sg.cs)+"\t");
-        if(sg.cs.getThreshold()!=0)
-          text.append("pidThreshold="+sg.cs.getThreshold());
-        if(sg.cs.conservationApplied())
-          text.append("consThreshold="+sg.cs.getConservationInc()+"\t");
+        text.append("description=" + sg.getDescription() + "\t");
       }
-      text.append("outlineColour="+
-                  jalview.util.Format.getHexString(sg.getOutlineColour())+"\t");
+      if (sg.cs != null)
+      {
+        text.append("colour=" + ColourSchemeProperty.getColourName(sg.cs) +
+                    "\t");
+        if (sg.cs.getThreshold() != 0)
+        {
+          text.append("pidThreshold=" + sg.cs.getThreshold());
+        }
+        if (sg.cs.conservationApplied())
+        {
+          text.append("consThreshold=" + sg.cs.getConservationInc() + "\t");
+        }
+      }
+      text.append("outlineColour=" +
+                  jalview.util.Format.getHexString(sg.getOutlineColour()) +
+                  "\t");
 
       text.append("displayBoxes=" + sg.getDisplayBoxes() + "\t");
       text.append("displayText=" + sg.getDisplayText() + "\t");
       text.append("colourText=" + sg.getColourText() + "\t");
 
       if (sg.textColour != java.awt.Color.black)
+      {
         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");
-      if(sg.thresholdTextColour!=0)
-      text.append("textColThreshold="+sg.thresholdTextColour);
+      }
+      if (sg.thresholdTextColour != 0)
+      {
+        text.append("textColThreshold=" + sg.thresholdTextColour);
+      }
 
       text.append("\n\n");
 
     }
   }
 
-
   SequenceI refSeq = null;
   public boolean readAnnotationFile(AlignmentI al,
                                     String file,
@@ -241,7 +272,7 @@ public class AnnotationFile
         URL url = new URL(file);
         in = new BufferedReader(new InputStreamReader(url.openStream()));
       }
-     else if (protocol.equals(AppletFormatAdapter.PASTE))
+      else if (protocol.equals(AppletFormatAdapter.PASTE))
       {
         in = new BufferedReader(new StringReader(file));
       }
@@ -252,14 +283,16 @@ public class AnnotationFile
         {
           in = new BufferedReader(new java.io.InputStreamReader(is));
         }
-    }
+      }
 
       String line, label, description, token;
       int graphStyle, index;
       int refSeqIndex = 1;
       int existingAnnotations = 0;
-      if(al.getAlignmentAnnotation()!=null)
-       existingAnnotations = al.getAlignmentAnnotation().length;
+      if (al.getAlignmentAnnotation() != null)
+      {
+        existingAnnotations = al.getAlignmentAnnotation().length;
+      }
 
       int alWidth = al.getWidth();
 
@@ -271,8 +304,10 @@ public class AnnotationFile
       boolean jvAnnotationFile = false;
       while ( (line = in.readLine()) != null)
       {
-        if (line.indexOf("#") == 0 )
+        if (line.indexOf("#") == 0)
+        {
           continue;
+        }
 
         if (line.indexOf("JALVIEW_ANNOTATION") > -1)
         {
@@ -281,7 +316,7 @@ public class AnnotationFile
         }
       }
 
-      if(!jvAnnotationFile)
+      if (!jvAnnotationFile)
       {
         in.close();
         return false;
@@ -289,20 +324,22 @@ public class AnnotationFile
 
       while ( (line = in.readLine()) != null)
       {
-        if(line.indexOf("#")==0
-           || line.indexOf("JALVIEW_ANNOTATION")>-1
-           || line.length()==0)
+        if (line.indexOf("#") == 0
+            || line.indexOf("JALVIEW_ANNOTATION") > -1
+            || line.length() == 0)
+        {
           continue;
+        }
 
         st = new StringTokenizer(line, "\t");
         token = st.nextToken();
-        if(token.equalsIgnoreCase("COLOUR"))
+        if (token.equalsIgnoreCase("COLOUR"))
         {
           colourAnnotations(al, st.nextToken(), st.nextToken());
           continue;
         }
 
-        else if(token.equalsIgnoreCase("COMBINE") )
+        else if (token.equalsIgnoreCase("COMBINE"))
         {
           combineAnnotations(al, st);
           continue;
@@ -314,46 +351,50 @@ public class AnnotationFile
           continue;
         }
 
-
-        else if(token.equalsIgnoreCase("SEQUENCE_REF") )
+        else if (token.equalsIgnoreCase("SEQUENCE_REF"))
         {
           refSeq = al.findName(st.nextToken());
-          try{
+          try
+          {
             refSeqIndex = Integer.parseInt(st.nextToken());
-            if(refSeqIndex<1)
+            if (refSeqIndex < 1)
             {
               refSeqIndex = 1;
-              System.out.println("WARNING: SEQUENCE_REF index must be > 0 in AnnotationFile");
+              System.out.println(
+                  "WARNING: SEQUENCE_REF index must be > 0 in AnnotationFile");
             }
           }
-          catch(Exception ex)
+          catch (Exception ex)
           {
             refSeqIndex = 1;
           }
 
-          continue;
+          continue ;
         }
 
-        else if(token.equalsIgnoreCase("SEQUENCE_GROUP"))
+        else if (token.equalsIgnoreCase("SEQUENCE_GROUP"))
         {
           addGroup(al, st);
           continue;
         }
 
-        else if(token.equalsIgnoreCase("PROPERTIES"))
+        else if (token.equalsIgnoreCase("PROPERTIES"))
         {
           addProperties(al, st);
           continue;
         }
 
-
         graphStyle = AlignmentAnnotation.getGraphValueFromString(token);
         label = st.nextToken();
 
-        if(st.countTokens()>1)
+        if (st.countTokens() > 1)
+        {
           description = st.nextToken();
+        }
         else
+        {
           description = null;
+        }
 
         line = st.nextToken();
 
@@ -363,14 +404,15 @@ public class AnnotationFile
         index = 0;
         boolean emptyColumn = true;
 
-
-        while (st.hasMoreElements() && index<alWidth)
+        while (st.hasMoreElements() && index < alWidth)
         {
           token = st.nextToken().trim();
-          if(token.equals("|"))
+          if (token.equals("|"))
           {
-            if(emptyColumn)
+            if (emptyColumn)
+            {
               index++;
+            }
 
             emptyColumn = true;
           }
@@ -381,28 +423,31 @@ public class AnnotationFile
           }
         }
 
-       annotation = new AlignmentAnnotation(label,
-                                          description,
-                                          annotations,
-                                          0,
-                                          0,
-                                          graphStyle);
+        annotation = new AlignmentAnnotation(label,
+                                             description,
+                                             annotations,
+                                             0,
+                                             0,
+                                             graphStyle);
 
-       if(refSeq!=null)
-       {
-         annotation.createSequenceMapping(refSeq, refSeqIndex, false);
-         refSeq.addAlignmentAnnotation(annotation);
-       }
+        if (refSeq != null)
+        {
+          annotation.createSequenceMapping(refSeq, refSeqIndex, false);
+          refSeq.addAlignmentAnnotation(annotation);
+        }
 
-       al.addAnnotation(annotation);
+        al.addAnnotation(annotation);
 
-       al.setAnnotationIndex(annotation,  al.getAlignmentAnnotation().length - existingAnnotations-1);
+        al.setAnnotationIndex(annotation,
+                              al.getAlignmentAnnotation().length - existingAnnotations -
+                              1);
       }
 
-    }catch(Exception ex)
+    }
+    catch (Exception ex)
     {
       ex.printStackTrace();
-      System.out.println("Problem reading annotation file: "+ex);
+      System.out.println("Problem reading annotation file: " + ex);
       return false;
     }
     return true;
@@ -410,45 +455,56 @@ public class AnnotationFile
 
   Annotation parseAnnotation(String string)
   {
-    String desc = null, displayChar="";
+    String desc = null, displayChar = "";
     char ss = ' '; // secondaryStructure
     float value = 0;
     boolean parsedValue = false;
     StringTokenizer st = new StringTokenizer(string, ",");
     String token;
-    while(st.hasMoreTokens())
+    while (st.hasMoreTokens())
     {
       token = st.nextToken().trim();
-      if(token.length()==0)
+      if (token.length() == 0)
+      {
         continue;
+      }
 
-      if(!parsedValue)
+      if (!parsedValue)
       {
-        try{
+        try
+        {
           displayChar = token;
           value = new Float(token).floatValue();
           parsedValue = true;
           continue;
-        }catch(NumberFormatException ex){}
+        }
+        catch (NumberFormatException ex)
+        {}
       }
 
-      if(token.equals("H") || token.equals("E"))
+      if (token.equals("H") || token.equals("E"))
       {
         // Either this character represents a helix or sheet
         // or an integer which can be displayed
         ss = token.charAt(0);
-        if(displayChar.equals(token.substring(0,1)))
+        if (displayChar.equals(token.substring(0, 1)))
+        {
           displayChar = "";
+        }
       }
-      else if(desc==null)
+      else if (desc == null)
+      {
         desc = token;
+      }
 
     }
 
-    if(desc == null)
-      desc = value+"";
+    if (desc == null)
+    {
+      desc = value + "";
+    }
 
-    if(displayChar.length()>1 && desc.length()==1)
+    if (displayChar.length() > 1 && desc.length() == 1)
     {
       String tmp = displayChar;
       displayChar = desc;
@@ -462,15 +518,17 @@ public class AnnotationFile
   {
     UserColourScheme ucs = new UserColourScheme(colour);
     Annotation[] annotations;
-    for(int i=0; i<al.getAlignmentAnnotation().length; i++)
+    for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
     {
-      if(al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(label))
+      if (al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(label))
       {
         annotations = al.getAlignmentAnnotation()[i].annotations;
-        for(int j=0; j<annotations.length; j++)
+        for (int j = 0; j < annotations.length; j++)
         {
-          if(annotations[j]!=null)
+          if (annotations[j] != null)
+          {
             annotations[j].colour = ucs.findColour('A');
+          }
         }
       }
     }
@@ -481,21 +539,21 @@ public class AnnotationFile
     int graphGroup = -1;
     String group = st.nextToken();
     //First make sure we are not overwriting the graphIndex
-    for(int i=0; i<al.getAlignmentAnnotation().length; i++)
+    for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
     {
-      if(al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(group))
+      if (al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(group))
       {
-        graphGroup = al.getAlignmentAnnotation()[i].graphGroup +1;
+        graphGroup = al.getAlignmentAnnotation()[i].graphGroup + 1;
         al.getAlignmentAnnotation()[i].graphGroup = graphGroup;
         break;
       }
     }
 
     //Now update groups
-    while(st.hasMoreTokens())
+    while (st.hasMoreTokens())
     {
       group = st.nextToken();
-      for(int i=0; i<al.getAlignmentAnnotation().length; i++)
+      for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
       {
         if (al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(group))
         {
@@ -520,12 +578,14 @@ public class AnnotationFile
       }
     }
 
-    if(annotation==null)
+    if (annotation == null)
+    {
       return;
+    }
     float value = new Float(st.nextToken()).floatValue();
-    String label = st.hasMoreTokens() ?  st.nextToken() : null;
+    String label = st.hasMoreTokens() ? st.nextToken() : null;
     java.awt.Color colour = null;
-    if(st.hasMoreTokens())
+    if (st.hasMoreTokens())
     {
       UserColourScheme ucs = new UserColourScheme(st.nextToken());
       colour = ucs.findColour('A');
@@ -538,11 +598,11 @@ public class AnnotationFile
   {
     SequenceGroup sg = new SequenceGroup();
     sg.setName(st.nextToken());
-    sg.setStartRes(Integer.parseInt(st.nextToken())-1);
-    sg.setEndRes(Integer.parseInt(st.nextToken())-1);
+    sg.setStartRes(Integer.parseInt(st.nextToken()) - 1);
+    sg.setEndRes(Integer.parseInt(st.nextToken()) - 1);
 
     String index = st.nextToken();
-    if(index.equals("-1"))
+    if (index.equals("-1"))
     {
       while (st.hasMoreElements())
       {
@@ -571,23 +631,27 @@ public class AnnotationFile
           int end = (Integer.parseInt(st3.nextToken()));
 
           if (end > start)
+          {
             for (int i = start; i <= end; i++)
-              sg.addSequence(al.getSequenceAt(i-1), false);
+            {
+              sg.addSequence(al.getSequenceAt(i - 1), false);
+            }
+          }
         }
         else
         {
-          sg.addSequence(al.getSequenceAt(Integer.parseInt(tmp)-1 ), false);
+          sg.addSequence(al.getSequenceAt(Integer.parseInt(tmp) - 1), false);
         }
       }
     }
 
-    if(refSeq!=null)
+    if (refSeq != null)
     {
-      sg.setStartRes( refSeq.findIndex( sg.getStartRes()+1 )-1 );
-      sg.setEndRes(   refSeq.findIndex( sg.getEndRes() +1) -1 );
+      sg.setStartRes(refSeq.findIndex(sg.getStartRes() + 1) - 1);
+      sg.setEndRes(refSeq.findIndex(sg.getEndRes() + 1) - 1);
     }
 
-    if(sg.getSize()>0)
+    if (sg.getSize() > 0)
     {
       al.addGroup(sg);
     }
@@ -599,35 +663,45 @@ public class AnnotationFile
     //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)
+    if (al.getGroups() == null)
+    {
       return;
+    }
     SequenceGroup sg = null;
 
     String name = st.nextToken();
 
     Vector groups = al.getGroups();
-    for(int i=0; i<groups.size(); i++)
+    for (int i = 0; i < groups.size(); i++)
     {
-      sg = (SequenceGroup)groups.elementAt(i);
-      if(sg.getName().equals(name))
+      sg = (SequenceGroup) groups.elementAt(i);
+      if (sg.getName().equals(name))
+      {
         break;
+      }
       else
+      {
         sg = null;
+      }
     }
 
-    if(sg!=null)
+    if (sg != null)
     {
       String keyValue, key, value;
-      while(st.hasMoreTokens())
+      while (st.hasMoreTokens())
       {
         keyValue = st.nextToken();
-        key = keyValue.substring(0,keyValue.indexOf("="));
-        value=keyValue.substring(keyValue.indexOf("=")+1);
+        key = keyValue.substring(0, keyValue.indexOf("="));
+        value = keyValue.substring(keyValue.indexOf("=") + 1);
 
-        if(key.equalsIgnoreCase("description"))
+        if (key.equalsIgnoreCase("description"))
+        {
           sg.setDescription(value);
-        else if(key.equalsIgnoreCase("colour"))
+        }
+        else if (key.equalsIgnoreCase("colour"))
+        {
           sg.cs = ColourSchemeProperty.getColour(al, value);
+        }
         else if (key.equalsIgnoreCase("pidThreshold"))
         {
           sg.cs.setThreshold(Integer.parseInt(value), true);
@@ -637,39 +711,47 @@ 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);
+          c.calculate();
+          c.verdict(false, 25);
 
-            sg.cs.setConservation(c);
+          sg.cs.setConservation(c);
 
         }
         else if (key.equalsIgnoreCase("outlineColour"))
-         {
-           sg.setOutlineColour(new UserColourScheme(value).findColour('A'));
-         }
+        {
+          sg.setOutlineColour(new UserColourScheme(value).findColour('A'));
+        }
         else if (key.equalsIgnoreCase("displayBoxes"))
-         sg.setDisplayBoxes( Boolean.valueOf(value).booleanValue() );
+        {
+          sg.setDisplayBoxes(Boolean.valueOf(value).booleanValue());
+        }
         else if (key.equalsIgnoreCase("displayText"))
-         sg.setDisplayText( Boolean.valueOf(value).booleanValue() );
+        {
+          sg.setDisplayText(Boolean.valueOf(value).booleanValue());
+        }
         else if (key.equalsIgnoreCase("colourText"))
-         sg.setColourText( Boolean.valueOf(value).booleanValue() );
+        {
+          sg.setColourText(Boolean.valueOf(value).booleanValue());
+        }
         else if (key.equalsIgnoreCase("textCol1"))
-         {
-           sg.textColour = new UserColourScheme(value).findColour('A');
-         }
+        {
+          sg.textColour = new UserColourScheme(value).findColour('A');
+        }
         else if (key.equalsIgnoreCase("textCol2"))
         {
           sg.textColour2 = new UserColourScheme(value).findColour('A');
         }
         else if (key.equalsIgnoreCase("textColThreshold"))
-         sg.thresholdTextColour = Integer.parseInt(value);
+        {
+          sg.thresholdTextColour = Integer.parseInt(value);
+        }
 
-       sg.recalcConservation();
+        sg.recalcConservation();
       }
     }
   }
diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 2e4ddc4..e4475ab 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -1,234 +1,240 @@
-    /*
-    * Jalview - A Sequence Alignment Editor and Viewer
-    * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-    *
-    * This program is free software; you can redistribute it and/or
-    * modify it under the terms of the GNU General Public License
-    * as published by the Free Software Foundation; either version 2
-    * of the License, or (at your option) any later version.
-    *
-    * This program is distributed in the hope that it will be useful,
-    * but WITHOUT ANY WARRANTY; without even the implied warranty of
-    * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    * GNU General Public License for more details.
-    *
-    * You should have received a copy of the GNU General Public License
-    * along 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.*;
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @author $author$
-     * @version $Revision$
-     */
-    public class AppletFormatAdapter
+/*
+ * 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.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class AppletFormatAdapter
+{
+  /** DOCUMENT ME!! */
+  public static final String[] READABLE_FORMATS = new String[]
+      {
+      "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH", "PDB"
+  };
+
+  public static final String[] WRITEABLE_FORMATS = new String[]
+      {
+      "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM" //, "AMSA"
+  };
+
+  public static String INVALID_CHARACTERS = "Contains invalid characters";
+
+  public static String SUPPORTED_FORMATS = "Formats currently supported are\n" +
+      "Fasta, MSF, Clustal, BLC, PIR, MSP, and PFAM";
+
+  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;
+
+  public static final boolean isValidFormat(String format)
+  {
+    boolean valid = false;
+    for (int i = 0; i < READABLE_FORMATS.length; i++)
     {
-        /** DOCUMENT ME!! */
-        public static final String [] READABLE_FORMATS = new String[]
-        {
-            "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH", "PDB"
-        };
-
-        public static final String [] WRITEABLE_FORMATS = new String[]
-        {
-            "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM"  //, "AMSA"
-        };
-
-
-        public static String INVALID_CHARACTERS = "Contains invalid characters";
-
-        public static String SUPPORTED_FORMATS = "Formats currently supported are\n" +
-                                                 "Fasta, MSF, Clustal, BLC, PIR, MSP, and PFAM";
-
-
-        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;
+      if (READABLE_FORMATS[i].equalsIgnoreCase(format))
+      {
+        return true;
+      }
+    }
 
-        public static final boolean isValidFormat(String format)
+    return valid;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param inFile DOCUMENT ME!
+   * @param type DOCUMENT ME!
+   * @param format DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Alignment readFile(String inFile, String type, String format)
+      throws java.io.IOException
+  {
+    this.inFile = inFile;
+    try
+    {
+      if (format.equals("FASTA"))
+      {
+        afile = new FastaFile(inFile, type);
+      }
+      else if (format.equals("MSF"))
+      {
+        afile = new MSFfile(inFile, type);
+      }
+      else if (format.equals("PileUp"))
+      {
+        afile = new PileUpfile(inFile, type);
+      }
+      else if (format.equals("CLUSTAL"))
+      {
+        afile = new ClustalFile(inFile, type);
+      }
+      else if (format.equals("BLC"))
+      {
+        afile = new BLCFile(inFile, type);
+      }
+      else if (format.equals("PIR"))
+      {
+        afile = new PIRFile(inFile, type);
+      }
+      else if (format.equals("PFAM"))
+      {
+        afile = new PfamFile(inFile, type);
+      }
+      else if (format.equals("JnetFile"))
+      {
+        afile = new JPredFile(inFile, type);
+        ( (JPredFile) afile).removeNonSequences();
+      }
+      else if (format.equals("PDB"))
+      {
+        afile = new MCview.PDBfile(inFile, type);
+      }
+      else if (format.equals("STH"))
+      {
+        afile = new StockholmFile(inFile, type);
+      }
+
+      Alignment al = new Alignment(afile.getSeqsAsArray());
+
+      afile.addAnnotations(al);
+
+      return al;
+    }
+    catch (Exception e)
+    {
+      e.printStackTrace();
+      System.err.println("Failed to read alignment using the '" + format +
+                         "' reader.\n" + e);
+
+      if (e.getMessage() != null &&
+          e.getMessage().startsWith(INVALID_CHARACTERS))
+      {
+        throw new java.io.IOException(e.getMessage());
+      }
+
+      // Finally test if the user has pasted just the sequence, no id
+      if (type.equalsIgnoreCase("Paste"))
+      {
+        try
         {
-          boolean valid = false;
-          for(int i=0; i<READABLE_FORMATS.length; i++)
-            if(READABLE_FORMATS[i].equalsIgnoreCase(format))
-              return true;
+          // Possible sequence is just residues with no label
+          afile = new FastaFile(">UNKNOWN\n" + inFile, "Paste");
+          Alignment al = new Alignment(afile.getSeqsAsArray());
+          afile.addAnnotations(al);
+          return al;
 
-          return valid;
         }
-
-        /**
-         * DOCUMENT ME!
-         *
-         * @param inFile DOCUMENT ME!
-         * @param type DOCUMENT ME!
-         * @param format DOCUMENT ME!
-         *
-         * @return DOCUMENT ME!
-         */
-        public Alignment readFile(String inFile, String type, String format)
-            throws java.io.IOException
+        catch (Exception ex)
         {
-            this.inFile = inFile;
-            try
-            {
-              if (format.equals("FASTA"))
-              {
-                afile = new FastaFile(inFile, type);
-              }
-              else if (format.equals("MSF"))
-              {
-                afile = new MSFfile(inFile, type);
-              }
-              else if (format.equals("PileUp"))
-              {
-                afile = new PileUpfile(inFile, type);
-              }
-              else if (format.equals("CLUSTAL"))
-              {
-                afile = new ClustalFile(inFile, type);
-              }
-              else if (format.equals("BLC"))
-              {
-                afile = new BLCFile(inFile, type);
-              }
-              else if (format.equals("PIR"))
-              {
-                afile = new PIRFile(inFile, type);
-              }
-              else if (format.equals("PFAM"))
-              {
-                afile = new PfamFile(inFile, type);
-              }
-              else if (format.equals("JnetFile"))
-              {
-                afile = new JPredFile(inFile, type);
-                ( (JPredFile) afile).removeNonSequences();
-              }
-              else if (format.equals("PDB"))
-              {
-                afile = new MCview.PDBfile(inFile, type);
-              }
-              else if (format.equals("STH"))
-              {
-                afile = new StockholmFile(inFile, type);
-              }
-
-              Alignment al = new Alignment(afile.getSeqsAsArray());
-
-              afile.addAnnotations(al);
-
-              return al;
-            }
-            catch (Exception e)
-            {
-              e.printStackTrace();
-              System.err.println("Failed to read alignment using the '" + format +
-                                 "' reader.\n"+e);
-
-              if(e.getMessage()!=null && e.getMessage().startsWith(INVALID_CHARACTERS))
-                throw new java.io.IOException(e.getMessage());
-
-              // Finally test if the user has pasted just the sequence, no id
-              if(type.equalsIgnoreCase("Paste"))
-              {
-                try{
-                  // Possible sequence is just residues with no label
-                  afile = new FastaFile(">UNKNOWN\n" + inFile, "Paste");
-                  Alignment al = new Alignment(afile.getSeqsAsArray());
-                  afile.addAnnotations(al);
-                  return al;
-
-                }
-                catch(Exception ex)
-                {
-                  if(ex.toString().startsWith(INVALID_CHARACTERS))
-                    throw new java.io.IOException(e.getMessage());
-
-                  ex.printStackTrace();
-                }
-              }
-
-              // If we get to this stage, the format was not supported
-              throw new java.io.IOException(SUPPORTED_FORMATS);
-            }
-        }
-
+          if (ex.toString().startsWith(INVALID_CHARACTERS))
+          {
+            throw new java.io.IOException(e.getMessage());
+          }
 
-        /**
-         * DOCUMENT ME!
-         *
-         * @param format DOCUMENT ME!
-         * @param seqs DOCUMENT ME!
-         *
-         * @return DOCUMENT ME!
-         */
-        public String formatSequences(String format,
-                                      AlignmentI alignment,
-                                      boolean jvsuffix)
-        {
-            try
-            {
-                AlignFile afile = null;
-
-                if (format.equalsIgnoreCase("FASTA"))
-                {
-                    afile = new FastaFile();
-                }
-                else if (format.equalsIgnoreCase("MSF"))
-                {
-                    afile = new MSFfile();
-                }
-                else if (format.equalsIgnoreCase("PileUp"))
-                {
-                    afile = new PileUpfile();
-                }
-                else if (format.equalsIgnoreCase("CLUSTAL"))
-                {
-                    afile = new ClustalFile();
-                }
-                else if (format.equalsIgnoreCase("BLC"))
-                {
-                    afile = new BLCFile();
-                }
-                else if (format.equalsIgnoreCase("PIR"))
-                {
-                    afile = new PIRFile();
-                }
-                else if (format.equalsIgnoreCase("PFAM"))
-                {
-                    afile = new PfamFile();
-                }
-                else if (format.equalsIgnoreCase("STH"))
-                {
-                  afile = new StockholmFile();
-                }
-                else if (format.equals("AMSA"))
-                {
-                  afile = new AMSAFile(alignment);
-                }
-
-                afile.addJVSuffix(jvsuffix);
-
-                afile.setSeqs( alignment.getSequencesArray() );
-
-                return afile.print();
-            }
-            catch (Exception e)
-            {
-                System.err.println("Failed to write alignment as a '" + format +
-                    "' file\n");
-                e.printStackTrace();
-            }
-
-            return null;
+          ex.printStackTrace();
         }
+      }
+
+      // If we get to this stage, the format was not supported
+      throw new java.io.IOException(SUPPORTED_FORMATS);
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param format DOCUMENT ME!
+   * @param seqs DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public String formatSequences(String format,
+                                AlignmentI alignment,
+                                boolean jvsuffix)
+  {
+    try
+    {
+      AlignFile afile = null;
+
+      if (format.equalsIgnoreCase("FASTA"))
+      {
+        afile = new FastaFile();
+      }
+      else if (format.equalsIgnoreCase("MSF"))
+      {
+        afile = new MSFfile();
+      }
+      else if (format.equalsIgnoreCase("PileUp"))
+      {
+        afile = new PileUpfile();
+      }
+      else if (format.equalsIgnoreCase("CLUSTAL"))
+      {
+        afile = new ClustalFile();
+      }
+      else if (format.equalsIgnoreCase("BLC"))
+      {
+        afile = new BLCFile();
+      }
+      else if (format.equalsIgnoreCase("PIR"))
+      {
+        afile = new PIRFile();
+      }
+      else if (format.equalsIgnoreCase("PFAM"))
+      {
+        afile = new PfamFile();
+      }
+      else if (format.equalsIgnoreCase("STH"))
+      {
+        afile = new StockholmFile();
+      }
+      else if (format.equals("AMSA"))
+      {
+        afile = new AMSAFile(alignment);
+      }
+
+      afile.addJVSuffix(jvsuffix);
+
+      afile.setSeqs(alignment.getSequencesArray());
+
+      return afile.print();
     }
+    catch (Exception e)
+    {
+      System.err.println("Failed to write alignment as a '" + format +
+                         "' file\n");
+      e.printStackTrace();
+    }
+
+    return null;
+  }
+}
diff --git a/src/jalview/io/BLCFile.java b/src/jalview/io/BLCFile.java
index 624e134..8958f7b 100755
--- a/src/jalview/io/BLCFile.java
+++ b/src/jalview/io/BLCFile.java
@@ -1,29 +1,27 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 jalview.io;
 
-import jalview.datamodel.*;
-
 import java.io.*;
-
 import java.util.*;
 
+import jalview.datamodel.*;
 
 /**
  * DOCUMENT ME!
@@ -31,176 +29,180 @@ import java.util.*;
  * @author $author$
  * @version $Revision$
  */
-public class BLCFile extends AlignFile
+public class BLCFile
+    extends AlignFile
 {
-    Vector titles;
-
-    /**
-     * Creates a new BLCFile object.
-     */
-    public BLCFile()
+  Vector titles;
+
+  /**
+   * Creates a new BLCFile object.
+   */
+  public BLCFile()
+  {
+  }
+
+  /**
+   * Creates a new BLCFile object.
+   *
+   * @param inFile DOCUMENT ME!
+   * @param type DOCUMENT ME!
+   *
+   * @throws IOException DOCUMENT ME!
+   */
+  public BLCFile(String inFile, String type)
+      throws IOException
+  {
+    super(inFile, type);
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void initData()
+  {
+    super.initData();
+    titles = new Vector();
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void parse()
+      throws IOException
+  {
+    boolean idsFound = false;
+    StringBuffer[] seqstrings;
+
+    String line = null;
+
+    do
     {
+      line = nextLine();
+
+      // seek end of ids
+      if (line.indexOf("*") > -1)
+      {
+        idsFound = true;
+
+        break;
+      }
+
+      int abracket = line.indexOf(">");
+
+      if (abracket > -1)
+      {
+        line = line.substring(abracket + 1);
+
+        Sequence seq = parseId(line);
+        seqs.addElement(seq);
+      }
     }
+    while (!idsFound);
 
+    int starCol = line.indexOf("*");
+    seqstrings = new StringBuffer[seqs.size()];
 
-    /**
-     * Creates a new BLCFile object.
-     *
-     * @param inFile DOCUMENT ME!
-     * @param type DOCUMENT ME!
-     *
-     * @throws IOException DOCUMENT ME!
-     */
-    public BLCFile(String inFile, String type) throws IOException
+    for (int i = 0; i < seqs.size(); i++)
     {
-        super(inFile, type);
+      if (seqstrings[i] == null)
+      {
+        seqstrings[i] = new StringBuffer();
+      }
     }
 
-    /**
-     * DOCUMENT ME!
-     */
-    public void initData()
+    while ( (line = nextLine()).indexOf("*") == -1)
     {
-        super.initData();
-        titles = new Vector();
+      for (int i = 0; i < seqs.size(); i++)
+      {
+        if (line.length() > (i + starCol))
+        {
+          seqstrings[i].append(line.charAt(i + starCol));
+        }
+      }
     }
 
-    /**
-     * DOCUMENT ME!
-     */
-    public void parse() throws IOException
+    for (int i = 0; i < seqs.size(); i++)
     {
-        boolean idsFound = false;
-        StringBuffer[] seqstrings;
-
-        String line = null;
-
-            do
-            {
-                line = nextLine();
-
-                // seek end of ids
-                if (line.indexOf("*") > -1)
-                {
-                    idsFound = true;
-
-                    break;
-                }
-
-                int abracket = line.indexOf(">");
-
-                if (abracket > -1)
-                {
-                  line = line.substring(abracket+1);
-
-                  Sequence seq = parseId(line);
-                  seqs.addElement(seq);
-                }
-            }
-            while (!idsFound);
-
-            int starCol = line.indexOf("*");
-            seqstrings = new StringBuffer[seqs.size()];
-
-            for (int i = 0; i < seqs.size(); i++)
-            {
-                if (seqstrings[i] == null)
-                {
-                    seqstrings[i] = new StringBuffer();
-                }
-            }
-
-            while ((line = nextLine()).indexOf("*") == -1)
-            {
-                for (int i = 0; i < seqs.size(); i++)
-                {
-                    if (line.length() > (i + starCol))
-                    {
-                        seqstrings[i].append(line.charAt(i + starCol));
-                    }
-                }
-            }
-
-            for (int i = 0; i < seqs.size(); i++)
-            {
-              Sequence newSeq = (Sequence) seqs.elementAt(i);
-
-              newSeq.setSequence(seqstrings[i].toString());
-            }
+      Sequence newSeq = (Sequence) seqs.elementAt(i);
 
+      newSeq.setSequence(seqstrings[i].toString());
     }
 
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public String print()
+  {
+    return print(getSeqsAsArray());
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param s DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public String print(SequenceI[] s)
+  {
+    StringBuffer out = new StringBuffer();
     /**
-     * DOCUMENT ME!
+     * A general parser for ids. Will look for dbrefs in
+     * Uniprot format source|id
+     * And also Jalview /start-end
      *
-     * @return DOCUMENT ME!
+     * @String id Id to be parsed
      */
-    public String print()
-    {
-        return print(getSeqsAsArray());
-    }
+    int i = 0;
+    int max = -1;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param s DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String print(SequenceI[] s)
+    while ( (i < s.length) && (s[i] != null))
     {
-        StringBuffer out = new StringBuffer();
-        /**
-         * 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;
+      out.append(">" + printId(s[i]));
+      if (s[i].getDescription() != null)
+      {
+        out.append(" " + s[i].getDescription());
+      }
 
-        while ((i < s.length) && (s[i] != null))
-        {
-            out.append(">" + printId(s[i]));
-            if(s[i].getDescription()!=null)
-              out.append(" "+s[i].getDescription());
+      out.append("\n");
 
-            out.append("\n");
+      if (s[i].getSequence().length > max)
+      {
+        max = s[i].getSequence().length;
+      }
 
-            if (s[i].getSequence().length > max)
-            {
-                max = s[i].getSequence().length;
-            }
+      i++;
+    }
 
-            i++;
-        }
+    out.append("* iteration 1\n");
 
-        out.append("* iteration 1\n");
+    for (int j = 0; j < max; j++)
+    {
+      i = 0;
 
-        for (int j = 0; j < max; j++)
+      while ( (i < s.length) && (s[i] != null))
+      {
+        if (s[i].getSequence().length > j)
+        {
+          out.append(s[i].getSequenceAsString(j, j + 1));
+        }
+        else
         {
-            i = 0;
-
-            while ((i < s.length) && (s[i] != null))
-            {
-                if (s[i].getSequence().length > j)
-                {
-                    out.append(s[i].getSequenceAsString(j, j + 1));
-                }
-                else
-                {
-                    out.append("-");
-                }
-
-                i++;
-            }
-
-            out.append("\n");
+          out.append("-");
         }
 
-        out.append("*\n");
+        i++;
+      }
 
-        return out.toString();
+      out.append("\n");
     }
+
+    out.append("*\n");
+
+    return out.toString();
+  }
 }
diff --git a/src/jalview/io/ClustalFile.java b/src/jalview/io/ClustalFile.java
index 90c22f9..5d7be8c 100755
--- a/src/jalview/io/ClustalFile.java
+++ b/src/jalview/io/ClustalFile.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -43,7 +43,8 @@ public class ClustalFile
     super.initData();
   }
 
-  public void parse() throws IOException
+  public void parse()
+      throws IOException
   {
     int i = 0;
     boolean flag = false;
@@ -97,7 +98,9 @@ public class ClustalFile
             }
           }
           else
+          {
             flag = true;
+          }
         }
       }
     }
@@ -124,7 +127,8 @@ public class ClustalFile
           }
 
           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);
         }
@@ -185,7 +189,7 @@ public class ClustalFile
 
       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;
diff --git a/src/jalview/io/DBRefFetcher.java b/src/jalview/io/DBRefFetcher.java
index bd3c733..445c90a 100644
--- a/src/jalview/io/DBRefFetcher.java
+++ b/src/jalview/io/DBRefFetcher.java
@@ -1,37 +1,31 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 jalview.io;
 
-import jalview.datamodel.*;
-
-import jalview.gui.*;
-
 import java.io.*;
-
 import java.util.*;
 
-import org.exolab.castor.mapping.Mapping;
-
+import org.exolab.castor.mapping.*;
 import org.exolab.castor.xml.*;
-import jalview.analysis.AlignSeq;
-
-
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.gui.*;
 
 /**
  * DOCUMENT ME!
@@ -39,7 +33,8 @@ import jalview.analysis.AlignSeq;
  * @author $author$
  * @version $Revision$
  */
-public class DBRefFetcher implements Runnable
+public class DBRefFetcher
+    implements Runnable
 {
   AlignmentI dataset;
   AlignFrame af;
@@ -73,10 +68,9 @@ public class DBRefFetcher implements Runnable
     }
     catch (Exception e)
     {
-      System.out.println("Error getUniprotEntries() "+e);
+      System.out.println("Error getUniprotEntries() " + e);
     }
 
-
     return uni.getUniprotEntries();
   }
 
@@ -98,13 +92,16 @@ public class DBRefFetcher implements Runnable
     thread.start();
     running = true;
 
-    if(waitTillFinished)
+    if (waitTillFinished)
     {
-      while(running)
+      while (running)
       {
-        try{
+        try
+        {
           Thread.sleep(500);
-        }catch(Exception ex){}
+        }
+        catch (Exception ex)
+        {}
       }
     }
 
@@ -122,15 +119,15 @@ public class DBRefFetcher implements Runnable
     key = key.toUpperCase();
 
     Vector seqs;
-    if(seqRefs.containsKey(key))
+    if (seqRefs.containsKey(key))
     {
-      seqs = (Vector)seqRefs.get(key);
+      seqs = (Vector) seqRefs.get(key);
 
-      if(seqs!=null && !seqs.contains(seq))
+      if (seqs != null && !seqs.contains(seq))
       {
         seqs.addElement(seq);
       }
-      else if(seqs==null)
+      else if (seqs == null)
       {
         seqs = new Vector();
         seqs.addElement(seq);
@@ -146,7 +143,6 @@ public class DBRefFetcher implements Runnable
     seqRefs.put(key, seqs);
   }
 
-
   /**
    * DOCUMENT ME!
    */
@@ -171,35 +167,39 @@ public class DBRefFetcher implements Runnable
              seqIndex++, i++)
         {
           Sequence sequence = (Sequence) sequences.get(seqIndex);
-          DBRefEntry [] uprefs = jalview.util.DBRefUtils.selectRefs(sequence.getDBRef(), new String[] {
+          DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(sequence.
+              getDBRef(), new String[]
+              {
               jalview.datamodel.DBRefSource.UNIPROT});
-          if (uprefs!=null)
+          if (uprefs != null)
           {
-            if(uprefs.length+i>50)
+            if (uprefs.length + i > 50)
+            {
               break;
+            }
 
-            for(int j=0; j<uprefs.length; j++)
+            for (int j = 0; j < uprefs.length; j++)
             {
               addSeqId(sequence, uprefs[j].getAccessionId());
-              queryString.append(uprefs[j].getAccessionId()+";");
+              queryString.append(uprefs[j].getAccessionId() + ";");
             }
           }
           else
           {
             StringTokenizer st = new StringTokenizer(sequence.getName(), "|");
-            if(st.countTokens()+i>50)
+            if (st.countTokens() + i > 50)
             {
               //Dont send more than 50 id strings to dbFetch!!
-              seqIndex --;
+              seqIndex--;
             }
             else
             {
-                while(st.hasMoreTokens())
-                {
-                  String token = st.nextToken();
-                  addSeqId(sequence, token);
-                  queryString.append(token+";");
-                }
+              while (st.hasMoreTokens())
+              {
+                String token = st.nextToken();
+                addSeqId(sequence, token);
+                queryString.append(token + ";");
+              }
             }
           }
         }
@@ -233,13 +233,12 @@ public class DBRefFetcher implements Runnable
     }
 
     af.setProgressBar("DBRef search completed", startTime);
-   // promptBeforeBlast();
+    // promptBeforeBlast();
 
-   running = false;
+    running = false;
 
   }
 
-
   /**
    * DOCUMENT ME!
    *
@@ -250,7 +249,9 @@ public class DBRefFetcher implements Runnable
   void ReadUniprotFile(File file)
   {
     if (!file.exists())
+    {
       return;
+    }
 
     SequenceI sequence = null;
 
@@ -275,7 +276,9 @@ public class DBRefFetcher implements Runnable
           {
             sequence = (SequenceI) seqs.elementAt(jj);
             if (!sequenceMatches.contains(sequence))
+            {
               sequenceMatches.addElement(sequence);
+            }
           }
         }
       }
@@ -289,7 +292,9 @@ public class DBRefFetcher implements Runnable
           {
             sequence = (SequenceI) seqs.elementAt(jj);
             if (!sequenceMatches.contains(sequence))
+            {
               sequenceMatches.addElement(sequence);
+            }
           }
         }
       }
@@ -353,7 +358,9 @@ public class DBRefFetcher implements Runnable
         {
           PDBEntry pdb = (PDBEntry) e.nextElement();
           if (!pdb.getType().equals(DBRefSource.PDB))
+          {
             continue;
+          }
 
           sequence.addDBRef(new DBRefEntry(DBRefSource.PDB,
                                            "0",
@@ -371,5 +378,3 @@ public class DBRefFetcher implements Runnable
     }
   }
 }
-
-
diff --git a/src/jalview/io/DasSequenceFeatureFetcher.java b/src/jalview/io/DasSequenceFeatureFetcher.java
index f6e6f9b..fbd7442 100755
--- a/src/jalview/io/DasSequenceFeatureFetcher.java
+++ b/src/jalview/io/DasSequenceFeatureFetcher.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,29 +18,19 @@
  */
 package jalview.io;
 
-import jalview.datamodel.*;
-
-import jalview.gui.*;
-
+import java.net.*;
 import java.util.*;
 
-import java.net.URL;
-
-import org.biojava.dasobert.das.FeatureThread;
-import org.biojava.dasobert.eventmodel.FeatureEvent;
-import org.biojava.dasobert.eventmodel.FeatureListener;
-import org.biojava.dasobert.dasregistry.DasSource;
-
-import org.biojava.dasobert.das2.io.DasSourceReaderImpl;
-import org.biojava.dasobert.dasregistry.Das1Source;
-import org.biojava.dasobert.dasregistry.DasSource;
-import org.biojava.dasobert.das2.Das2Source;
-import org.biojava.dasobert.das2.DasSourceConverter;
+import javax.swing.*;
 
+import org.biojava.dasobert.das.*;
+import org.biojava.dasobert.das2.*;
+import org.biojava.dasobert.das2.io.*;
+import org.biojava.dasobert.dasregistry.*;
+import org.biojava.dasobert.eventmodel.*;
 import jalview.bin.Cache;
-import org.biojava.dasobert.dasregistry.DasCoordinateSystem;
-
-import javax.swing.*;
+import jalview.datamodel.*;
+import jalview.gui.*;
 
 /**
  * DOCUMENT ME!
@@ -124,13 +114,17 @@ public class DasSequenceFeatureFetcher
         thread.start();
       }
       else
+      {
         startFetching();
+      }
     }
     else
+    {
       startFetching();
-
     }
 
+  }
+
   class FetchDBRefs
       implements Runnable
   {
@@ -142,173 +136,176 @@ public class DasSequenceFeatureFetcher
     }
   }
 
+  /**
+   * Spawns a number of dasobert Fetcher threads to add features to sequences in the dataset
+   */
+  void startFetching()
+  {
+    cancelled = false;
+    startTime = System.currentTimeMillis();
+    af.setProgressBar("Fetching DAS Sequence Features", startTime);
+
+    DasSource[] sources = new jalview.gui.DasSourceBrowser().getDASSource();
+
+    if (selectedSources == null || selectedSources.size() == 0)
+    {
+      String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE",
+          "uniprot");
+      StringTokenizer st = new StringTokenizer(active, "\t");
+      Vector selectedSources = new Vector();
+      String token;
+      while (st.hasMoreTokens())
+      {
+        token = st.nextToken();
+        for (int i = 0; i < sources.length; i++)
+        {
+          if (sources[i].getNickname().equals(token))
+          {
+            selectedSources.addElement(sources[i]);
+            break;
+          }
+        }
+      }
+    }
+
+    if (selectedSources == null || selectedSources.size() == 0)
+    {
+      System.out.println("No DAS Sources active");
+      af.setProgressBar("No DAS Sources Active", startTime);
+      return;
+    }
+
+    sourcesRemaining = selectedSources.size();
+    //Now sending requests one at a time to each server
+    for (int sourceIndex = 0;
+         sourceIndex < selectedSources.size()
+         && !cancelled;
+         sourceIndex++)
+    {
+      DasSource dasSource = (DasSource) selectedSources.elementAt(
+          sourceIndex);
+
+      nextSequence(dasSource, sequences[0]);
+    }
+  }
+
+  public void cancel()
+  {
+    af.setProgressBar("DAS Feature Fetching Cancelled", startTime);
+    cancelled = true;
+  }
+
+  int sourcesRemaining = 0;
+  void responseComplete(DasSource dasSource, SequenceI seq)
+  {
+    if (seq != null)
+    {
+      for (int seqIndex = 0;
+           seqIndex < sequences.length - 1
+           && !cancelled; seqIndex++)
+      {
+        if (sequences[seqIndex] == seq)
+        {
+          nextSequence(dasSource, sequences[++seqIndex]);
+          return;
+        }
+      }
+    }
+
+    sourcesRemaining--;
+
+    if (sourcesRemaining == 0)
+    {
+      af.setProgressBar("DAS Feature Fetching Complete", startTime);
+
+      if (af.featureSettings != null)
+      {
+        af.featureSettings.setTableData();
+      }
+
+      fsettings.complete();
+    }
+
+  }
 
-   /**
-    * Spawns a number of dasobert Fetcher threads to add features to sequences in the dataset
-    */
-   void startFetching()
-   {
-     cancelled = false;
-     startTime = System.currentTimeMillis();
-     af.setProgressBar("Fetching DAS Sequence Features", startTime);
-
-     DasSource[] sources = new jalview.gui.DasSourceBrowser().getDASSource();
-
-     if (selectedSources == null || selectedSources.size() == 0)
-     {
-       String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE",
-           "uniprot");
-       StringTokenizer st = new StringTokenizer(active, "\t");
-       Vector selectedSources = new Vector();
-       String token;
-       while (st.hasMoreTokens())
-       {
-         token = st.nextToken();
-         for (int i = 0; i < sources.length; i++)
-         {
-           if (sources[i].getNickname().equals(token))
-           {
-             selectedSources.addElement(sources[i]);
-             break;
-           }
-         }
-       }
-     }
-
-     if (selectedSources == null || selectedSources.size() == 0)
-     {
-       System.out.println("No DAS Sources active");
-       af.setProgressBar("No DAS Sources Active", startTime);
-       return;
-     }
-
-       sourcesRemaining = selectedSources.size();
-       //Now sending requests one at a time to each server
-       for (int sourceIndex = 0;
-            sourceIndex < selectedSources.size()
-            && !cancelled;
-            sourceIndex++)
-       {
-         DasSource dasSource = (DasSource) selectedSources.elementAt(
-             sourceIndex);
-
-         nextSequence(dasSource, sequences[0]);
-       }
-   }
-
-   public void cancel()
-   {
-     af.setProgressBar("DAS Feature Fetching Cancelled", startTime);
-     cancelled = true;
-   }
-
-   int sourcesRemaining=0;
-   void responseComplete(DasSource dasSource, SequenceI seq)
-   {
-     if (seq != null)
-     {
-       for (int seqIndex = 0;
-            seqIndex < sequences.length-1
-            && !cancelled; seqIndex++)
-       {
-         if (sequences[seqIndex] == seq)
-         {
-           nextSequence(dasSource, sequences[++seqIndex]);
-           return;
-         }
-       }
-     }
-
-     sourcesRemaining --;
-
-     if(sourcesRemaining==0)
-     {
-       af.setProgressBar("DAS Feature Fetching Complete", startTime);
-
-       if(af.featureSettings!=null)
-         af.featureSettings.setTableData();
-
-       fsettings.complete();
-     }
-
-   }
-
-   void featuresAdded(SequenceI seq)
-   {
-     af.getFeatureRenderer().featuresAdded();
-
-     int start = af.getViewport().getStartSeq();
-     int end = af.getViewport().getEndSeq();
-     int index;
-     for(index=start; index<end; index++)
-      if(seq == af.getViewport().getAlignment().getSequenceAt(index).getDatasetSequence())
-       {
-         af.alignPanel.repaint();
-         break;
-       }
-   }
+  void featuresAdded(SequenceI seq)
+  {
+    af.getFeatureRenderer().featuresAdded();
 
+    int start = af.getViewport().getStartSeq();
+    int end = af.getViewport().getEndSeq();
+    int index;
+    for (index = start; index < end; index++)
+    {
+      if (seq ==
+          af.getViewport().getAlignment().getSequenceAt(index).getDatasetSequence())
+      {
+        af.alignPanel.repaint();
+        break;
+      }
+    }
+  }
 
   void nextSequence(DasSource dasSource, SequenceI seq)
   {
-      DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(seq.getDBRef(),
-          new String[]
-          {
+    DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(seq.getDBRef(),
+        new String[]
+        {
         //  jalview.datamodel.DBRefSource.PDB,
-          jalview.datamodel.DBRefSource.UNIPROT
-      });
+        jalview.datamodel.DBRefSource.UNIPROT
+    });
 
-        if (uprefs != null)
+    if (uprefs != null)
+    {
+      // we know the id for this entry, so don't note its ID in the unknownSequences list
+      // for (int j = 0; j < uprefs.length; j++)
+      {
+        // 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
+        DasCoordinateSystem cs[] = dasSource.getCoordinateSystem();
+        if (cs.length > 0)
         {
-          // we know the id for this entry, so don't note its ID in the unknownSequences list
-         // for (int j = 0; j < uprefs.length; j++)
+          // for (int l = 0; l < cs.length; l++)
           {
-            // 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
-            DasCoordinateSystem cs[] = dasSource.getCoordinateSystem();
-            if(cs.length>0)
+            //
+            if (jalview.util.DBRefUtils
+                .isDasCoordinateSystem(cs[0].getName(), uprefs[0]))
             {
-             // for (int l = 0; l < cs.length; l++)
-              {
-               //
-               if (jalview.util.DBRefUtils
-                    .isDasCoordinateSystem(cs[0].getName(), uprefs[0]))
-                {
-                  Cache.log.debug("Launched fetcher for coordinate system " +
-                                  cs[0].getName());
-
-                  createFeatureFetcher(seq,
-                                       dasSource,
-                                       uprefs[0].getAccessionId());
-                }
-              }
+              Cache.log.debug("Launched fetcher for coordinate system " +
+                              cs[0].getName());
+
+              createFeatureFetcher(seq,
+                                   dasSource,
+                                   uprefs[0].getAccessionId());
             }
           }
         }
-        else
-        {
-          String id = null;
-          // try and use the name as the sequence id
-          if (seq.getName().indexOf("|") > -1)
-          {
-            id = seq.getName().substring(
-                seq.getName().lastIndexOf("|") + 1);
-          }
-          else
-          {
-            id = seq.getName();
-          }
-          if (id != null)
-          {
-            // Should try to call a general feature fetcher that
-            // queries many sources with name to discover applicable ID references
-            createFeatureFetcher(seq,
-                                 dasSource,
-                                 id);
-          }
-        }
+      }
+    }
+    else
+    {
+      String id = null;
+      // try and use the name as the sequence id
+      if (seq.getName().indexOf("|") > -1)
+      {
+        id = seq.getName().substring(
+            seq.getName().lastIndexOf("|") + 1);
+      }
+      else
+      {
+        id = seq.getName();
+      }
+      if (id != null)
+      {
+        // Should try to call a general feature fetcher that
+        // queries many sources with name to discover applicable ID references
+        createFeatureFetcher(seq,
+                             dasSource,
+                             id);
+      }
+    }
 
-   }
+  }
 
   /**
    * fetch and add das features to a sequence using the given source URL and Id to create a feature request
@@ -369,8 +366,8 @@ 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);
 
@@ -404,7 +401,9 @@ public class DasSequenceFeatureFetcher
        */
       String desc = new String();
       if (dasfeature.containsKey("NOTE"))
+      {
         desc += (String) dasfeature.get("NOTE");
+      }
 
       int start = 0, end = 0;
       float score = 0f;
@@ -498,4 +497,3 @@ public class DasSequenceFeatureFetcher
   }
 
 }
-
diff --git a/src/jalview/io/EBIFetchClient.java b/src/jalview/io/EBIFetchClient.java
index 12fab86..b71e152 100755
--- a/src/jalview/io/EBIFetchClient.java
+++ b/src/jalview/io/EBIFetchClient.java
@@ -1,34 +1,31 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 jalview.io;
 
 import java.io.*;
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.StringTokenizer;
-
-import org.apache.axis.client.*;
-import org.apache.axis.encoding.XMLType;
-
-import javax.xml.namespace.QName;
-import javax.xml.rpc.ParameterMode;
+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!
@@ -38,199 +35,225 @@ import javax.xml.rpc.ParameterMode;
  */
 public class EBIFetchClient
 {
-    Call call;
-    String format = "default";
-    String style = "raw";
-
-    /**
-     * Creates a new EBIFetchClient object.
-     */
-    public EBIFetchClient()
+  Call call;
+  String format = "default";
+  String style = "raw";
+
+  /**
+   * Creates a new EBIFetchClient object.
+   */
+  public EBIFetchClient()
+  {
+    try
     {
-        try
-        {
-            call = (Call) new Service().createCall();
-            call.setTargetEndpointAddress(new java.net.URL(
-                    "http://www.ebi.ac.uk/ws/services/Dbfetch"));
-        }
-        catch (Exception ex)
-        {
-        }
+      call = (Call)new Service().createCall();
+      call.setTargetEndpointAddress(new java.net.URL(
+          "http://www.ebi.ac.uk/ws/services/Dbfetch"));
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String[] getSupportedDBs()
+    catch (Exception ex)
     {
-        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()
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public String[] getSupportedDBs()
+  {
+    try
     {
-        try
-        {
-            call.setOperationName(new QName("urn:Dbfetch", "getSupportedFormats"));
-            call.setReturnType(XMLType.SOAP_ARRAY);
-
-            return (String[]) call.invoke(new Object[] {  });
-        }
-        catch (Exception ex)
-        {
-            return null;
-        }
+      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[] getSupportedStyles()
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public String[] getSupportedFormats()
+  {
+    try
     {
-        try
-        {
-            call.setOperationName(new QName("urn:Dbfetch", "getSupportedStyles"));
-            call.setReturnType(XMLType.SOAP_ARRAY);
-
-            return (String[]) call.invoke(new Object[] {  });
-        }
-        catch (Exception ex)
-        {
-            return null;
-        }
+      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);
 
-    public static void main (String [] args)
+      return (String[]) call.invoke(new Object[]
+                                    {});
+    }
+    catch (Exception ex)
     {
-      EBIFetchClient ebi = new EBIFetchClient();
-      String[] result = ebi.fetchData("uniprot:25KD_SARPE;G6PD_HUMAN",
-                           "xml", null);
+      return null;
+    }
+  }
+
+  public static void main(String[] args)
+  {
+    EBIFetchClient ebi = new EBIFetchClient();
+    String[] result = ebi.fetchData("uniprot:25KD_SARPE;G6PD_HUMAN",
+                                    "xml", null);
 
-     try{
-       java.io.PrintWriter out = new java.io.PrintWriter(
-      new java.io.FileWriter("out.xml"));
+    try
+    {
+      java.io.PrintWriter out = new java.io.PrintWriter(
+          new java.io.FileWriter("out.xml"));
 
+      for (int i = 0; i < result.length; i++)
+      {
+        out.println(result[i]);
+      }
+      out.close();
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
 
-       for(int i=0; i<result.length; i++)
-       {
-         out.println(result[i]);
-       }
-       out.close();
-     }catch(Exception ex){ex.printStackTrace();}
+  }
 
+  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;
 
-    public File fetchDataAsFile(String ids, String f, String s)
+    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 && (p + 3 < query.length()))
+      {
+        db = query.substring(0, p);
+        query = query.substring(p + 1);
+      }
+      if (querystring == null)
+      {
+        querystring = new StringBuffer(query);
+      }
+      else
+      {
+        querystring.append("," + query);
+      }
+    }
+    if (db == null)
     {
-      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;
+      System.err.println("Invalid Query string : '" + ids +
+                         "'\nShould be of form 'dbname:q1;q2;q3;q4'");
     }
+    return fetchBatch(querystring.toString(), db, f, s);
+  }
 
-    /**
-     * 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)
+  public String[] fetchBatch(String ids, String db, String f, String s)
+  {
+    // max 50 ids can be added at one time
+    try
     {
-        // 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 && (p+3<query.length())) {
-                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);
+      //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;
     }
-    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;
-        }
+    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/io/FastaFile.java b/src/jalview/io/FastaFile.java
index 684f867..c69b8ce 100755
--- a/src/jalview/io/FastaFile.java
+++ b/src/jalview/io/FastaFile.java
@@ -1,29 +1,26 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 jalview.io;
 
-import jalview.datamodel.*;
-
 import java.io.*;
 
-import java.util.*;
-
+import jalview.datamodel.*;
 
 /**
  * DOCUMENT ME!
@@ -31,7 +28,8 @@ import java.util.*;
  * @author $author$
  * @version $Revision$
  */
-public class FastaFile extends AlignFile
+public class FastaFile
+    extends AlignFile
 {
   /**
    * Length of a sequence line
@@ -40,170 +38,180 @@ public class FastaFile extends AlignFile
 
   StringBuffer out;
 
-    /**
-     * Creates a new FastaFile object.
-     */
-    public FastaFile()
-    {
-    }
+  /**
+   * Creates a new FastaFile object.
+   */
+  public FastaFile()
+  {
+  }
 
-    /**
-     * Creates a new FastaFile object.
-     *
-     * @param inFile DOCUMENT ME!
-     * @param type DOCUMENT ME!
-     *
-     * @throws IOException DOCUMENT ME!
-     */
-    public FastaFile(String inFile, String type) throws IOException
-    {
-        super(inFile, type);
-    }
+  /**
+   * Creates a new FastaFile object.
+   *
+   * @param inFile DOCUMENT ME!
+   * @param type DOCUMENT ME!
+   *
+   * @throws IOException DOCUMENT ME!
+   */
+  public FastaFile(String inFile, String type)
+      throws IOException
+  {
+    super(inFile, type);
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @throws IOException DOCUMENT ME!
-     */
-    public void parse() throws IOException
-    {
-        StringBuffer sb = new StringBuffer();
-        boolean firstLine = true;
+  /**
+   * DOCUMENT ME!
+   *
+   * @throws IOException DOCUMENT ME!
+   */
+  public void parse()
+      throws IOException
+  {
+    StringBuffer sb = new StringBuffer();
+    boolean firstLine = true;
 
-        String line;
-        Sequence seq = null;
+    String line;
+    Sequence seq = null;
 
-        boolean annotation = false;
+    boolean annotation = false;
 
-        while ((line = nextLine()) != null)
+    while ( (line = nextLine()) != null)
+    {
+      line = line.trim();
+      if (line.length() > 0)
+      {
+        if (line.charAt(0) == '>')
         {
-            line = line.trim();
-            if (line.length() > 0)
+          if (line.startsWith(">#_"))
+          {
+            if (annotation)
             {
-              if (line.charAt(0)=='>')
-                {
-                  if (line.startsWith(">#_"))
-                  {
-                    if (annotation)
-                    {
-                      Annotation[] anots = new Annotation[sb.length()];
-                      String anotString = sb.toString();
-                      for (int i = 0; i < sb.length(); i++)
-                      {
-                        anots[i] = new Annotation(anotString.substring(i, i+1),
-                                                  null,
-                                                  ' ', 0);
-                      }
-                      AlignmentAnnotation aa = new AlignmentAnnotation(
-                          seq.getName().substring(2), seq.getDescription(),
-                          anots);
-
-                      annotations.addElement(aa);
-                    }
-                  }
-                  else
-                    annotation = false;
-
-                    if (!firstLine)
-                    {
-                       seq.setSequence(sb.toString());
-
-                       if (!annotation)
-                         seqs.addElement(seq);
-                    }
-
-                    seq = parseId(line.substring(1));
-                    firstLine = false;
-
-                    sb = new StringBuffer();
-
-                    if (line.startsWith(">#_"))
-                      annotation = true;
-                }
-                else
-                {
-                    sb.append(line);
-                }
+              Annotation[] anots = new Annotation[sb.length()];
+              String anotString = sb.toString();
+              for (int i = 0; i < sb.length(); i++)
+              {
+                anots[i] = new Annotation(anotString.substring(i, i + 1),
+                                          null,
+                                          ' ', 0);
+              }
+              AlignmentAnnotation aa = new AlignmentAnnotation(
+                  seq.getName().substring(2), seq.getDescription(),
+                  anots);
+
+              annotations.addElement(aa);
             }
-        }
+          }
+          else
+          {
+            annotation = false;
+          }
 
-        if (annotation)
-        {
-          Annotation[] anots = new Annotation[sb.length()];
-          String anotString = sb.toString();
-          for (int i = 0; i < sb.length(); i++)
+          if (!firstLine)
           {
-            anots[i] = new Annotation(anotString.substring(i, i + 1),
-                                      null,
-                                      ' ', 0);
+            seq.setSequence(sb.toString());
+
+            if (!annotation)
+            {
+              seqs.addElement(seq);
+            }
           }
-          AlignmentAnnotation aa = new AlignmentAnnotation(
-              seq.getName().substring(2), seq.getDescription(),
-              anots);
 
-          annotations.addElement(aa);
-        }
+          seq = parseId(line.substring(1));
+          firstLine = false;
+
+          sb = new StringBuffer();
 
-        else if (!firstLine)
+          if (line.startsWith(">#_"))
+          {
+            annotation = true;
+          }
+        }
+        else
         {
-            seq.setSequence(sb.toString());
-            seqs.addElement(seq);
+          sb.append(line);
         }
+      }
     }
 
-    /**
-     * 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)
+    if (annotation)
     {
-        out = new StringBuffer();
-        int i = 0;
+      Annotation[] anots = new Annotation[sb.length()];
+      String anotString = sb.toString();
+      for (int i = 0; i < sb.length(); i++)
+      {
+        anots[i] = new Annotation(anotString.substring(i, i + 1),
+                                  null,
+                                  ' ', 0);
+      }
+      AlignmentAnnotation aa = new AlignmentAnnotation(
+          seq.getName().substring(2), seq.getDescription(),
+          anots);
+
+      annotations.addElement(aa);
+    }
 
-        while ((i < s.length) && (s[i] != null))
-        {
-            out.append(">" + printId(s[i]));
-            if(s[i].getDescription()!=null)
-              out.append(" "+s[i].getDescription());
+    else if (!firstLine)
+    {
+      seq.setSequence(sb.toString());
+      seqs.addElement(seq);
+    }
+  }
 
-            out.append("\n");
+  /**
+   * 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)
+  {
+    out = new StringBuffer();
+    int i = 0;
 
-            int nochunks = (s[i].getLength() / len) + 1;
+    while ( (i < s.length) && (s[i] != null))
+    {
+      out.append(">" + printId(s[i]));
+      if (s[i].getDescription() != null)
+      {
+        out.append(" " + s[i].getDescription());
+      }
 
-            for (int j = 0; j < nochunks; j++)
-            {
-                int start = j * len;
-                int end = start + len;
-
-                if (end < s[i].getLength())
-                {
-                    out.append(s[i].getSequenceAsString(start, end) + "\n");
-                }
-                else if (start < s[i].getLength())
-                {
-                    out.append(s[i].getSequenceAsString(start, s[i].getLength()) + "\n");
-                }
-            }
+      out.append("\n");
+
+      int nochunks = (s[i].getLength() / len) + 1;
 
-            i++;
+      for (int j = 0; j < nochunks; j++)
+      {
+        int start = j * len;
+        int end = start + len;
+
+        if (end < s[i].getLength())
+        {
+          out.append(s[i].getSequenceAsString(start, end) + "\n");
         }
+        else if (start < s[i].getLength())
+        {
+          out.append(s[i].getSequenceAsString(start, s[i].getLength()) + "\n");
+        }
+      }
 
-        return out.toString();
+      i++;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String print()
-    {
-        return print(getSeqsAsArray());
-    }
+    return out.toString();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public String print()
+  {
+    return print(getSeqsAsArray());
+  }
 }
diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index 2c0b6d7..6b9ee67 100755
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -1,29 +1,28 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 jalview.io;
 
-import jalview.datamodel.*;
-
 import java.io.*;
 import java.util.*;
-import jalview.schemes.UserColourScheme;
 
+import jalview.datamodel.*;
+import jalview.schemes.*;
 
 /**
  * DOCUMENT ME!
@@ -31,506 +30,561 @@ import jalview.schemes.UserColourScheme;
  * @author $author$
  * @version $Revision$
  */
-public class FeaturesFile extends AlignFile
+public class FeaturesFile
+    extends AlignFile
 {
-    /**
-     * Creates a new FeaturesFile object.
-     */
-    public FeaturesFile()
-    {
-    }
+  /**
+   * Creates a new FeaturesFile object.
+   */
+  public FeaturesFile()
+  {
+  }
 
+  /**
+   * Creates a new FeaturesFile object.
+   *
+   * @param inFile DOCUMENT ME!
+   * @param type DOCUMENT ME!
+   *
+   * @throws IOException DOCUMENT ME!
+   */
+  public FeaturesFile(String inFile, String type)
+      throws IOException
+  {
+    super(inFile, type);
+  }
 
-    /**
-     * Creates a new FeaturesFile object.
-     *
-     * @param inFile DOCUMENT ME!
-     * @param type DOCUMENT ME!
-     *
-     * @throws IOException DOCUMENT ME!
-     */
-    public FeaturesFile(String inFile, String type)
-       throws IOException
-    {
-        super(inFile, type);
-    }
+  /**
+   * The Application can render HTML, but the applet will
+   * remove HTML tags and replace links with %LINK%
+   * Both need to read links in HTML however
+   *
+   * @throws IOException DOCUMENT ME!
+   */
+  public boolean parse(AlignmentI align,
+                       Hashtable colours,
+                       boolean removeHTML)
+  {
+    return parse(align, colours, null, removeHTML);
+  }
 
-    /**
-     * The Application can render HTML, but the applet will
-     * remove HTML tags and replace links with %LINK%
-     * Both need to read links in HTML however
-     *
-     * @throws IOException DOCUMENT ME!
-     */
-    public boolean parse(AlignmentI align,
-                         Hashtable colours,
-                         boolean removeHTML)
+  /**
+   * The Application can render HTML, but the applet will
+   * remove HTML tags and replace links with %LINK%
+   * Both need to read links in HTML however
+   *
+   * @throws IOException DOCUMENT ME!
+   */
+  public boolean parse(AlignmentI align,
+                       Hashtable colours,
+                       Hashtable featureLink,
+                       boolean removeHTML)
+  {
+    String line = null;
+    try
     {
-      return parse(align, colours, null, removeHTML);
-    }
-    /**
-     * The Application can render HTML, but the applet will
-     * remove HTML tags and replace links with %LINK%
-     * Both need to read links in HTML however
-     *
-     * @throws IOException DOCUMENT ME!
-     */
-    public boolean parse(AlignmentI align,
-                         Hashtable colours,
-                         Hashtable featureLink,
-                         boolean removeHTML)
-    {
-      String line = null;
-      try
-      {
-        SequenceI seq = null;
-        String type, desc, token=null;
+      SequenceI seq = null;
+      String type, desc, token = null;
 
-        int index, start, end;
-        float score;
-        StringTokenizer st;
-        SequenceFeature sf;
-        String featureGroup = null, groupLink = null;
-        Hashtable typeLink = new Hashtable();
+      int index, start, end;
+      float score;
+      StringTokenizer st;
+      SequenceFeature sf;
+      String featureGroup = null, groupLink = null;
+      Hashtable typeLink = new Hashtable();
 
-        boolean GFFFile = true;
+      boolean GFFFile = true;
 
-        while ( (line = nextLine()) != null)
+      while ( (line = nextLine()) != null)
+      {
+        if (line.startsWith("#"))
         {
-          if(line.startsWith("#"))
-            continue;
+          continue;
+        }
 
-          st = new StringTokenizer(line, "\t");
-          if (st.countTokens()>1 && st.countTokens() < 4 )
+        st = new StringTokenizer(line, "\t");
+        if (st.countTokens() > 1 && st.countTokens() < 4)
+        {
+          GFFFile = false;
+          type = st.nextToken();
+          if (type.equalsIgnoreCase("startgroup"))
           {
-            GFFFile = false;
-            type = st.nextToken();
-            if (type.equalsIgnoreCase("startgroup"))
+            featureGroup = st.nextToken();
+            if (st.hasMoreElements())
             {
-              featureGroup = st.nextToken();
-              if (st.hasMoreElements())
-              {
-                groupLink = st.nextToken();
-                featureLink.put(featureGroup, groupLink);
-              }
-            }
-            else if (type.equalsIgnoreCase("endgroup"))
-            {
-              //We should check whether this is the current group,
-              //but at present theres no way of showing more than 1 group
-              st.nextToken();
-              featureGroup = null;
-              groupLink = null;
+              groupLink = st.nextToken();
+              featureLink.put(featureGroup, groupLink);
             }
-            else
+          }
+          else if (type.equalsIgnoreCase("endgroup"))
+          {
+            //We should check whether this is the current group,
+            //but at present theres no way of showing more than 1 group
+            st.nextToken();
+            featureGroup = null;
+            groupLink = null;
+          }
+          else
+          {
+            UserColourScheme ucs = new UserColourScheme(st.nextToken());
+            colours.put(type, ucs.findColour('A'));
+            if (st.hasMoreElements())
             {
-              UserColourScheme ucs = new UserColourScheme(st.nextToken());
-              colours.put(type, ucs.findColour('A'));
-              if (st.hasMoreElements())
+              String link = st.nextToken();
+              typeLink.put(type, link);
+              if (featureLink == null)
               {
-                String link = st.nextToken();
-                typeLink.put(type, link);
-                if(featureLink==null)
-                  featureLink = new Hashtable();
-                featureLink.put(type, link);
+                featureLink = new Hashtable();
               }
-
+              featureLink.put(type, link);
             }
-            continue;
+
           }
+          continue;
+        }
 
-          while (st.hasMoreElements())
-          {
+        while (st.hasMoreElements())
+        {
 
-            if(GFFFile)
+          if (GFFFile)
+          {
+            // Still possible this is an old Jalview file,
+            // which does not have type colours at the beginning
+            token = st.nextToken();
+            seq = align.findName(token);
+            if (seq != null)
             {
-              // Still possible this is an old Jalview file,
-              // which does not have type colours at the beginning
-              token = st.nextToken();
-              seq = align.findName(token);
-              if(seq != null)
+              desc = st.nextToken();
+              type = st.nextToken();
+              start = Integer.parseInt(st.nextToken());
+              end = Integer.parseInt(st.nextToken());
+              try
               {
-                desc = st.nextToken();
-                type = st.nextToken();
-                start = Integer.parseInt(st.nextToken());
-                end = Integer.parseInt(st.nextToken());
-                try
-                {
-                  score =  new Float(st.nextToken()).floatValue();
-                }
-                catch (NumberFormatException ex)
-                {
-                  score = 0;
-                }
+                score = new Float(st.nextToken()).floatValue();
+              }
+              catch (NumberFormatException ex)
+              {
+                score = 0;
+              }
 
-                sf = new SequenceFeature(type, desc, start, end, score, null);
+              sf = new SequenceFeature(type, desc, start, end, score, null);
 
-                try
-                {
-                  sf.setValue("STRAND", st.nextToken());
-                  sf.setValue("FRAME", st.nextToken());
-                }
-                catch (Exception ex)
-                {}
+              try
+              {
+                sf.setValue("STRAND", st.nextToken());
+                sf.setValue("FRAME", st.nextToken());
+              }
+              catch (Exception ex)
+              {}
 
-                if(st.hasMoreTokens())
+              if (st.hasMoreTokens())
+              {
+                StringBuffer attributes = new StringBuffer();
+                while (st.hasMoreTokens())
                 {
-                  StringBuffer attributes = new StringBuffer();
-                  while (st.hasMoreTokens())
-                  {
-                    attributes.append("\t"+st.nextElement());
-                  }
-                  sf.setValue("ATTRIBUTES", attributes.toString());
+                  attributes.append("\t" + st.nextElement());
                 }
-
-                seq.addSequenceFeature(sf);
-
-                break;
+                sf.setValue("ATTRIBUTES", attributes.toString());
               }
-            }
 
-            if(GFFFile && seq==null)
-            {
-              desc = token;
+              seq.addSequenceFeature(sf);
+
+              break;
             }
-            else
-              desc = st.nextToken();
+          }
 
+          if (GFFFile && seq == null)
+          {
+            desc = token;
+          }
+          else
+          {
+            desc = st.nextToken();
+          }
 
-            token = st.nextToken();
-            if (!token.equals("ID_NOT_SPECIFIED"))
+          token = st.nextToken();
+          if (!token.equals("ID_NOT_SPECIFIED"))
+          {
+            seq = align.findName(token);
+            st.nextToken();
+          }
+          else
+          {
+            try
             {
-              seq = align.findName(token);
-              st.nextToken();
+              index = Integer.parseInt(st.nextToken());
+              seq = align.getSequenceAt(index);
             }
-            else
+            catch (NumberFormatException ex)
             {
-              try{
-                index = Integer.parseInt(st.nextToken());
-                seq = align.getSequenceAt(index);
-              }
-              catch(NumberFormatException ex)
-              {
-                seq = null;
-              }
+              seq = null;
             }
+          }
 
-            if(seq==null)
-            {
-              System.out.println("Sequence not found: "+line);
-              break;
-            }
+          if (seq == null)
+          {
+            System.out.println("Sequence not found: " + line);
+            break;
+          }
 
-            start = Integer.parseInt(st.nextToken());
-            end = Integer.parseInt(st.nextToken());
+          start = Integer.parseInt(st.nextToken());
+          end = Integer.parseInt(st.nextToken());
 
-            type = st.nextToken();
+          type = st.nextToken();
 
-            if (!colours.containsKey(type))
-            {
-              // Probably the old style groups file
-              UserColourScheme ucs = new UserColourScheme(type);
-              colours.put(type, ucs.findColour('A'));
-            }
+          if (!colours.containsKey(type))
+          {
+            // Probably the old style groups file
+            UserColourScheme ucs = new UserColourScheme(type);
+            colours.put(type, ucs.findColour('A'));
+          }
 
-            sf = new SequenceFeature(type, desc, "", start, end, featureGroup);
+          sf = new SequenceFeature(type, desc, "", start, end, featureGroup);
 
-            seq.addSequenceFeature(sf);
+          seq.addSequenceFeature(sf);
 
-            if(groupLink!=null && removeHTML)
-            {
-              sf.addLink(groupLink);
-              sf.description += "%LINK%";
-            }
-            if(typeLink.containsKey(type) && removeHTML)
-            {
-              sf.addLink(typeLink.get(type).toString());
-              sf.description += "%LINK%";
-            }
+          if (groupLink != null && removeHTML)
+          {
+            sf.addLink(groupLink);
+            sf.description += "%LINK%";
+          }
+          if (typeLink.containsKey(type) && removeHTML)
+          {
+            sf.addLink(typeLink.get(type).toString());
+            sf.description += "%LINK%";
+          }
 
-            parseDescriptionHTML(sf, removeHTML);
+          parseDescriptionHTML(sf, removeHTML);
 
-            //If we got here, its not a GFFFile
-            GFFFile = false;
-          }
+          //If we got here, its not a GFFFile
+          GFFFile = false;
         }
       }
-      catch (Exception ex)
-      {
-        System.out.println(line);
-        System.out.println("Error parsing feature file: " + ex +"\n"+line);
-        return false;
-      }
+    }
+    catch (Exception ex)
+    {
+      System.out.println(line);
+      System.out.println("Error parsing feature file: " + ex + "\n" + line);
+      return false;
+    }
+
+    return true;
+  }
+
+  public void parseDescriptionHTML(SequenceFeature sf, boolean removeHTML)
+  {
+    if (sf.getDescription() == null)
+    {
+      return;
+    }
 
-      return true;
+    if (removeHTML && sf.getDescription().toUpperCase().indexOf("<HTML>") == -1)
+    {
+      removeHTML = false;
     }
 
-    public void parseDescriptionHTML(SequenceFeature sf, boolean removeHTML)
+    StringBuffer sb = new StringBuffer();
+    StringTokenizer st = new StringTokenizer(sf.getDescription(), "<");
+    String token, link;
+    int startTag;
+    String tag = null;
+    while (st.hasMoreElements())
     {
-      if(sf.getDescription()==null)
-        return;
-
-      if(removeHTML && sf.getDescription().toUpperCase().indexOf("<HTML>")==-1)
-        removeHTML = false;
-
-      StringBuffer sb = new StringBuffer();
-      StringTokenizer st = new StringTokenizer(sf.getDescription(), "<");
-      String token,  link;
-      int startTag;
-      String tag=null;
-      while(st.hasMoreElements())
+      token = st.nextToken("&>");
+      if (token.equalsIgnoreCase("html") || token.startsWith("/"))
       {
-        token = st.nextToken("&>");
-        if(token.equalsIgnoreCase("html") || token.startsWith("/"))
-        {
-          continue;
-        }
+        continue;
+      }
 
-        tag = null;
-        startTag = token.indexOf("<");
+      tag = null;
+      startTag = token.indexOf("<");
 
-        if (startTag > -1)
-        {
-          tag = token.substring(startTag+1);
-          token = token.substring(0, startTag);
-        }
+      if (startTag > -1)
+      {
+        tag = token.substring(startTag + 1);
+        token = token.substring(0, startTag);
+      }
 
-        if (tag != null && tag.toUpperCase().startsWith("A HREF="))
-        {
-          if(token.length()>0)
-            sb.append(token);
-          link = tag.substring(tag.indexOf("\"") + 1, tag.length() - 1);
-          String label = st.nextToken("<>");
-          sf.addLink(label + "|" + link);
-          sb.append(label + "%LINK%");
-        }
-        else if (tag != null && tag.equalsIgnoreCase("br"))
-          sb.append("\n");
-        else if (token.startsWith("lt;"))
-          sb.append("<" + token.substring(3));
-        else if (token.startsWith("gt;"))
-          sb.append(">" + token.substring(3));
-        else if (token.startsWith("amp;"))
-          sb.append("&" + token.substring(4));
-        else
+      if (tag != null && tag.toUpperCase().startsWith("A HREF="))
+      {
+        if (token.length() > 0)
         {
           sb.append(token);
         }
+        link = tag.substring(tag.indexOf("\"") + 1, tag.length() - 1);
+        String label = st.nextToken("<>");
+        sf.addLink(label + "|" + link);
+        sb.append(label + "%LINK%");
+      }
+      else if (tag != null && tag.equalsIgnoreCase("br"))
+      {
+        sb.append("\n");
+      }
+      else if (token.startsWith("lt;"))
+      {
+        sb.append("<" + token.substring(3));
+      }
+      else if (token.startsWith("gt;"))
+      {
+        sb.append(">" + token.substring(3));
+      }
+      else if (token.startsWith("amp;"))
+      {
+        sb.append("&" + token.substring(4));
       }
+      else
+      {
+        sb.append(token);
+      }
+    }
 
-      if(removeHTML)
-        sf.description = sb.toString();
+    if (removeHTML)
+    {
+      sf.description = sb.toString();
+    }
 
   }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param s DOCUMENT ME!
-     * @param len DOCUMENT ME!
-     * @param gaps DOCUMENT ME!
-     * @param displayId DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String printJalviewFormat(SequenceI [] seqs,
-                                     Hashtable visible)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param s DOCUMENT ME!
+   * @param len DOCUMENT ME!
+   * @param gaps DOCUMENT ME!
+   * @param displayId DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public String printJalviewFormat(SequenceI[] seqs,
+                                   Hashtable visible)
+  {
+    StringBuffer out = new StringBuffer();
+    SequenceFeature[] next;
+
+    if (visible == null || visible.size() < 1)
     {
-        StringBuffer out = new StringBuffer();
-        SequenceFeature [] next;
-
-        if(visible==null || visible.size()<1)
-          return "No Features Visible";
+      return "No Features Visible";
+    }
 
-        Enumeration en = visible.keys();
-        String type;
-        int color;
-        while( en.hasMoreElements() )
-        {
-          type = en.nextElement().toString();
-          color = Integer.parseInt( visible.get(type).toString() );
-          out.append(type + "\t"
-                     + jalview.util.Format.getHexString(
-                         new java.awt.Color(color)  )
-                     +"\n");
-        }
+    Enumeration en = visible.keys();
+    String type;
+    int color;
+    while (en.hasMoreElements())
+    {
+      type = en.nextElement().toString();
+      color = Integer.parseInt(visible.get(type).toString());
+      out.append(type + "\t"
+                 + jalview.util.Format.getHexString(
+                     new java.awt.Color(color))
+                 + "\n");
+    }
 
-        //Work out which groups are both present and visible
-        Vector groups = new Vector();
-        int groupIndex = 0;
+    //Work out which groups are both present and visible
+    Vector groups = new Vector();
+    int groupIndex = 0;
 
-        for(int i=0; i<seqs.length; i++)
+    for (int i = 0; i < seqs.length; i++)
+    {
+      next = seqs[i].getSequenceFeatures();
+      if (next != null)
+      {
+        for (int j = 0; j < next.length; j++)
         {
-          next = seqs[i].getSequenceFeatures();
-          if(next!=null)
+          if (!visible.containsKey(next[j].type))
           {
-            for(int j=0; j<next.length; j++)
-            {
-              if (!visible.containsKey(next[j].type))
-                continue;
+            continue;
+          }
 
-              if (    next[j].featureGroup != null
-                  && !groups.contains(next[j].featureGroup))
-                groups.addElement(next[j].featureGroup);
-            }
+          if (next[j].featureGroup != null
+              && !groups.contains(next[j].featureGroup))
+          {
+            groups.addElement(next[j].featureGroup);
           }
         }
+      }
+    }
 
-        String group = null;
+    String group = null;
 
-        do
-        {
+    do
+    {
 
+      if (groups.size() > 0 && groupIndex < groups.size())
+      {
+        group = groups.elementAt(groupIndex).toString();
+        out.append("\nSTARTGROUP\t" + group + "\n");
+      }
+      else
+      {
+        group = null;
+      }
 
-          if (groups.size() > 0 && groupIndex < groups.size())
+      for (int i = 0; i < seqs.length; i++)
+      {
+        next = seqs[i].getSequenceFeatures();
+        if (next != null)
+        {
+          for (int j = 0; j < next.length; j++)
           {
-            group = groups.elementAt(groupIndex).toString();
-            out.append("\nSTARTGROUP\t" + group + "\n");
-          }
-          else
-            group = null;
+            if (!visible.containsKey(next[j].type))
+            {
+              continue;
+            }
 
-          for (int i = 0; i < seqs.length; i++)
-          {
-            next = seqs[i].getSequenceFeatures();
-            if (next != null)
+            if (group != null
+                && (next[j].featureGroup == null
+                    || !next[j].featureGroup.equals(group))
+                )
             {
-              for (int j = 0; j < next.length; j++)
-              {
-                if (!visible.containsKey(next[j].type))
-                  continue;
+              continue;
+            }
 
-                if (group != null
-                    && (next[j].featureGroup==null
-                        || !next[j].featureGroup.equals(group))
-                  )
-                  continue;
+            if (group == null && next[j].featureGroup != null)
+            {
+              continue;
+            }
 
-                if(group==null && next[j].featureGroup!=null)
-                  continue;
+            if (next[j].description == null || next[j].description.equals(""))
+            {
+              out.append(next[j].type + "\t");
+            }
+            else
+            {
+              if (next[j].links != null
+                  && next[j].getDescription().indexOf("<html>") == -1)
+              {
+                out.append("<html>");
+              }
 
-                if(next[j].description==null || next[j].description.equals(""))
-                  out.append(next[j].type+"\t");
-                else
+              out.append(next[j].description + " ");
+              if (next[j].links != null)
+              {
+                for (int l = 0; l < next[j].links.size(); l++)
                 {
-                  if(next[j].links!=null
-                     && next[j].getDescription().indexOf("<html>")==-1)
-                    out.append("<html>");
-
-                  out.append(next[j].description+" ");
-                  if(next[j].links!=null)
-                    {
-                      for(int l=0; l<next[j].links.size(); l++)
-                      {
-                        String label = next[j].links.elementAt(l).toString();
-                        String href = label.substring(label.indexOf("|")+1);
-                        label = label.substring(0, label.indexOf("|"));
-
-                        if(next[j].description.indexOf(href)==-1)
-                        {
-                          out.append("<a href=\""
-                                     + href
-                                     + "\">"
-                                     + label
-                                     + "</a>");
-                        }
-                      }
-
-                      if (next[j].getDescription().indexOf("</html>") == -1)
-                        out.append("</html>");
-                    }
-
-
-                   out.append("\t");
-                }
+                  String label = next[j].links.elementAt(l).toString();
+                  String href = label.substring(label.indexOf("|") + 1);
+                  label = label.substring(0, label.indexOf("|"));
 
+                  if (next[j].description.indexOf(href) == -1)
+                  {
+                    out.append("<a href=\""
+                               + href
+                               + "\">"
+                               + label
+                               + "</a>");
+                  }
+                }
 
-                out.append(  seqs[i].getName() + "\t-1\t"
-                           + next[j].begin + "\t"
-                           + next[j].end + "\t"
-                           + next[j].type + "\n"
-                    );
+                if (next[j].getDescription().indexOf("</html>") == -1)
+                {
+                  out.append("</html>");
+                }
               }
+
+              out.append("\t");
             }
-          }
 
-          if(group!=null)
-          {
-            out.append("ENDGROUP\t"+group+"\n");
-            groupIndex++;
+            out.append(seqs[i].getName() + "\t-1\t"
+                       + next[j].begin + "\t"
+                       + next[j].end + "\t"
+                       + next[j].type + "\n"
+                );
           }
-          else
-            break;
-
         }
-        while(groupIndex < groups.size()+1);
+      }
 
+      if (group != null)
+      {
+        out.append("ENDGROUP\t" + group + "\n");
+        groupIndex++;
+      }
+      else
+      {
+        break;
+      }
 
-      return out.toString();
     }
+    while (groupIndex < groups.size() + 1);
 
-    public String printGFFFormat(SequenceI [] seqs, Hashtable visible)
-    {
-      StringBuffer out = new StringBuffer();
-      SequenceFeature [] next;
-      String source;
+    return out.toString();
+  }
+
+  public String printGFFFormat(SequenceI[] seqs, Hashtable visible)
+  {
+    StringBuffer out = new StringBuffer();
+    SequenceFeature[] next;
+    String source;
 
-      for(int i=0; i<seqs.length; i++)
+    for (int i = 0; i < seqs.length; i++)
+    {
+      if (seqs[i].getSequenceFeatures() != null)
       {
-        if(seqs[i].getSequenceFeatures()!=null)
+        next = seqs[i].getSequenceFeatures();
+        for (int j = 0; j < next.length; j++)
         {
-          next = seqs[i].getSequenceFeatures();
-          for(int j=0; j<next.length; j++)
+          if (!visible.containsKey(next[j].type))
           {
-            if(!visible.containsKey(next[j].type))
-              continue;
+            continue;
+          }
 
-            source = next[j].featureGroup;
-            if(source==null)
-              source = next[j].getDescription();
+          source = next[j].featureGroup;
+          if (source == null)
+          {
+            source = next[j].getDescription();
+          }
 
-            out.append(seqs[i].getName() + "\t"
-                       + source + "\t"
-                       + next[j].type  + "\t"
-                       + next[j].begin + "\t"
-                       + next[j].end   + "\t"
-                       + next[j].score + "\t"
-                      );
+          out.append(seqs[i].getName() + "\t"
+                     + source + "\t"
+                     + next[j].type + "\t"
+                     + next[j].begin + "\t"
+                     + next[j].end + "\t"
+                     + next[j].score + "\t"
+              );
 
-            if(next[j].getValue("STRAND")!=null)
-              out.append(next[j].getValue("STRAND")+"\t");
-            else
-              out.append(".\t");
+          if (next[j].getValue("STRAND") != null)
+          {
+            out.append(next[j].getValue("STRAND") + "\t");
+          }
+          else
+          {
+            out.append(".\t");
+          }
 
-            if(next[j].getValue("FRAME")!=null)
-              out.append(next[j].getValue("FRAME"));
-            else
-              out.append(".");
+          if (next[j].getValue("FRAME") != null)
+          {
+            out.append(next[j].getValue("FRAME"));
+          }
+          else
+          {
+            out.append(".");
+          }
 
-            if(next[j].getValue("ATTRIBUTES")!=null)
-              out.append(next[j].getValue("ATTRIBUTES"));
+          if (next[j].getValue("ATTRIBUTES") != null)
+          {
+            out.append(next[j].getValue("ATTRIBUTES"));
+          }
 
-            out.append("\n");
+          out.append("\n");
 
-          }
         }
       }
-
-      return out.toString();
     }
 
-    public void parse()
-    {
-      //IGNORED
-    }
+    return out.toString();
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String print()
-    {
-        return "USE printGFFFormat() or printJalviewFormat()";
-    }
+  public void parse()
+  {
+    //IGNORED
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public String print()
+  {
+    return "USE printGFFFormat() or printJalviewFormat()";
+  }
 }
diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 34e5886..86c1cf4 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -1,35 +1,33 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 jalview.io;
 
-import jalview.gui.AlignFrame;
-import jalview.gui.Jalview2XML;
-import javax.swing.JOptionPane;
+import java.util.*;
+
+import javax.swing.*;
 
-import jalview.gui.*;
 import jalview.datamodel.*;
-import java.util.Vector;
-import java.util.StringTokenizer;
-import javax.swing.SwingUtilities;
+import jalview.gui.*;
 
-public class FileLoader implements Runnable
+public class FileLoader
+    implements Runnable
 {
   String file;
   String protocol;
@@ -37,14 +35,13 @@ public class FileLoader implements Runnable
   AlignViewport viewport;
   AlignFrame alignFrame;
 
-  public void LoadFile(AlignViewport viewport, String file, String protocol, String format)
+  public void LoadFile(AlignViewport viewport, String file, String protocol,
+                       String format)
   {
     this.viewport = viewport;
     LoadFile(file, protocol, format);
   }
 
-
-
   public void LoadFile(String file, String protocol, String format)
   {
     this.file = file;
@@ -62,9 +59,8 @@ public class FileLoader implements Runnable
     });
   }
 
-
   public AlignFrame LoadFileWaitTillLoaded(String file, String protocol,
-                                                  String format)
+                                           String format)
   {
     this.file = file;
     this.protocol = protocol;
@@ -86,8 +82,6 @@ public class FileLoader implements Runnable
     return alignFrame;
   }
 
-
-
   public void updateRecentlyOpened()
   {
     Vector recent = new Vector();
@@ -123,122 +117,130 @@ public class FileLoader implements Runnable
 
     jalview.bin.Cache.setProperty(type, newHistory.toString());
 
-    if(type.equals(FormatAdapter.FILE))
+    if (type.equals(FormatAdapter.FILE))
+    {
       jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format);
+    }
   }
 
-    public void run()
+  public void run()
+  {
+    try
     {
-      try{
-        if (Desktop.instance != null)
-          Desktop.instance.startLoading(file);
+      if (Desktop.instance != null)
+      {
+        Desktop.instance.startLoading(file);
+      }
 
-        Alignment al = null;
+      Alignment al = null;
 
-        if (format.equalsIgnoreCase("Jalview"))
+      if (format.equalsIgnoreCase("Jalview"))
+      {
+        alignFrame = new Jalview2XML().LoadJalviewAlign(file);
+      }
+      else
+      {
+        String error = AppletFormatAdapter.SUPPORTED_FORMATS;
+
+        if (FormatAdapter.isValidFormat(format))
         {
-          alignFrame = new Jalview2XML().LoadJalviewAlign(file);
+          try
+          {
+            al = new FormatAdapter().readFile(file, protocol, format);
+          }
+          catch (java.io.IOException ex)
+          {
+            error = ex.getMessage();
+          }
         }
-        else
-        {
-          String error = AppletFormatAdapter.SUPPORTED_FORMATS;
 
-          if (FormatAdapter.isValidFormat(format))
+        if ( (al != null) && (al.getHeight() > 0))
+        {
+          if (viewport != null)
           {
-            try
+            for (int i = 0; i < al.getHeight(); i++)
             {
-              al = new FormatAdapter().readFile(file, protocol, format);
+              viewport.getAlignment().addSequence(al.getSequenceAt(i));
             }
-            catch (java.io.IOException ex)
-            {
-              error = ex.getMessage();
-            }
-          }
+            viewport.firePropertyChange("alignment", null,
+                                        viewport.getAlignment().getSequences());
 
-          if ( (al != null) && (al.getHeight() > 0))
+          }
+          else
           {
-            if (viewport != null)
-            {
-              for (int i = 0; i < al.getHeight(); i++)
-              {
-                viewport.getAlignment().addSequence(al.getSequenceAt(i));
-              }
-              viewport.firePropertyChange("alignment", null,
-                                          viewport.getAlignment().getSequences());
+            alignFrame = new AlignFrame(al,
+                                        AlignFrame.DEFAULT_WIDTH,
+                                        AlignFrame.DEFAULT_HEIGHT);
+
+            alignFrame.statusBar.setText("Successfully loaded file " + file);
+            alignFrame.setFileName(file, format);
+
+            Desktop.addInternalFrame(alignFrame, file,
+                                     AlignFrame.DEFAULT_WIDTH,
+                                     AlignFrame.DEFAULT_HEIGHT);
 
+            try
+            {
+              alignFrame.setMaximum(jalview.bin.Cache.getDefault(
+                  "SHOW_FULLSCREEN", false));
             }
-            else
+            catch (java.beans.PropertyVetoException ex)
             {
-              alignFrame = new AlignFrame(al,
-                                           AlignFrame.DEFAULT_WIDTH,
-                                           AlignFrame.DEFAULT_HEIGHT);
-
-              alignFrame.statusBar.setText("Successfully loaded file " + file);
-              alignFrame.setFileName(file, format);
-
-
-              Desktop.addInternalFrame(alignFrame, file,
-                                       AlignFrame.DEFAULT_WIDTH,
-                                       AlignFrame.DEFAULT_HEIGHT);
-
-              try
-              {
-               alignFrame.setMaximum(jalview.bin.Cache.getDefault(
-                   "SHOW_FULLSCREEN", false));
-              }
-              catch (java.beans.PropertyVetoException ex)
-              {
-              }
             }
           }
-          else
+        }
+        else
+        {
+          if (Desktop.instance != null)
           {
-            if (Desktop.instance != null)
-              Desktop.instance.stopLoading();
+            Desktop.instance.stopLoading();
+          }
 
-            final String errorMessage = "Couldn't load file " + file + "\n" +
-                error;
+          final String errorMessage = "Couldn't load file " + file + "\n" +
+              error;
 
-            javax.swing.SwingUtilities.invokeLater(new Runnable()
+          javax.swing.SwingUtilities.invokeLater(new Runnable()
+          {
+            public void run()
             {
-              public void run()
-              {
-                JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                    errorMessage,
-                    "Error loading file",
-                    JOptionPane.WARNING_MESSAGE);
-              }
-            });
-          }
+              JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                  errorMessage,
+                  "Error loading file",
+                  JOptionPane.WARNING_MESSAGE);
+            }
+          });
         }
+      }
 
-         updateRecentlyOpened();
+      updateRecentlyOpened();
 
-      }
-      catch (OutOfMemoryError er)
-      {
+    }
+    catch (OutOfMemoryError er)
+    {
 
-        er.printStackTrace();
-        alignFrame = null;
+      er.printStackTrace();
+      alignFrame = null;
 
-        javax.swing.SwingUtilities.invokeLater(new Runnable()
+      javax.swing.SwingUtilities.invokeLater(new Runnable()
+      {
+        public void run()
         {
-          public void run()
-          {
-            javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                "Out of memory loading file "+file+"!!"
-                +
-                "\nSee help files for increasing Java Virtual Machine memory."
-                , "Out of memory",
-                javax.swing.JOptionPane.WARNING_MESSAGE);
-          }
-        });
-      }
-
-     System.gc();
-     if (Desktop.instance != null)
-        Desktop.instance.stopLoading();
+          javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
+              "Out of memory loading file " + file + "!!"
+              +
+              "\nSee help files for increasing Java Virtual Machine memory."
+              , "Out of memory",
+              javax.swing.JOptionPane.WARNING_MESSAGE);
+        }
+      });
+    }
 
+    System.gc();
+    if (Desktop.instance != null)
+    {
+      Desktop.instance.stopLoading();
     }
 
+  }
+
 }
diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index 46f223a..982a9ee 100755
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -46,7 +46,7 @@ public class FileParse
       URL url = new URL(fileStr);
       dataIn = new BufferedReader(new InputStreamReader(url.openStream()));
     }
-   else if (type.equals(AppletFormatAdapter.PASTE))
+    else if (type.equals(AppletFormatAdapter.PASTE))
     {
       dataIn = new BufferedReader(new StringReader(fileStr));
     }
diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 15d4dc3..3cd9345 100755
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -1,126 +1,125 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 jalview.io;
 
 import jalview.datamodel.*;
 
-
 /**
  * DOCUMENT ME!
  *
  * @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)
+  {
+    if (omitHiddenColumns != null)
     {
-      if(omitHiddenColumns!=null)
+      SequenceI[] tmp = new SequenceI[seqs.length];
+      for (int i = 0; i < seqs.length; i++)
       {
-        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].setDescription(seqs[i].getDescription());
-        }
-        seqs = tmp;
+        tmp[i] = new Sequence(
+            seqs[i].getName(), omitHiddenColumns[i],
+            seqs[i].getStart(), seqs[i].getEnd());
+        tmp[i].setDescription(seqs[i].getDescription());
       }
-
-      return formatSequences(format, seqs);
+      seqs = tmp;
     }
 
+    return formatSequences(format, seqs);
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param format DOCUMENT ME!
-     * @param seqs DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String formatSequences(String format,
-                                  SequenceI [] seqs)
-    {
+  /**
+   * DOCUMENT ME!
+   *
+   * @param format DOCUMENT ME!
+   * @param seqs DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public String formatSequences(String format,
+                                SequenceI[] seqs)
+  {
 
-        try
-        {
-            AlignFile afile = null;
-
-            if (format.equalsIgnoreCase("FASTA"))
-            {
-                afile = new FastaFile();
-                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));
-            }
-            else if (format.equalsIgnoreCase("PileUp"))
-            {
-                afile = new PileUpfile();
-                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));
-            }
-            else if (format.equalsIgnoreCase("BLC"))
-            {
-                afile = new BLCFile();
-                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));
-            }
-            else if (format.equalsIgnoreCase("PFAM"))
-            {
-                afile = new PfamFile();
-                afile.addJVSuffix(
-                    jalview.bin.Cache.getDefault("PFAM_JVSUFFIX", true));
-            }
+    try
+    {
+      AlignFile afile = null;
 
-            afile.setSeqs(seqs);
+      if (format.equalsIgnoreCase("FASTA"))
+      {
+        afile = new FastaFile();
+        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));
+      }
+      else if (format.equalsIgnoreCase("PileUp"))
+      {
+        afile = new PileUpfile();
+        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));
+      }
+      else if (format.equalsIgnoreCase("BLC"))
+      {
+        afile = new BLCFile();
+        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));
+      }
+      else if (format.equalsIgnoreCase("PFAM"))
+      {
+        afile = new PfamFile();
+        afile.addJVSuffix(
+            jalview.bin.Cache.getDefault("PFAM_JVSUFFIX", true));
+      }
 
-            return afile.print();
-        }
-        catch (Exception e)
-        {
-            System.err.println("Failed to write alignment as a '" + format +
-                "' file\n");
-            e.printStackTrace();
-        }
+      afile.setSeqs(seqs);
 
-        return null;
+      return afile.print();
     }
+    catch (Exception e)
+    {
+      System.err.println("Failed to write alignment as a '" + format +
+                         "' file\n");
+      e.printStackTrace();
+    }
+
+    return null;
+  }
 }
diff --git a/src/jalview/io/HTMLOutput.java b/src/jalview/io/HTMLOutput.java
index 32d8a1f..6c2c51e 100755
--- a/src/jalview/io/HTMLOutput.java
+++ b/src/jalview/io/HTMLOutput.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -137,8 +137,7 @@ public class HTMLOutput
       String id = seq.getDisplayId(av.getShowJVSuffix());
 
       out.println("<tr><td nowrap>" + id +
-                    "&nbsp;&nbsp;</td>");
-
+                  "&nbsp;&nbsp;</td>");
 
       for (int res = 0; res < seq.getLength(); res++)
       {
@@ -149,10 +148,11 @@ public class HTMLOutput
           color = fr.findFeatureColour(color, seq, res);
         }
         else
-            color = Color.white;
-
+        {
+          color = Color.white;
+        }
 
-       if (color.getRGB() < -1)
+        if (color.getRGB() < -1)
         {
           out.println("<td bgcolor=\"#" +
                       jalview.util.Format.getHexString(color) + "\">" +
@@ -196,15 +196,18 @@ public class HTMLOutput
         endRes = al.getWidth();
       }
 
-      if(av.getScaleAboveWrapped())
+      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)
         {
@@ -220,25 +223,27 @@ public class HTMLOutput
         out.println("<tr>");
         seq = al.getSequenceAt(s);
 
-        startPos = seq.findPosition( startRes );
-        endPos =   seq.findPosition( endRes )-1;
+        startPos = seq.findPosition(startRes);
+        endPos = seq.findPosition(endRes) - 1;
 
         String id = seq.getDisplayId(av.getShowJVSuffix());
 
         out.println("<td nowrap>" + id +
-                      "&nbsp;&nbsp;</td>");
-
+                    "&nbsp;&nbsp;</td>");
 
-        if(av.getScaleLeftWrapped())
+        if (av.getScaleLeftWrapped())
         {
-          if(startPos > seq.getEnd() || endPos==0)
+          if (startPos > seq.getEnd() || endPos == 0)
+          {
             out.println("<td nowrap>&nbsp;</td>");
+          }
           else
+          {
             out.println("<td nowrap>" + startPos +
-                      "&nbsp;&nbsp;</td>");
+                        "&nbsp;&nbsp;</td>");
+          }
         }
 
-
         for (int res = startRes; res < endRes; res++)
         {
           if (!jalview.util.Comparison.isGap(seq.getCharAt(res)))
@@ -248,11 +253,14 @@ public class HTMLOutput
             color = fr.findFeatureColour(color, seq, res);
           }
           else
+          {
             color = Color.white;
+          }
 
           if (color.getRGB() < -1)
           {
-            out.println("<td bgcolor=\"#" + jalview.util.Format.getHexString(color) + "\">" +
+            out.println("<td bgcolor=\"#" +
+                        jalview.util.Format.getHexString(color) + "\">" +
                         seq.getCharAt(res) + "</td>");
           }
           else
@@ -260,24 +268,22 @@ public class HTMLOutput
             out.println("<td>" + seq.getCharAt(res) + "</td>");
           }
 
-
         }
 
-        if(av.getScaleRightWrapped() &&
-           endRes < startRes + av.getWrappedWidth())
+        if (av.getScaleRightWrapped() &&
+            endRes < startRes + av.getWrappedWidth())
         {
-         out.println("<td colspan=\""+ (startRes+av.getWrappedWidth()-endRes) +"\">"
-                     +"&nbsp;&nbsp;</td>");
-       }
-
+          out.println("<td colspan=\"" +
+                      (startRes + av.getWrappedWidth() - endRes) + "\">"
+                      + "&nbsp;&nbsp;</td>");
+        }
 
-        if(av.getScaleRightWrapped() && startPos<endPos)
+        if (av.getScaleRightWrapped() && startPos < endPos)
         {
           out.println("<td nowrap>&nbsp;" + endPos +
                       "&nbsp;&nbsp;</td>");
         }
 
-
         out.println("</tr>");
       }
 
@@ -294,88 +300,90 @@ public class HTMLOutput
   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");
+        "<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 01282ea..f1dfffe 100755
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -1,28 +1,26 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 jalview.io;
 
 import java.io.*;
-
 import java.net.*;
 
-
 /**
  * DOCUMENT ME!
  *
@@ -31,142 +29,142 @@ import java.net.*;
  */
 public class IdentifyFile
 {
-    /**
-     * DOCUMENT ME!
-     *
-     * @param file DOCUMENT ME!
-     * @param protocol DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String Identify(String file, String protocol)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param file DOCUMENT ME!
+   * @param protocol DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public String Identify(String file, String protocol)
+  {
+    String reply = "PFAM";
+    String error = "FILE NOT FOUND";
+    try
     {
-        String reply = "PFAM";
-        String error =  "FILE NOT FOUND";
-        try
+      BufferedReader reader = null;
+
+      if (protocol.equals(AppletFormatAdapter.FILE))
+      {
+        reader = new BufferedReader(new FileReader(file));
+      }
+      else if (protocol.equals(AppletFormatAdapter.URL))
+      {
+        error = "URL NOT FOUND";
+        URL url = new URL(file);
+        reader = new BufferedReader(new InputStreamReader(
+            url.openStream()));
+
+      }
+      else if (protocol.equals(AppletFormatAdapter.PASTE))
+      {
+        reader = new BufferedReader(new StringReader(file));
+      }
+      else if (protocol.equals(AppletFormatAdapter.CLASSLOADER))
+      {
+        java.io.InputStream is = getClass().getResourceAsStream("/" +
+            file);
+        reader = new BufferedReader(new java.io.InputStreamReader(is));
+      }
+
+      String data;
+
+      while ( (data = reader.readLine()) != null)
+      {
+        data = data.toUpperCase();
+
+        if ( (data.indexOf("# STOCKHOLM") > -1))
         {
-            BufferedReader reader = null;
+          reply = "STH";
 
-            if (protocol.equals(AppletFormatAdapter.FILE))
-            {
-              reader = new BufferedReader(new FileReader(file));
-            }
-            else if (protocol.equals(AppletFormatAdapter.URL))
-            {
-              error = "URL NOT FOUND";
-              URL url = new URL(file);
-              reader = new BufferedReader(new InputStreamReader(
-                  url.openStream()));
+          break;
+        }
 
-            }
-            else if (protocol.equals(AppletFormatAdapter.PASTE))
-            {
-              reader = new BufferedReader(new StringReader(file));
-            }
-            else if (protocol.equals(AppletFormatAdapter.CLASSLOADER))
-            {
-              java.io.InputStream is = getClass().getResourceAsStream("/" +
-                  file);
-              reader = new BufferedReader(new java.io.InputStreamReader(is));
-            }
+        if ( (data.indexOf("#") == 0) || (data.length() < 1))
+        {
+          continue;
+        }
 
-            String data;
+        if (data.indexOf("PILEUP") > -1)
+        {
+          reply = "PileUp";
 
-            while ((data = reader.readLine()) != null)
+          break;
+        }
+
+        if ( (data.indexOf("//") == 0) ||
+            ( (data.indexOf("!!") > -1) &&
+             (data.indexOf("!!") < data.indexOf(
+                 "_MULTIPLE_ALIGNMENT "))))
+        {
+          reply = "MSF";
+
+          break;
+        }
+        else if (data.indexOf("CLUSTAL") > -1)
+        {
+          reply = "CLUSTAL";
+
+          break;
+        }
+        else if ( (data.indexOf(">P1;") > -1) ||
+                 (data.indexOf(">DL;") > -1))
+        {
+          reply = "PIR";
+
+          break;
+        }
+        else if (data.indexOf(">") > -1)
+        {
+          // could be BLC file, read next line to confirm
+          data = reader.readLine();
+
+          if (data.indexOf(">") > -1)
+          {
+            reply = "BLC";
+          }
+          else
+          {
+            //Is this a single line BLC file?
+            reader.readLine();
+            String data2 = reader.readLine();
+            if (data2 != null
+                && data.indexOf("*") > -1
+                && data.indexOf("*") == data2.indexOf("*"))
             {
-                data = data.toUpperCase();
-
-                if ( (data.indexOf("# STOCKHOLM") > -1))
-                {
-                  reply = "STH";
-
-                  break;
-                }
-
-                if ((data.indexOf("#") == 0) || (data.length() < 1))
-                {
-                    continue;
-                }
-
-                if (data.indexOf("PILEUP") > -1)
-                {
-                    reply = "PileUp";
-
-                    break;
-                }
-
-                if ((data.indexOf("//") == 0) ||
-                        ((data.indexOf("!!") > -1) &&
-                        (data.indexOf("!!") < data.indexOf(
-                            "_MULTIPLE_ALIGNMENT "))))
-                {
-                    reply = "MSF";
-
-                    break;
-                }
-                else if (data.indexOf("CLUSTAL") > -1)
-                {
-                    reply = "CLUSTAL";
-
-                    break;
-                }
-                else if ((data.indexOf(">P1;") > -1) ||
-                        (data.indexOf(">DL;") > -1))
-                {
-                    reply = "PIR";
-
-                    break;
-                }
-                else if (data.indexOf(">") > -1)
-                {
-                    // could be BLC file, read next line to confirm
-                    data = reader.readLine();
-
-                    if (data.indexOf(">") > -1)
-                    {
-                        reply = "BLC";
-                    }
-                    else
-                    {
-                      //Is this a single line BLC file?
-                      reader.readLine();
-                      String data2 = reader.readLine();
-                      if ( data2 != null
-                           && data.indexOf("*")>-1
-                           && data.indexOf("*")==data2.indexOf("*"))
-                      {
-                        reply = "BLC";
-                      }
-                      else
-                      {
-                        reply = "FASTA";
-                      }
-                    }
-
-                    break;
-                  }
-                  else if (data.indexOf("HEADER") == 0 ||
-                           data.indexOf("ATOM") == 0)
-                  {
-                    reply = "PDB";
-                    break;
-                  }
-                  else if (data.indexOf(":") < data.indexOf(",")) //  && data.indexOf(",")<data.indexOf(",", data.indexOf(",")))
-                  {
-                    // file looks like a concise JNet file
-                    reply = "JnetFile";
-                    break;
-                  }
+              reply = "BLC";
             }
+            else
+            {
+              reply = "FASTA";
+            }
+          }
 
-            reader.close();
+          break;
         }
-        catch (Exception ex)
+        else if (data.indexOf("HEADER") == 0 ||
+                 data.indexOf("ATOM") == 0)
         {
-            System.err.println("File Identification failed!\n" + ex);
-            return error;
+          reply = "PDB";
+          break;
         }
+        else if (data.indexOf(":") < data.indexOf(",")) //  && data.indexOf(",")<data.indexOf(",", data.indexOf(",")))
+        {
+          // file looks like a concise JNet file
+          reply = "JnetFile";
+          break;
+        }
+      }
 
-        return reply;
+      reader.close();
+    }
+    catch (Exception ex)
+    {
+      System.err.println("File Identification failed!\n" + ex);
+      return error;
     }
+
+    return reply;
+  }
 }
diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java
index 3f308be..30cd181 100755
--- a/src/jalview/io/JPredFile.java
+++ b/src/jalview/io/JPredFile.java
@@ -1,21 +1,21 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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
+ */
 
 /**
  * PredFile.java
@@ -29,330 +29,338 @@ import java.util.*;
 
 import jalview.datamodel.*;
 
-
 /**
  * DOCUMENT ME!
  *
  * @author $author$
  * @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
-    private int QuerySeqPosition;
-
-
-    /**
-     * Creates a new JPredFile object.
-     *
-     * @param inFile DOCUMENT ME!
-     * @param type DOCUMENT ME!
-     *
-     * @throws IOException DOCUMENT ME!
-     */
-    public JPredFile(String inFile, String type) throws IOException
-    {
-        super(inFile, type);
-    }
+  Vector ids;
+  Vector conf;
+  Hashtable Scores; // Hash of names and score vectors
+  Hashtable Symscores; // indexes of symbol annotation properties in sequenceI vector
+  private int QuerySeqPosition;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param QuerySeqPosition DOCUMENT ME!
-     */
-    public void setQuerySeqPosition(int QuerySeqPosition)
-    {
-        this.QuerySeqPosition = QuerySeqPosition;
-    }
+  /**
+   * Creates a new JPredFile object.
+   *
+   * @param inFile DOCUMENT ME!
+   * @param type DOCUMENT ME!
+   *
+   * @throws IOException DOCUMENT ME!
+   */
+  public JPredFile(String inFile, String type)
+      throws IOException
+  {
+    super(inFile, type);
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getQuerySeqPosition()
-    {
-        return QuerySeqPosition;
-    }
+  /**
+   * DOCUMENT ME!
+   *
+   * @param QuerySeqPosition DOCUMENT ME!
+   */
+  public void setQuerySeqPosition(int QuerySeqPosition)
+  {
+    this.QuerySeqPosition = QuerySeqPosition;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Hashtable getScores()
-    {
-        return Scores;
-    }
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public int getQuerySeqPosition()
+  {
+    return QuerySeqPosition;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Hashtable getSymscores()
-    {
-        return Symscores;
-    }
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Hashtable getScores()
+  {
+    return Scores;
+  }
 
-    /**
-     * DOCUMENT ME!
-     */
-    public void initData()
-    {
-        super.initData();
-        Scores = new Hashtable();
-        ids = null;
-        conf = null;
-    }
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Hashtable getSymscores()
+  {
+    return Symscores;
+  }
 
-    /**
- * parse a JPred concise file into a sequence-alignment like object.
- */
-    public void parse() throws IOException
+  /**
+   * DOCUMENT ME!
+   */
+  public void initData()
+  {
+    super.initData();
+    Scores = new Hashtable();
+    ids = null;
+    conf = null;
+  }
+
+  /**
+   * parse a JPred concise file into a sequence-alignment like object.
+   */
+  public void parse()
+      throws IOException
+  {
+    // JBPNote log.System.out.println("all read in ");
+    String line;
+    QuerySeqPosition = -1;
+    noSeqs = 0;
+
+    Vector seq_entries = new Vector();
+    Vector ids = new Vector();
+    Hashtable Symscores = new Hashtable();
+
+    while ( (line = nextLine()) != null)
     {
-        // JBPNote log.System.out.println("all read in ");
-        String line;
-        QuerySeqPosition = -1;
-        noSeqs = 0;
+      // Concise format allows no comments or non comma-formatted data
+      StringTokenizer str = new StringTokenizer(line, ":");
+      String id = "";
+
+      if (!str.hasMoreTokens())
+      {
+        continue;
+      }
+
+      id = str.nextToken();
+
+      String seqsym = str.nextToken();
+      StringTokenizer symbols = new StringTokenizer(seqsym, ",");
+
+      // decide if we have more than just alphanumeric symbols
+      int numSymbols = symbols.countTokens();
+
+      if (numSymbols == 0)
+      {
+        continue;
+      }
+
+      if (seqsym.length() != (2 * numSymbols))
+      {
+        // Set of scalars for some property
+        if (Scores.containsKey(id))
+        {
+          int i = 1;
+
+          while (Scores.containsKey(id + "_" + i))
+          {
+            i++;
+          }
+
+          id = id + "_" + i;
+        }
+
+        Vector scores = new Vector();
+
+        // Typecheck from first entry
+        int i = 0;
+        String ascore = "dead";
 
-        Vector seq_entries = new Vector();
-        Vector ids = new Vector();
-        Hashtable Symscores = new Hashtable();
+        try
+        {
+          // store elements as floats...
+          while (symbols.hasMoreTokens())
+          {
+            ascore = symbols.nextToken();
+
+            Float score = new Float(ascore);
+            scores.addElement( (Object) score);
+          }
 
-        while ((line = nextLine()) != null)
+          Scores.put(id, scores);
+        }
+        catch (Exception e)
         {
-            // Concise format allows no comments or non comma-formatted data
-            StringTokenizer str = new StringTokenizer(line, ":");
-            String id = "";
-
-            if (!str.hasMoreTokens())
-            {
-                continue;
-            }
-
-            id = str.nextToken();
-
-            String seqsym = str.nextToken();
-            StringTokenizer symbols = new StringTokenizer(seqsym, ",");
-
-            // decide if we have more than just alphanumeric symbols
-            int numSymbols = symbols.countTokens();
-
-            if (numSymbols == 0)
-            {
-                continue;
-            }
-
-            if (seqsym.length() != (2 * numSymbols))
-            {
-                // Set of scalars for some property
-                if (Scores.containsKey(id))
-                {
-                    int i = 1;
-
-                    while (Scores.containsKey(id + "_" + i))
-                    {
-                        i++;
-                    }
-
-                    id = id + "_" + i;
-                }
-
-                Vector scores = new Vector();
-
-                // Typecheck from first entry
-                int i = 0;
-                String ascore = "dead";
-
-                try
-                {
-                    // store elements as floats...
-                    while (symbols.hasMoreTokens())
-                    {
-                        ascore = symbols.nextToken();
-
-                        Float score = new Float(ascore);
-                        scores.addElement((Object) score);
-                    }
-
-                    Scores.put(id, scores);
-                }
-                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.addElement((Object) ascore);
-
-                    while (symbols.hasMoreTokens())
-                    {
-                        ascore = symbols.nextToken();
-                        scores.addElement((Object) ascore);
-                    }
-
-                    Scores.put(id, scores);
-                }
-            }
-            else if (id.equals("jnetconf"))
-            {
-                // log.debug System.out.println("here");
-                id = "Prediction Confidence";
-                this.conf = new Vector(numSymbols);
-
-                for (int i = 0; i < numSymbols; i++)
-                {
-                    conf.setElementAt( symbols.nextToken(), i);
-                }
-            }
-            else
-            {
-                // Sequence or a prediction string (rendered as sequence)
-                StringBuffer newseq = new StringBuffer();
-
-                for (int i = 0; i < numSymbols; i++)
-                {
-                    newseq.append(symbols.nextToken());
-                }
-
-                if (id.indexOf(";") > -1)
-                {
-                    seq_entries.addElement(newseq);
-
-                    int i = 1;
-                    String name = id.substring(id.indexOf(";") + 1);
-
-                    while (ids.lastIndexOf(name) > -1)
-                    {
-                        name = id.substring(id.indexOf(";") + 1) + "_" + ++i;
-                    }
-
-                    ids.addElement(name);
-
-                    noSeqs++;
-                }
-                else
-                {
-                    if (id.equals("JNETPRED"))
-                    {
-                        id = "Predicted Secondary Structure";
-                    }
-
-                    seq_entries.addElement(newseq.toString());
-                    ids.addElement(id);
-                    Symscores.put((Object) id,
-                        (Object) new Integer(ids.size() - 1));
-                }
-            }
+          // 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.addElement( (Object) ascore);
+
+          while (symbols.hasMoreTokens())
+          {
+            ascore = symbols.nextToken();
+            scores.addElement( (Object) ascore);
+          }
+
+          Scores.put(id, scores);
         }
-        /* leave it to the parser user to actually check this.
-        if (noSeqs < 1)
+      }
+      else if (id.equals("jnetconf"))
+      {
+        // log.debug System.out.println("here");
+        id = "Prediction Confidence";
+        this.conf = new Vector(numSymbols);
+
+        for (int i = 0; i < numSymbols; i++)
         {
-            throw new IOException(
-                "JpredFile Parser: No sequence in the prediction!");
-        }*/
+          conf.setElementAt(symbols.nextToken(), i);
+        }
+      }
+      else
+      {
+        // Sequence or a prediction string (rendered as sequence)
+        StringBuffer newseq = new StringBuffer();
 
-        maxLength = seq_entries.elementAt(0).toString().length();
+        for (int i = 0; i < numSymbols; i++)
+        {
+          newseq.append(symbols.nextToken());
+        }
 
-        for (int i = 0; i < ids.size(); i++)
+        if (id.indexOf(";") > -1)
         {
-            // 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());
-
-
-            if (maxLength != seq_entries.elementAt(i).toString().length())
-            {
-                throw new IOException("JPredConcise: Entry (" +
-                    ids.elementAt(i).toString() +
-                    ") has an unexpected number of columns");
-            }
-
-            if (newSeq.getName().startsWith("QUERY") &&
-                    (QuerySeqPosition == -1))
-            {
-                QuerySeqPosition = seqs.size();
-            }
-
-            seqs.addElement(newSeq);
+          seq_entries.addElement(newseq);
+
+          int i = 1;
+          String name = id.substring(id.indexOf(";") + 1);
+
+          while (ids.lastIndexOf(name) > -1)
+          {
+            name = id.substring(id.indexOf(";") + 1) + "_" + ++i;
+          }
+
+          ids.addElement(name);
+
+          noSeqs++;
+        }
+        else
+        {
+          if (id.equals("JNETPRED"))
+          {
+            id = "Predicted Secondary Structure";
+          }
+
+          seq_entries.addElement(newseq.toString());
+          ids.addElement(id);
+          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!");
+             }*/
 
-    /**
- * print
- *
- * @return String
-   */
-    public String print()
+    maxLength = seq_entries.elementAt(0).toString().length();
+
+    for (int i = 0; i < ids.size(); i++)
     {
-        return "Not Supported";
+      // 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());
+
+      if (maxLength != seq_entries.elementAt(i).toString().length())
+      {
+        throw new IOException("JPredConcise: Entry (" +
+                              ids.elementAt(i).toString() +
+                              ") has an unexpected number of columns");
+      }
+
+      if (newSeq.getName().startsWith("QUERY") &&
+          (QuerySeqPosition == -1))
+      {
+        QuerySeqPosition = seqs.size();
+      }
+
+      seqs.addElement(newSeq);
     }
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param args DOCUMENT ME!
-     */
-    public static void main(String[] args)
+  /**
+   * print
+   *
+   * @return String
+   */
+  public String print()
+  {
+    return "Not Supported";
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param args DOCUMENT ME!
+   */
+  public static void main(String[] args)
+  {
+    try
     {
-        try
-        {
-            JPredFile blc = new JPredFile(args[0], "File");
-
-            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");
-            }
-        }
-        catch (java.io.IOException e)
-        {
-            System.err.println("Exception " + e);
-            e.printStackTrace();
-        }
+      JPredFile blc = new JPredFile(args[0], "File");
+
+      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");
+      }
+    }
+    catch (java.io.IOException e)
+    {
+      System.err.println("Exception " + e);
+      e.printStackTrace();
     }
-    Vector annotSeqs=null;
+  }
+
+  Vector annotSeqs = null;
   /**
    * removeNonSequences
    */
   public void removeNonSequences()
   {
-    if (annotSeqs!=null)
+    if (annotSeqs != null)
+    {
       return;
+    }
     annotSeqs = new Vector();
     Vector newseqs = new Vector();
-    int i=0;
-    int j=seqs.size();
-    for (; i<QuerySeqPosition; i++)
-        annotSeqs.addElement(seqs.elementAt(i));
-      // check that no stray annotations have been added at the end.
+    int i = 0;
+    int j = seqs.size();
+    for (; i < QuerySeqPosition; i++)
+    {
+      annotSeqs.addElement(seqs.elementAt(i));
+    }
+    // check that no stray annotations have been added at the end.
+    {
+      SequenceI sq = (SequenceI) seqs.elementAt(j - 1);
+      if (sq.getName().toUpperCase().startsWith("JPRED"))
       {
-        SequenceI sq = (SequenceI) seqs.elementAt(j-1);
-        if (sq.getName().toUpperCase().startsWith("JPRED")) {
-          annotSeqs.addElement(sq);
-          seqs.removeElementAt(--j);
-        }
+        annotSeqs.addElement(sq);
+        seqs.removeElementAt(--j);
       }
-    for (; i<j; i++)
-        newseqs.addElement(seqs.elementAt(i));
+    }
+    for (; i < j; i++)
+    {
+      newseqs.addElement(seqs.elementAt(i));
+    }
 
     seqs.removeAllElements();
     seqs = newseqs;
   }
 }
 
-
 /*
  StringBuffer out = new StringBuffer();
 
diff --git a/src/jalview/io/JalviewFileChooser.java b/src/jalview/io/JalviewFileChooser.java
index 39f4aaf..556bb72 100755
--- a/src/jalview/io/JalviewFileChooser.java
+++ b/src/jalview/io/JalviewFileChooser.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -21,10 +21,11 @@
 package jalview.io;
 
 import java.io.*;
+import java.util.*;
+
 import java.awt.*;
-import javax.swing.*;
 import java.awt.event.*;
-import java.util.*;
+import javax.swing.*;
 
 public class JalviewFileChooser
     extends JFileChooser
@@ -43,7 +44,7 @@ public class JalviewFileChooser
                             boolean selectAll)
   {
     super(dir);
-    init( suffix, desc, selected, selectAll);
+    init(suffix, desc, selected, selectAll);
   }
 
   public JalviewFileChooser(String dir,
@@ -52,7 +53,7 @@ public class JalviewFileChooser
                             String selected)
   {
     super(dir);
-    init( suffix, desc, selected, true);
+    init(suffix, desc, selected, true);
   }
 
   void init(String[] suffix,
@@ -86,14 +87,13 @@ public class JalviewFileChooser
     setAccessory(new RecentlyOpened());
   }
 
-
   public void setFileFilter(javax.swing.filechooser.FileFilter filter)
   {
     super.setFileFilter(filter);
 
-
-    try{
-      if(getUI() instanceof javax.swing.plaf.basic.BasicFileChooserUI)
+    try
+    {
+      if (getUI() instanceof javax.swing.plaf.basic.BasicFileChooserUI)
       {
         final javax.swing.plaf.basic.BasicFileChooserUI ui = (javax.swing.plaf.
             basic.BasicFileChooserUI) getUI();
@@ -116,7 +116,8 @@ public class JalviewFileChooser
           }
         });
       }
-    }catch(Exception ex)
+    }
+    catch (Exception ex)
     {
       ex.printStackTrace();
       // Some platforms do not have BasicFileChooserUI
@@ -125,7 +126,7 @@ public class JalviewFileChooser
 
   public String getSelectedFormat()
   {
-    if(getFileFilter()==null)
+    if (getFileFilter() == null)
     {
       return null;
     }
@@ -169,7 +170,6 @@ public class JalviewFileChooser
   {
     this.setAccessory(null);
 
-
     setDialogType(SAVE_DIALOG);
 
     int ret = showDialog(parent, "Save");
@@ -218,10 +218,11 @@ public class JalviewFileChooser
       }
     }
 
-     setSelectedFile( file );
+    setSelectedFile(file);
   }
 
-  class RecentlyOpened extends JPanel
+  class RecentlyOpened
+      extends JPanel
   {
     JList list;
     public RecentlyOpened()
@@ -246,14 +247,13 @@ public class JalviewFileChooser
       dlcr.setHorizontalAlignment(DefaultListCellRenderer.RIGHT);
       list.setCellRenderer(dlcr);
 
-
       list.addMouseListener(new MouseAdapter()
-          {
-            public void mousePressed(MouseEvent evt)
-            {
-              recentListSelectionChanged(list.getSelectedValue().toString());
-            }
-          });
+      {
+        public void mousePressed(MouseEvent evt)
+        {
+          recentListSelectionChanged(list.getSelectedValue().toString());
+        }
+      });
 
       this.setBorder(new javax.swing.border.TitledBorder("Recently Opened"));
 
@@ -270,13 +270,7 @@ public class JalviewFileChooser
         }
       });
 
-
     }
 
   }
 }
-
-
-
-
-
diff --git a/src/jalview/io/JalviewFileFilter.java b/src/jalview/io/JalviewFileFilter.java
index c68fe3f..fd8bcd3 100755
--- a/src/jalview/io/JalviewFileFilter.java
+++ b/src/jalview/io/JalviewFileFilter.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -77,7 +77,7 @@ public class JalviewFileFilter
 
       if (f.isDirectory())
       {
-          return true;
+        return true;
       }
 
       if ( (extension != null) && (filters.get(getExtension(f)) != null))
diff --git a/src/jalview/io/JalviewFileView.java b/src/jalview/io/JalviewFileView.java
index d81a419..b32cbb6 100755
--- a/src/jalview/io/JalviewFileView.java
+++ b/src/jalview/io/JalviewFileView.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
diff --git a/src/jalview/io/JnetAnnotationMaker.java b/src/jalview/io/JnetAnnotationMaker.java
index b334a5c..be063c8 100755
--- a/src/jalview/io/JnetAnnotationMaker.java
+++ b/src/jalview/io/JnetAnnotationMaker.java
@@ -1,20 +1,20 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 jalview.io;
 
 import jalview.datamodel.*;
@@ -22,9 +22,12 @@ import jalview.datamodel.*;
 public class JnetAnnotationMaker
 {
   public static void add_annotation(JPredFile prediction, AlignmentI al,
-                                    int firstSeq, boolean noMsa) throws Exception {
-    JnetAnnotationMaker.add_annotation(prediction, al, firstSeq, noMsa, (int[]) null);
+                                    int firstSeq, boolean noMsa)
+      throws Exception
+  {
+    JnetAnnotationMaker.add_annotation(prediction, al, firstSeq, noMsa, (int[])null);
   }
+
   /**
    * adds the annotation parsed by prediction to al.
    * @param prediction JPredFile
@@ -44,10 +47,12 @@ 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 ('" +
+          "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 +
@@ -58,9 +63,10 @@ public class JnetAnnotationMaker
     Annotation[] annotations = null;
 
     int existingAnnotations = 0;
-    if(al.getAlignmentAnnotation()!=null)
-       existingAnnotations = al.getAlignmentAnnotation().length;
-
+    if (al.getAlignmentAnnotation() != null)
+    {
+      existingAnnotations = al.getAlignmentAnnotation().length;
+    }
 
     while (i < preds.length)
     {
@@ -73,19 +79,22 @@ public class JnetAnnotationMaker
         /*        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 (delMap==null) {
+          if (delMap == null)
+          {
             for (int j = 0; j < width; j++)
             {
               annotations[gapmap[j]] = new Annotation("", "",
                   preds[i].getCharAt(j), 0);
             }
-          } else {
+          }
+          else
+          {
             for (int j = 0; j < width; j++)
             {
               annotations[gapmap[delMap[j]]] = new Annotation("", "",
@@ -95,39 +104,47 @@ public class JnetAnnotationMaker
         }
         else if (id.equals("JNETCONF"))
         {
-          if (delMap==null) {
+          if (delMap == null)
+          {
             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);
+                  j) + "").floatValue();
+              annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(
+                  j) + "", "", preds[i].getCharAt(j),
+                  value);
             }
-          } else {
+          }
+          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),
+              annotations[gapmap[delMap[j]]] = new Annotation(preds[i].
+                  getCharAt(
+                      j) + "", "", preds[i].getCharAt(j),
                   value);
-              }
             }
+          }
         }
         else
         {
-          if (delMap==null) {
+          if (delMap == null)
+          {
             for (int j = 0; j < width; j++)
             {
               annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(
                   j) + "", "", ' ', 0);
             }
-          } else {
+          }
+          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);
             }
           }
         }
diff --git a/src/jalview/io/MSFfile.java b/src/jalview/io/MSFfile.java
index f21a106..b9a14ba 100755
--- a/src/jalview/io/MSFfile.java
+++ b/src/jalview/io/MSFfile.java
@@ -1,31 +1,28 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 jalview.io;
 
-import jalview.datamodel.*;
-
-import jalview.util.*;
-
 import java.io.*;
-
 import java.util.*;
 
+import jalview.datamodel.*;
+import jalview.util.*;
 
 /**
  * DOCUMENT ME!
@@ -33,364 +30,370 @@ import java.util.*;
  * @author $author$
  * @version $Revision$
  */
-public class MSFfile extends AlignFile
+public class MSFfile
+    extends AlignFile
 {
 
-
-    /**
-     * Creates a new MSFfile object.
-     */
-    public MSFfile()
-    {
-    }
-
-
-    /**
-     * Creates a new MSFfile object.
-     *
-     * @param inFile DOCUMENT ME!
-     * @param type DOCUMENT ME!
-     *
-     * @throws IOException DOCUMENT ME!
-     */
-    public MSFfile(String inFile, String type) throws IOException
+  /**
+   * Creates a new MSFfile object.
+   */
+  public MSFfile()
+  {
+  }
+
+  /**
+   * Creates a new MSFfile object.
+   *
+   * @param inFile DOCUMENT ME!
+   * @param type DOCUMENT ME!
+   *
+   * @throws IOException DOCUMENT ME!
+   */
+  public MSFfile(String inFile, String type)
+      throws IOException
+  {
+    super(inFile, type);
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void parse()
+      throws IOException
+  {
+    int i = 0;
+    boolean seqFlag = false;
+    String key = new String();
+    Vector headers = new Vector();
+    Hashtable seqhash = new Hashtable();
+    String line;
+
+    try
     {
-        super(inFile, type);
-    }
-
-    /**
-     * DOCUMENT ME!
-     */
-    public void parse() throws IOException
-    {
-        int i = 0;
-        boolean seqFlag = false;
-        String key = new String();
-        Vector headers = new Vector();
-        Hashtable seqhash = new Hashtable();
-        String line;
-
-        try
-        {
-            while ((line = nextLine()) != null)
-            {
-                StringTokenizer str = new StringTokenizer(line);
-
-                while (str.hasMoreTokens())
-                {
-                    String inStr = str.nextToken();
-
-                    //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 (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
-                        key = inStr;
-
-                        StringBuffer tempseq;
-
-                        //Get sequence from hash if it exists
-                        if (seqhash.containsKey(key))
-                        {
-                            tempseq = (StringBuffer) seqhash.get(key);
-                        }
-                        else
-                        {
-                            tempseq = new StringBuffer();
-                            seqhash.put(key, tempseq);
-                        }
-
-                        //loop through the rest of the words
-                        while (str.hasMoreTokens())
-                        {
-                            //append the word to the sequence
-                            tempseq.append(str.nextToken());
-                        }
-                    }
-                }
-            }
-        }
-        catch (IOException e)
-        {
-            System.err.println("Exception parsing MSFFile " + e);
-            e.printStackTrace();
-        }
-
-        this.noSeqs = headers.size();
+      while ( (line = nextLine()) != null)
+      {
+        StringTokenizer str = new StringTokenizer(line);
 
-        //Add sequences to the hash
-        for (i = 0; i < headers.size(); i++)
+        while (str.hasMoreTokens())
         {
-            if (seqhash.get(headers.elementAt(i)) != null)
-            {
-                String head = headers.elementAt(i).toString();
-                String seq = seqhash.get(head).toString();
+          String inStr = str.nextToken();
 
-                if (maxLength < head.length())
-                {
-                    maxLength = head.length();
-                }
+          //If line has header information add to the headers vector
+          if (inStr.indexOf("Name:") != -1)
+          {
+            key = str.nextToken();
+            headers.addElement(key);
+          }
 
-                // Replace ~ with a sensible gap character
-                seq = seq.replace('~', '-');
+          //if line has // set SeqFlag to 1 so we know sequences are coming
+          if (inStr.indexOf("//") != -1)
+          {
+            seqFlag = true;
+          }
 
-                Sequence newSeq = parseId(head);
+          //Process lines as sequence lines if seqFlag is set
+          if ( (inStr.indexOf("//") == -1) && (seqFlag == true))
+          {
+            //seqeunce id is the first field
+            key = inStr;
 
-                newSeq.setSequence(seq);
+            StringBuffer tempseq;
 
-                seqs.addElement(newSeq);
+            //Get sequence from hash if it exists
+            if (seqhash.containsKey(key))
+            {
+              tempseq = (StringBuffer) seqhash.get(key);
             }
             else
             {
-                System.err.println("MSFFile Parser: Can't find sequence for " +
-                    headers.elementAt(i));
+              tempseq = new StringBuffer();
+              seqhash.put(key, tempseq);
+            }
+
+            //loop through the rest of the words
+            while (str.hasMoreTokens())
+            {
+              //append the word to the sequence
+              tempseq.append(str.nextToken());
             }
+          }
         }
+      }
+    }
+    catch (IOException e)
+    {
+      System.err.println("Exception parsing MSFFile " + e);
+      e.printStackTrace();
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param seq DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int checkSum(String seq)
+    this.noSeqs = headers.size();
+
+    //Add sequences to the hash
+    for (i = 0; i < headers.size(); i++)
     {
-        int check = 0;
-        String sequence = seq.toUpperCase();
+      if (seqhash.get(headers.elementAt(i)) != null)
+      {
+        String head = headers.elementAt(i).toString();
+        String seq = seqhash.get(head).toString();
 
-        for (int i = 0; i < sequence.length(); i++)
+        if (maxLength < head.length())
         {
-            try
-            {
-
-                    int value = sequence.charAt(i);
-                    if (value!=-1)
-                    {
-                        check += (i % 57 +1) * value;
-                    }
-            }
-            catch (Exception e)
-            {
-                System.err.println("Exception during MSF Checksum calculation");
-                e.printStackTrace();
-            }
+          maxLength = head.length();
         }
 
-        return check % 10000;
-    }
+        // Replace ~ with a sensible gap character
+        seq = seq.replace('~', '-');
 
+        Sequence newSeq = parseId(head);
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param s DOCUMENT ME!
-     * @param is_NA DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String print(SequenceI[] seqs)
-    {
+        newSeq.setSequence(seq);
 
-      boolean is_NA = jalview.util.Comparison.isNucleotide(seqs);
+        seqs.addElement(newSeq);
+      }
+      else
+      {
+        System.err.println("MSFFile Parser: Can't find sequence for " +
+                           headers.elementAt(i));
+      }
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param seq DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public int checkSum(String seq)
+  {
+    int check = 0;
+    String sequence = seq.toUpperCase();
+
+    for (int i = 0; i < sequence.length(); i++)
+    {
+      try
+      {
 
-      SequenceI [] s = new SequenceI[seqs.length];
+        int value = sequence.charAt(i);
+        if (value != -1)
+        {
+          check += (i % 57 + 1) * value;
+        }
+      }
+      catch (Exception e)
+      {
+        System.err.println("Exception during MSF Checksum calculation");
+        e.printStackTrace();
+      }
+    }
 
-        StringBuffer out = new StringBuffer("!!" + (is_NA ? "NA" : "AA") +
-                "_MULTIPLE_ALIGNMENT 1.0\n\n"); // TODO: JBPNote : Jalview doesn't remember NA or AA yet.
+    return check % 10000;
+  }
 
-        int max = 0;
-        int maxid = 0;
-        int i = 0;
+  /**
+   * DOCUMENT ME!
+   *
+   * @param s DOCUMENT ME!
+   * @param is_NA DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public String print(SequenceI[] seqs)
+  {
 
-        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('-', '.'));
+    boolean is_NA = jalview.util.Comparison.isNucleotide(seqs);
 
-          StringBuffer sb = new StringBuffer();
-          sb.append(s[i].getSequence());
+    SequenceI[] s = new SequenceI[seqs.length];
 
-          for (int ii = 0; ii < sb.length(); ii++)
-          {
-            if (sb.charAt(ii) == '.')
-            {
-              sb.setCharAt(ii, '~');
-            }
-            else
-              break;
-          }
+    StringBuffer out = new StringBuffer("!!" + (is_NA ? "NA" : "AA") +
+                                        "_MULTIPLE_ALIGNMENT 1.0\n\n"); // TODO: JBPNote : Jalview doesn't remember NA or AA yet.
 
-          for (int ii = sb.length() - 1; ii > 0; ii--)
-          {
-            if (sb.charAt(ii) == '.')
-            {
-              sb.setCharAt(ii,'~');
-            }
-            else
-              break;
-          }
+    int max = 0;
+    int maxid = 0;
+    int i = 0;
 
-            s[i].setSequence(sb.toString());
+    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('-', '.'));
 
-            if (s[i].getSequence().length > max)
-            {
-                max = s[i].getSequence().length;
-            }
+      StringBuffer sb = new StringBuffer();
+      sb.append(s[i].getSequence());
 
-            i++;
+      for (int ii = 0; ii < sb.length(); ii++)
+      {
+        if (sb.charAt(ii) == '.')
+        {
+          sb.setCharAt(ii, '~');
         }
+        else
+        {
+          break;
+        }
+      }
 
-        Format maxLenpad = new Format("%" + (new String("" + max)).length() +
-                "d");
-        Format maxChkpad = new Format("%" + (new String("1" + max)).length() +
-                "d");
-        i = 0;
-
-        int bigChecksum = 0;
-        int [] checksums = new int[s.length];
-        while ( i < s.length )
+      for (int ii = sb.length() - 1; ii > 0; ii--)
+      {
+        if (sb.charAt(ii) == '.')
+        {
+          sb.setCharAt(ii, '~');
+        }
+        else
         {
-          checksums[i] = checkSum(s[i].getSequenceAsString());
-          bigChecksum += checksums[i];
-          i++;
+          break;
         }
+      }
 
-        long maxNB = 0;
-        out.append("   MSF: " + s[0].getSequence().length + "   Type: " +
-            (is_NA ? "N" : "P") + "    Check:  " + (bigChecksum%10000) + "   ..\n\n\n");
+      s[i].setSequence(sb.toString());
 
-        String[] nameBlock = new String[s.length];
-        String[] idBlock = new String[s.length];
+      if (s[i].getSequence().length > max)
+      {
+        max = s[i].getSequence().length;
+      }
 
-        i=0;
-        while ((i < s.length) && (s[i] != null))
-        {
+      i++;
+    }
 
-            nameBlock[i] = new String("  Name: " + printId(s[i])+" ");
+    Format maxLenpad = new Format("%" + (new String("" + max)).length() +
+                                  "d");
+    Format maxChkpad = new Format("%" + (new String("1" + max)).length() +
+                                  "d");
+    i = 0;
 
-            idBlock[i] = new String("Len: " +
-                    maxLenpad.form(s[i].getSequence().length) + "  Check: " +
-                    maxChkpad.form(checksums[i]) + "  Weight: 1.00\n");
+    int bigChecksum = 0;
+    int[] checksums = new int[s.length];
+    while (i < s.length)
+    {
+      checksums[i] = checkSum(s[i].getSequenceAsString());
+      bigChecksum += checksums[i];
+      i++;
+    }
 
-            if (s[i].getName().length() > maxid)
-            {
-                maxid = s[i].getName().length();
-            }
+    long maxNB = 0;
+    out.append("   MSF: " + s[0].getSequence().length + "   Type: " +
+               (is_NA ? "N" : "P") + "    Check:  " + (bigChecksum % 10000) +
+               "   ..\n\n\n");
 
-            if (nameBlock[i].length() > maxNB)
-            {
-                maxNB = nameBlock[i].length();
-            }
+    String[] nameBlock = new String[s.length];
+    String[] idBlock = new String[s.length];
 
-            i++;
-        }
+    i = 0;
+    while ( (i < s.length) && (s[i] != null))
+    {
 
-        if (maxid < 10)
-        {
-            maxid = 10;
-        }
+      nameBlock[i] = new String("  Name: " + printId(s[i]) + " ");
 
-        if (maxNB < 15)
-        {
-            maxNB = 15;
-        }
+      idBlock[i] = new String("Len: " +
+                              maxLenpad.form(s[i].getSequence().length) +
+                              "  Check: " +
+                              maxChkpad.form(checksums[i]) + "  Weight: 1.00\n");
 
-        Format nbFormat = new Format("%-" + maxNB + "s");
+      if (s[i].getName().length() > maxid)
+      {
+        maxid = s[i].getName().length();
+      }
 
-        for (i = 0; (i < s.length) && (s[i] != null); i++)
-        {
-            out.append(nbFormat.form(nameBlock[i]) + idBlock[i]);
-        }
+      if (nameBlock[i].length() > maxNB)
+      {
+        maxNB = nameBlock[i].length();
+      }
 
-        maxid++;
-        out.append("\n\n//\n\n");
+      i++;
+    }
 
-        int len = 50;
+    if (maxid < 10)
+    {
+      maxid = 10;
+    }
 
-        int nochunks = (max / len) + 1;
+    if (maxNB < 15)
+    {
+      maxNB = 15;
+    }
 
-        if ((max % len) == 0)
-        {
-            nochunks--;
-        }
+    Format nbFormat = new Format("%-" + maxNB + "s");
+
+    for (i = 0; (i < s.length) && (s[i] != null); i++)
+    {
+      out.append(nbFormat.form(nameBlock[i]) + idBlock[i]);
+    }
+
+    maxid++;
+    out.append("\n\n//\n\n");
+
+    int len = 50;
+
+    int nochunks = (max / len) + 1;
+
+    if ( (max % len) == 0)
+    {
+      nochunks--;
+    }
+
+    for (i = 0; i < nochunks; i++)
+    {
+      int j = 0;
 
-        for (i = 0; i < nochunks; i++)
+      while ( (j < s.length) && (s[j] != null))
+      {
+        String name = printId(s[j]);
+
+        out.append(new Format("%-" + maxid + "s").form(name + " "));
+
+        for (int k = 0; k < 5; k++)
         {
-            int j = 0;
+          int start = (i * 50) + (k * 10);
+          int end = start + 10;
+
+          if ( (end < s[j].getSequence().length) &&
+              (start < s[j].getSequence().length))
+          {
+            out.append(s[j].getSequence(start, end));
 
-            while ((j < s.length) && (s[j] != null))
+            if (k < 4)
             {
-                String name = printId( s[j] );
-
-                out.append(new Format("%-" + maxid + "s").form(name+" "));
-
-
-                for (int k = 0; k < 5; k++)
-                {
-                    int start = (i * 50) + (k * 10);
-                    int end = start + 10;
-
-                    if ((end < s[j].getSequence().length) &&
-                            (start < s[j].getSequence().length))
-                    {
-                        out.append(s[j].getSequence(start, end));
-
-                        if (k < 4)
-                        {
-                             out.append(" ");
-                        }
-                        else
-                        {
-                            out.append("\n");
-                        }
-                    }
-                    else
-                    {
-                        if (start < s[j].getSequence().length)
-                        {
-                            out.append(s[j].getSequenceAsString().substring(start));
-                            out.append("\n");
-                        }
-                        else
-                        {
-                            if (k == 0)
-                            {
-                                out.append("\n");
-                            }
-                        }
-                    }
-                }
-
-                j++;
+              out.append(" ");
             }
-
-            out.append("\n");
+            else
+            {
+              out.append("\n");
+            }
+          }
+          else
+          {
+            if (start < s[j].getSequence().length)
+            {
+              out.append(s[j].getSequenceAsString().substring(start));
+              out.append("\n");
+            }
+            else
+            {
+              if (k == 0)
+              {
+                out.append("\n");
+              }
+            }
+          }
         }
 
-        return out.toString();
-    }
+        j++;
+      }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String print()
-    {
-        return print(getSeqsAsArray());
+      out.append("\n");
     }
+
+    return out.toString();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public String print()
+  {
+    return print(getSeqsAsArray());
+  }
 }
diff --git a/src/jalview/io/ModellerDescription.java b/src/jalview/io/ModellerDescription.java
index 13431c1..fa6ef6d 100755
--- a/src/jalview/io/ModellerDescription.java
+++ b/src/jalview/io/ModellerDescription.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,16 +18,16 @@
  */
 package jalview.io;
 
-import jalview.datamodel.SequenceI;
-import java.util.Vector;
+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 =
+  /**
+   * 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 =
@@ -87,7 +87,8 @@ public class ModellerDescription
   private resCode validResidueCode(String field)
   {
     Integer val = null;
-    com.stevesoft.pat.Regex r = new com.stevesoft.pat.Regex("\\s*((([-0-9]+).?)|FIRST|LAST|@)");
+    com.stevesoft.pat.Regex r = new com.stevesoft.pat.Regex(
+        "\\s*((([-0-9]+).?)|FIRST|LAST|@)");
 
     if (!r.search(field))
     {
@@ -98,8 +99,8 @@ public class ModellerDescription
     {
       value = r.stringMatched(1);
     }
-   // jalview.bin.Cache.log.debug("from '" + field + "' matched '" + value +
-   //                             "'");
+    // jalview.bin.Cache.log.debug("from '" + field + "' matched '" + value +
+    //                             "'");
     try
     {
       val = Integer.valueOf(value);
@@ -124,7 +125,7 @@ public class ModellerDescription
       field = st.nextToken(":");
       do
       {
-        if (seqTypes[i].equalsIgnoreCase(field) )
+        if (seqTypes[i].equalsIgnoreCase(field))
         {
           break;
         }
@@ -150,8 +151,8 @@ public class ModellerDescription
               }
               else
               {
-          //      jalview.bin.Cache.log.debug(
-         //           "Ignoring non-Modeller description: invalid integer-like field '" + field + "'");
+                //      jalview.bin.Cache.log.debug(
+                //           "Ignoring non-Modeller description: invalid integer-like field '" + field + "'");
                 type = -1; /* invalid field! - throw the FieldSet away */
               }
               ;
@@ -242,7 +243,7 @@ public class ModellerDescription
       if (seq.getDatasetSequence() != null &&
           seq.getDatasetSequence().getDBRef() != null)
       {
-        jalview.datamodel.DBRefEntry [] dbr = seq.getDatasetSequence().getDBRef();
+        jalview.datamodel.DBRefEntry[] dbr = seq.getDatasetSequence().getDBRef();
         int i, j;
         for (i = 0, j = dbr.length; i < j; i++)
         {
@@ -388,4 +389,3 @@ public class ModellerDescription
     return false;
   }
 }
-
diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java
index d7d7ec6..5d43f78 100755
--- a/src/jalview/io/NewickFile.java
+++ b/src/jalview/io/NewickFile.java
@@ -1,21 +1,21 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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
+ */
 
 // NewickFile.java
 // Tree I/O
@@ -25,10 +25,9 @@
 // TODO: Extended SequenceNodeI to hold parsed NHX strings
 package jalview.io;
 
-import jalview.datamodel.*;
-
 import java.io.*;
 
+import jalview.datamodel.*;
 
 /**
  * DOCUMENT ME!
@@ -36,757 +35,767 @@ import java.io.*;
  * @author $author$
  * @version $Revision$
  */
-public class NewickFile extends FileParse
+public class NewickFile
+    extends FileParse
 {
-    SequenceNode root;
-    private boolean HasBootstrap = false;
-    private boolean HasDistances = false;
-    private boolean RootHasDistance = false;
-
-    // File IO Flags
-    boolean ReplaceUnderscores = false;
-    boolean printRootInfo = false;
-    private com.stevesoft.pat.Regex[] NodeSafeName = new com.stevesoft.pat.Regex[]
-        {
-            new com.stevesoft.pat.Regex().perlCode("m/[\\[,:'()]/"), // test for requiring quotes
-            new com.stevesoft.pat.Regex().perlCode("s/'/''/"), // escaping quote characters
-            new com.stevesoft.pat.Regex().perlCode("s/\\/w/_/") // unqoted whitespace transformation
-        };
-    char QuoteChar = '\'';
-
-    /**
-     * Creates a new NewickFile object.
-     *
-     * @param inStr DOCUMENT ME!
-     *
-     * @throws IOException DOCUMENT ME!
-     */
-    public NewickFile(String inStr) throws IOException
-    {
-        super(inStr, "Paste");
+  SequenceNode root;
+  private boolean HasBootstrap = false;
+  private boolean HasDistances = false;
+  private boolean RootHasDistance = false;
+
+  // File IO Flags
+  boolean ReplaceUnderscores = false;
+  boolean printRootInfo = false;
+  private com.stevesoft.pat.Regex[] NodeSafeName = new com.stevesoft.pat.Regex[]
+      {
+      new com.stevesoft.pat.Regex().perlCode("m/[\\[,:'()]/"), // test for requiring quotes
+      new com.stevesoft.pat.Regex().perlCode("s/'/''/"), // escaping quote characters
+      new com.stevesoft.pat.Regex().perlCode("s/\\/w/_/") // unqoted whitespace transformation
+  };
+  char QuoteChar = '\'';
+
+  /**
+   * Creates a new NewickFile object.
+   *
+   * @param inStr DOCUMENT ME!
+   *
+   * @throws IOException DOCUMENT ME!
+   */
+  public NewickFile(String inStr)
+      throws IOException
+  {
+    super(inStr, "Paste");
+  }
+
+  /**
+   * Creates a new NewickFile object.
+   *
+   * @param inFile DOCUMENT ME!
+   * @param type DOCUMENT ME!
+   *
+   * @throws IOException DOCUMENT ME!
+   */
+  public NewickFile(String inFile, String type)
+      throws IOException
+  {
+    super(inFile, type);
+  }
+
+  /**
+   * Creates a new NewickFile object.
+   *
+   * @param newtree DOCUMENT ME!
+   */
+  public NewickFile(SequenceNode newtree)
+  {
+    root = newtree;
+  }
+
+  /**
+   * Creates a new NewickFile object.
+   *
+   * @param newtree DOCUMENT ME!
+   * @param bootstrap DOCUMENT ME!
+   */
+  public NewickFile(SequenceNode newtree, boolean bootstrap)
+  {
+    HasBootstrap = bootstrap;
+    root = newtree;
+  }
+
+  /**
+   * Creates a new NewickFile object.
+   *
+   * @param newtree DOCUMENT ME!
+   * @param bootstrap DOCUMENT ME!
+   * @param distances DOCUMENT ME!
+   */
+  public NewickFile(SequenceNode newtree, boolean bootstrap, boolean distances)
+  {
+    root = newtree;
+    HasBootstrap = bootstrap;
+    HasDistances = distances;
+  }
+
+  /**
+   * Creates a new NewickFile object.
+   *
+   * @param newtree DOCUMENT ME!
+   * @param bootstrap DOCUMENT ME!
+   * @param distances DOCUMENT ME!
+   * @param rootdistance DOCUMENT ME!
+   */
+  public NewickFile(SequenceNode newtree, boolean bootstrap,
+                    boolean distances, boolean rootdistance)
+  {
+    root = newtree;
+    HasBootstrap = bootstrap;
+    HasDistances = distances;
+    RootHasDistance = rootdistance;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param Error DOCUMENT ME!
+   * @param Er DOCUMENT ME!
+   * @param r DOCUMENT ME!
+   * @param p DOCUMENT ME!
+   * @param s DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  private String ErrorStringrange(String Error, String Er, int r, int p,
+                                  String s)
+  {
+    return ( (Error == null) ? "" : Error) + Er + " at position " + p +
+        " ( " +
+        s.substring( ( (p - r) < 0) ? 0 : (p - r),
+                    ( (p + r) > s.length()) ? s.length() : (p + r)) + " )\n";
+  }
+
+  // @tree annotations
+  // These are set automatically by the reader
+  public boolean HasBootstrap()
+  {
+    return HasBootstrap;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public boolean HasDistances()
+  {
+    return HasDistances;
+  }
+
+  public boolean HasRootDistance()
+  {
+    return RootHasDistance;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @throws IOException DOCUMENT ME!
+   */
+  public void parse()
+      throws IOException
+  {
+    String nf;
+
+    { // fill nf with complete tree file
+
+      StringBuffer file = new StringBuffer();
+
+      while ( (nf = nextLine()) != null)
+      {
+        file.append(nf);
+      }
+
+      nf = file.toString();
     }
 
-    /**
-     * Creates a new NewickFile object.
-     *
-     * @param inFile DOCUMENT ME!
-     * @param type DOCUMENT ME!
-     *
-     * @throws IOException DOCUMENT ME!
-     */
-    public NewickFile(String inFile, String type) throws IOException
-    {
-        super(inFile, type);
-    }
+    root = new SequenceNode();
 
-    /**
-     * Creates a new NewickFile object.
-     *
-     * @param newtree DOCUMENT ME!
-     */
-    public NewickFile(SequenceNode newtree)
-    {
-        root = newtree;
-    }
+    SequenceNode realroot = null;
+    SequenceNode c = root;
 
-    /**
-     * Creates a new NewickFile object.
-     *
-     * @param newtree DOCUMENT ME!
-     * @param bootstrap DOCUMENT ME!
-     */
-    public NewickFile(SequenceNode newtree, boolean bootstrap)
-    {
-        HasBootstrap = bootstrap;
-        root = newtree;
-    }
+    int d = -1;
+    int cp = 0;
+    //int flen = nf.length();
 
-    /**
-     * Creates a new NewickFile object.
-     *
-     * @param newtree DOCUMENT ME!
-     * @param bootstrap DOCUMENT ME!
-     * @param distances DOCUMENT ME!
-     */
-    public NewickFile(SequenceNode newtree, boolean bootstrap, boolean distances)
-    {
-        root = newtree;
-        HasBootstrap = bootstrap;
-        HasDistances = distances;
-    }
+    String Error = null;
+    String nodename = null;
 
-    /**
-     * Creates a new NewickFile object.
-     *
-     * @param newtree DOCUMENT ME!
-     * @param bootstrap DOCUMENT ME!
-     * @param distances DOCUMENT ME!
-     * @param rootdistance DOCUMENT ME!
-     */
-    public NewickFile(SequenceNode newtree, boolean bootstrap,
-        boolean distances, boolean rootdistance)
-    {
-        root = newtree;
-        HasBootstrap = bootstrap;
-        HasDistances = distances;
-        RootHasDistance = rootdistance;
-    }
+    float DefDistance = (float) 0.001; // @param Default distance for a node - very very small
+    int DefBootstrap = 0; // @param Default bootstrap for a node
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param Error DOCUMENT ME!
-     * @param Er DOCUMENT ME!
-     * @param r DOCUMENT ME!
-     * @param p DOCUMENT ME!
-     * @param s DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    private String ErrorStringrange(String Error, String Er, int r, int p,
-        String s)
-    {
-        return ((Error == null) ? "" : Error) + Er + " at position " + p +
-        " ( " +
-        s.substring(((p - r) < 0) ? 0 : (p - r),
-            ((p + r) > s.length()) ? s.length() : (p + r)) + " )\n";
-    }
+    float distance = DefDistance;
+    int bootstrap = DefBootstrap;
 
-    // @tree annotations
-    // These are set automatically by the reader
-    public boolean HasBootstrap()
-    {
-        return HasBootstrap;
-    }
+    boolean ascending = false; // flag indicating that we are leaving the current node
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean HasDistances()
-    {
-        return HasDistances;
-    }
+    com.stevesoft.pat.Regex majorsyms = new com.stevesoft.pat.Regex(
+        "[(\\['),;]");
 
-    public boolean HasRootDistance()
+    while (majorsyms.searchFrom(nf, cp) && (Error == null))
     {
-        return RootHasDistance;
-    }
-    /**
-     * DOCUMENT ME!
-     *
-     * @throws IOException DOCUMENT ME!
-     */
-    public void parse() throws IOException
-    {
-        String nf;
-
-        { // fill nf with complete tree file
-
-            StringBuffer file = new StringBuffer();
-
-            while ((nf = nextLine()) != null)
+      int fcp = majorsyms.matchedFrom();
+
+      switch (nf.charAt(fcp))
+      {
+        case '[': // Comment or structured/extended NH format info
+
+          com.stevesoft.pat.Regex comment = new com.stevesoft.pat.Regex(
+              "]");
+
+          if (comment.searchFrom(nf, fcp))
+          {
+            // Skip the comment field
+            cp = 1 + comment.matchedFrom();
+          }
+          else
+          {
+            Error = ErrorStringrange(Error, "Unterminated comment", 3,
+                                     fcp, nf);
+          }
+
+          ;
+
+          break;
+
+        case '(':
+
+          // ascending should not be set
+          // New Internal node
+          if (ascending)
+          {
+            Error = ErrorStringrange(Error, "Unexpected '('", 7, fcp, nf);
+
+            continue;
+          }
+
+          ;
+          d++;
+
+          if (c.right() == null)
+          {
+            c.setRight(new SequenceNode(null, c, null, DefDistance,
+                                        DefBootstrap, false));
+            c = (SequenceNode) c.right();
+          }
+          else
+          {
+            if (c.left() != null)
             {
-                file.append(nf);
+              // Dummy node for polytomy - keeps c.left free for new node
+              SequenceNode tmpn = new SequenceNode(null, c, null, 0,
+                  0, true);
+              tmpn.SetChildren(c.left(), c.right());
+              c.setRight(tmpn);
             }
 
-            nf = file.toString();
-        }
-
-        root = new SequenceNode();
-
-        SequenceNode realroot = null;
-        SequenceNode c = root;
-
-        int d = -1;
-        int cp = 0;
-        //int flen = nf.length();
-
-        String Error = null;
-        String nodename = null;
-
-        float DefDistance = (float) 0.001; // @param Default distance for a node - very very small
-        int DefBootstrap = 0; // @param Default bootstrap for a node
-
-        float distance = DefDistance;
-        int bootstrap = DefBootstrap;
-
-        boolean ascending = false; // flag indicating that we are leaving the current node
-
-        com.stevesoft.pat.Regex majorsyms = new com.stevesoft.pat.Regex(
-                "[(\\['),;]");
-
-        while (majorsyms.searchFrom(nf, cp) && (Error == null))
-        {
-            int fcp = majorsyms.matchedFrom();
-
-            switch (nf.charAt(fcp))
+            c.setLeft(new SequenceNode(null, c, null, DefDistance,
+                                       DefBootstrap, false));
+            c = (SequenceNode) c.left();
+          }
+
+          if (realroot == null)
+          {
+            realroot = c;
+          }
+
+          nodename = null;
+          distance = DefDistance;
+          bootstrap = DefBootstrap;
+          cp = fcp + 1;
+
+          break;
+
+          // Deal with quoted fields
+        case '\'':
+
+          com.stevesoft.pat.Regex qnodename = new com.stevesoft.pat.Regex(
+              "([^']|'')+'");
+
+          if (qnodename.searchFrom(nf, fcp))
+          {
+            int nl = qnodename.stringMatched().length();
+            nodename = new String(qnodename.stringMatched().substring(0,
+                nl - 1));
+            cp = fcp + nl + 1;
+          }
+          else
+          {
+            Error = ErrorStringrange(Error,
+                                     "Unterminated quotes for nodename", 7, fcp,
+                                     nf);
+          }
+
+          break;
+
+        case ';':
+
+          if (d != -1)
+          {
+            Error = ErrorStringrange(Error,
+                                     "Wayward semicolon (depth=" + d + ")", 7,
+                                     fcp, nf);
+          }
+
+          // cp advanced at the end of default
+        default:
+
+          // Parse simpler field strings
+          String fstring = nf.substring(cp, fcp);
+          com.stevesoft.pat.Regex uqnodename = new com.stevesoft.pat.Regex(
+              "\\b([^' :;\\](),]+)");
+          com.stevesoft.pat.Regex nbootstrap = new com.stevesoft.pat.Regex(
+              "\\S+([0-9+]+)\\S*:");
+          com.stevesoft.pat.Regex ndist = new com.stevesoft.pat.Regex(
+              ":([-0-9Ee.+]+)");
+
+          if (uqnodename.search(fstring) &&
+              ( (uqnodename.matchedFrom(1) == 0) ||
+               (fstring.charAt(uqnodename.matchedFrom(1) - 1) != ':'))) // JBPNote HACK!
+          {
+            if (nodename == null)
             {
-            case '[': // Comment or structured/extended NH format info
-
-                com.stevesoft.pat.Regex comment = new com.stevesoft.pat.Regex(
-                        "]");
-
-                if (comment.searchFrom(nf, fcp))
-                {
-                    // Skip the comment field
-                    cp = 1 + comment.matchedFrom();
-                }
-                else
-                {
-                    Error = ErrorStringrange(Error, "Unterminated comment", 3,
-                            fcp, nf);
-                }
-
-                ;
-
-                break;
-
-            case '(':
-
-                // ascending should not be set
-                // New Internal node
-                if (ascending)
-                {
-                    Error = ErrorStringrange(Error, "Unexpected '('", 7, fcp, nf);
-
-                    continue;
-                }
-
-                ;
-                d++;
-
-                if (c.right() == null)
-                {
-                    c.setRight(new SequenceNode(null, c, null, DefDistance,
-                            DefBootstrap, false));
-                    c = (SequenceNode) c.right();
-                }
-                else
-                {
-                    if (c.left() != null)
-                    {
-                        // Dummy node for polytomy - keeps c.left free for new node
-                        SequenceNode tmpn = new SequenceNode(null, c, null, 0,
-                                0, true);
-                        tmpn.SetChildren(c.left(), c.right());
-                        c.setRight(tmpn);
-                    }
-
-                    c.setLeft(new SequenceNode(null, c, null, DefDistance,
-                            DefBootstrap, false));
-                    c = (SequenceNode) c.left();
-                }
-
-                if (realroot == null)
-                {
-                    realroot = c;
-                }
-
-                nodename = null;
-                distance = DefDistance;
-                bootstrap = DefBootstrap;
-                cp = fcp + 1;
-
-                break;
-
-            // Deal with quoted fields
-            case '\'':
-
-                com.stevesoft.pat.Regex qnodename = new com.stevesoft.pat.Regex(
-                        "([^']|'')+'");
-
-                if (qnodename.searchFrom(nf, fcp))
-                {
-                    int nl = qnodename.stringMatched().length();
-                    nodename = new String(qnodename.stringMatched().substring(0,
-                                nl - 1));
-                    cp = fcp + nl + 1;
-                }
-                else
-                {
-                    Error = ErrorStringrange(Error,
-                            "Unterminated quotes for nodename", 7, fcp, nf);
-                }
-
-                break;
-
-            case ';':
-
-                if (d != -1)
-                {
-                    Error = ErrorStringrange(Error,
-                            "Wayward semicolon (depth=" + d + ")", 7, fcp, nf);
-                }
-
-            // cp advanced at the end of default
-            default:
-
-                // Parse simpler field strings
-                String fstring = nf.substring(cp, fcp);
-                com.stevesoft.pat.Regex uqnodename = new com.stevesoft.pat.Regex(
-                        "\\b([^' :;\\](),]+)");
-                com.stevesoft.pat.Regex nbootstrap = new com.stevesoft.pat.Regex(
-                        "\\S+([0-9+]+)\\S*:");
-                com.stevesoft.pat.Regex ndist = new com.stevesoft.pat.Regex(
-                        ":([-0-9Ee.+]+)");
-
-                if (uqnodename.search(fstring) &&
-                        ((uqnodename.matchedFrom(1) == 0) ||
-                        (fstring.charAt(uqnodename.matchedFrom(1) - 1) != ':'))) // JBPNote HACK!
-                {
-                    if (nodename == null)
-                    {
-                        if (ReplaceUnderscores)
-                        {
-                            nodename = uqnodename.stringMatched(1).replace('_',
-                                    ' ');
-                        }
-                        else
-                        {
-                            nodename = uqnodename.stringMatched(1);
-                        }
-                    }
-                    else
-                    {
-                        Error = ErrorStringrange(Error,
-                                "File has broken algorithm - overwritten nodename",
-                                10, fcp, nf);
-                    }
-                }
-
-                if (nbootstrap.search(fstring) &&
-                        (nbootstrap.matchedFrom(1) > (uqnodename.matchedFrom(1) +
-                        uqnodename.stringMatched().length())))
-                {
-                    try
-                    {
-                        bootstrap = (new Integer(nbootstrap.stringMatched(1))).intValue();
-                        HasBootstrap = true;
-                    }
-                    catch (Exception e)
-                    {
-                        Error = ErrorStringrange(Error,
-                                "Can't parse bootstrap value", 4,
-                                cp + nbootstrap.matchedFrom(), nf);
-                    }
-                }
+              if (ReplaceUnderscores)
+              {
+                nodename = uqnodename.stringMatched(1).replace('_',
+                    ' ');
+              }
+              else
+              {
+                nodename = uqnodename.stringMatched(1);
+              }
+            }
+            else
+            {
+              Error = ErrorStringrange(Error,
+                                       "File has broken algorithm - overwritten nodename",
+                                       10, fcp, nf);
+            }
+          }
 
-                boolean nodehasdistance = false;
+          if (nbootstrap.search(fstring) &&
+              (nbootstrap.matchedFrom(1) > (uqnodename.matchedFrom(1) +
+                                            uqnodename.stringMatched().length())))
+          {
+            try
+            {
+              bootstrap = (new Integer(nbootstrap.stringMatched(1))).intValue();
+              HasBootstrap = true;
+            }
+            catch (Exception e)
+            {
+              Error = ErrorStringrange(Error,
+                                       "Can't parse bootstrap value", 4,
+                                       cp + nbootstrap.matchedFrom(), nf);
+            }
+          }
 
-                if (ndist.search(fstring))
-                {
-                    try
-                    {
-                        distance = (new Float(ndist.stringMatched(1))).floatValue();
-                        HasDistances = true;
-                        nodehasdistance = true;
-                    }
-                    catch (Exception e)
-                    {
-                        Error = ErrorStringrange(Error,
-                                "Can't parse node distance value", 7,
-                                cp + ndist.matchedFrom(), nf);
-                    }
-                }
+          boolean nodehasdistance = false;
 
-                if (ascending)
-                {
-                    // Write node info here
-                    c.setName(nodename);
-                    // Trees without distances still need a render distance
-                    c.dist = (HasDistances) ? distance : DefDistance;
-                    // be consistent for internal bootstrap defaults too
-                    c.setBootstrap((HasBootstrap) ? bootstrap : DefBootstrap);
-                    if (c == realroot)
-                    {
-                        RootHasDistance = nodehasdistance; // JBPNote This is really UGLY!!! Ensure root node gets its given distance
-                    }
-                }
-                else
-                {
-                    // Find a place to put the leaf
-                    SequenceNode newnode = new SequenceNode(null, c, nodename,
-                            (HasDistances) ? distance : DefDistance,
-                            (HasBootstrap) ? bootstrap : DefBootstrap, false);
-
-                    if (c.right() == null)
-                    {
-                        c.setRight(newnode);
-                    }
-                    else
-                    {
-                        if (c.left() == null)
-                        {
-                            c.setLeft(newnode);
-                        }
-                        else
-                        {
-                            // Insert a dummy node for polytomy
-                            // dummy nodes have distances
-                            SequenceNode newdummy = new SequenceNode(null, c,
-                                    null, (HasDistances ? 0 : DefDistance), 0, true);
-                            newdummy.SetChildren(c.left(), newnode);
-                            c.setLeft(newdummy);
-                        }
-                    }
-                }
+          if (ndist.search(fstring))
+          {
+            try
+            {
+              distance = (new Float(ndist.stringMatched(1))).floatValue();
+              HasDistances = true;
+              nodehasdistance = true;
+            }
+            catch (Exception e)
+            {
+              Error = ErrorStringrange(Error,
+                                       "Can't parse node distance value", 7,
+                                       cp + ndist.matchedFrom(), nf);
+            }
+          }
+
+          if (ascending)
+          {
+            // Write node info here
+            c.setName(nodename);
+            // Trees without distances still need a render distance
+            c.dist = (HasDistances) ? distance : DefDistance;
+            // be consistent for internal bootstrap defaults too
+            c.setBootstrap( (HasBootstrap) ? bootstrap : DefBootstrap);
+            if (c == realroot)
+            {
+              RootHasDistance = nodehasdistance; // JBPNote This is really UGLY!!! Ensure root node gets its given distance
+            }
+          }
+          else
+          {
+            // Find a place to put the leaf
+            SequenceNode newnode = new SequenceNode(null, c, nodename,
+                (HasDistances) ? distance : DefDistance,
+                (HasBootstrap) ? bootstrap : DefBootstrap, false);
+
+            if (c.right() == null)
+            {
+              c.setRight(newnode);
+            }
+            else
+            {
+              if (c.left() == null)
+              {
+                c.setLeft(newnode);
+              }
+              else
+              {
+                // Insert a dummy node for polytomy
+                // dummy nodes have distances
+                SequenceNode newdummy = new SequenceNode(null, c,
+                    null, (HasDistances ? 0 : DefDistance), 0, true);
+                newdummy.SetChildren(c.left(), newnode);
+                c.setLeft(newdummy);
+              }
+            }
+          }
 
-                if (ascending)
-                {
-                    // move back up the tree from preceding closure
-                    c = c.AscendTree();
-
-                    if ((d > -1) && (c == null))
-                    {
-                        Error = ErrorStringrange(Error,
-                                "File broke algorithm: Lost place in tree (is there an extra ')' ?)",
-                                7, fcp, nf);
-                    }
-                }
+          if (ascending)
+          {
+            // move back up the tree from preceding closure
+            c = c.AscendTree();
 
-                if (nf.charAt(fcp) == ')')
-                {
-                    d--;
-                    ascending = true;
-                }
-                else
+            if ( (d > -1) && (c == null))
+            {
+              Error = ErrorStringrange(Error,
+                                       "File broke algorithm: Lost place in tree (is there an extra ')' ?)",
+                                       7, fcp, nf);
+            }
+          }
+
+          if (nf.charAt(fcp) == ')')
+          {
+            d--;
+            ascending = true;
+          }
+          else
+          {
+            if (nf.charAt(fcp) == ',')
+            {
+              if (ascending)
+              {
+                ascending = false;
+              }
+              else
+              {
+                // Just advance focus, if we need to
+                if ( (c.left() != null) && (!c.left().isLeaf()))
                 {
-                    if (nf.charAt(fcp) == ',')
-                    {
-                        if (ascending)
-                        {
-                            ascending = false;
-                        }
-                        else
-                        {
-                            // Just advance focus, if we need to
-                            if ((c.left() != null) && (!c.left().isLeaf()))
-                            {
-                                c = (SequenceNode) c.left();
-                            }
-                        }
-                    }
-
-                    // else : We do nothing if ';' is encountered.
+                  c = (SequenceNode) c.left();
                 }
-
-                // Reset new node properties to obvious fakes
-                nodename = null;
-                distance = DefDistance;
-                bootstrap = DefBootstrap;
-
-                cp = fcp + 1;
+              }
             }
-        }
 
-        if (Error != null)
-        {
-            throw (new IOException("NewickFile: " + Error + "\n"));
-        }
+            // else : We do nothing if ';' is encountered.
+          }
 
-        root = (SequenceNode) root.right().detach(); // remove the imaginary root.
+          // Reset new node properties to obvious fakes
+          nodename = null;
+          distance = DefDistance;
+          bootstrap = DefBootstrap;
 
-        if (!RootHasDistance)
-        {
-            root.dist = (HasDistances) ? 0 : DefDistance;
-        }
+          cp = fcp + 1;
+      }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public SequenceNode getTree()
+    if (Error != null)
     {
-        return root;
+      throw (new IOException("NewickFile: " + Error + "\n"));
     }
 
-    /**
-     * Generate a newick format tree according to internal flags
-     * for bootstraps, distances and root distances.
-     *
-     * @return new hampshire tree in a single line
-     */
-    public String print()
-    {
-        synchronized (this)
-        {
-            StringBuffer tf = new StringBuffer();
-            print(tf, root);
+    root = (SequenceNode) root.right().detach(); // remove the imaginary root.
 
-            return (tf.append(";").toString());
-        }
+    if (!RootHasDistance)
+    {
+      root.dist = (HasDistances) ? 0 : DefDistance;
     }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public SequenceNode getTree()
+  {
+    return root;
+  }
+
+  /**
+   * Generate a newick format tree according to internal flags
+   * for bootstraps, distances and root distances.
+   *
+   * @return new hampshire tree in a single line
+   */
+  public String print()
+  {
+    synchronized (this)
+    {
+      StringBuffer tf = new StringBuffer();
+      print(tf, root);
 
-    /**
-     *
-     *
-     * Generate a newick format tree according to internal flags
-     * for distances and root distances and user specificied writing of
-     * bootstraps.
-     * @param withbootstraps controls if bootstrap values are explicitly written.
-     *
-     * @return new hampshire tree in a single line
-     */
-    public String print(boolean withbootstraps)
+      return (tf.append(";").toString());
+    }
+  }
+
+  /**
+   *
+   *
+   * Generate a newick format tree according to internal flags
+   * for distances and root distances and user specificied writing of
+   * bootstraps.
+   * @param withbootstraps controls if bootstrap values are explicitly written.
+   *
+   * @return new hampshire tree in a single line
+   */
+  public String print(boolean withbootstraps)
+  {
+    synchronized (this)
     {
-        synchronized (this)
-        {
-            boolean boots = this.HasBootstrap;
-            this.HasBootstrap = withbootstraps;
+      boolean boots = this.HasBootstrap;
+      this.HasBootstrap = withbootstraps;
 
-            String rv = print();
-            this.HasBootstrap = boots;
+      String rv = print();
+      this.HasBootstrap = boots;
 
-            return rv;
-        }
+      return rv;
     }
-
-    /**
-     *
-     * Generate newick format tree according to internal flags
-     * for writing root node distances.
-     *
-     * @param withbootstraps explicitly write bootstrap values
-     * @param withdists explicitly write distances
-     *
-     * @return new hampshire tree in a single line
-     */
-    public String print(boolean withbootstraps, boolean withdists)
+  }
+
+  /**
+   *
+   * Generate newick format tree according to internal flags
+   * for writing root node distances.
+   *
+   * @param withbootstraps explicitly write bootstrap values
+   * @param withdists explicitly write distances
+   *
+   * @return new hampshire tree in a single line
+   */
+  public String print(boolean withbootstraps, boolean withdists)
+  {
+    synchronized (this)
     {
-        synchronized (this)
-        {
-            boolean dists = this.HasDistances;
-            this.HasDistances = withdists;
+      boolean dists = this.HasDistances;
+      this.HasDistances = withdists;
 
-            String rv = print(withbootstraps);
-            this.HasDistances = dists;
+      String rv = print(withbootstraps);
+      this.HasDistances = dists;
 
-            return rv;
-        }
+      return rv;
     }
-
-    /**
-     * Generate newick format tree according to user specified flags
-     *
-     * @param withbootstraps explicitly write bootstrap values
-     * @param withdists explicitly write distances
-     * @param printRootInfo explicitly write root distance
-     *
-     * @return new hampshire tree in a single line
-     */
-    public String print(boolean withbootstraps, boolean withdists,
-        boolean printRootInfo)
+  }
+
+  /**
+   * Generate newick format tree according to user specified flags
+   *
+   * @param withbootstraps explicitly write bootstrap values
+   * @param withdists explicitly write distances
+   * @param printRootInfo explicitly write root distance
+   *
+   * @return new hampshire tree in a single line
+   */
+  public String print(boolean withbootstraps, boolean withdists,
+                      boolean printRootInfo)
+  {
+    synchronized (this)
     {
-        synchronized (this)
-        {
-            boolean rootinfo = printRootInfo;
-            this.printRootInfo = printRootInfo;
+      boolean rootinfo = printRootInfo;
+      this.printRootInfo = printRootInfo;
 
-            String rv = print(withbootstraps, withdists);
-            this.printRootInfo = rootinfo;
+      String rv = print(withbootstraps, withdists);
+      this.printRootInfo = rootinfo;
 
-            return rv;
-        }
+      return rv;
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    char getQuoteChar()
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  char getQuoteChar()
+  {
+    return QuoteChar;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param c DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  char setQuoteChar(char c)
+  {
+    char old = QuoteChar;
+    QuoteChar = c;
+
+    return old;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param name DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  private String nodeName(String name)
+  {
+    if (NodeSafeName[0].search(name))
     {
-        return QuoteChar;
+      return QuoteChar + NodeSafeName[1].replaceAll(name) + QuoteChar;
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param c DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    char setQuoteChar(char c)
+    else
     {
-        char old = QuoteChar;
-        QuoteChar = c;
-
-        return old;
+      return NodeSafeName[2].replaceAll(name);
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param name DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    private String nodeName(String name)
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param c DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  private String printNodeField(SequenceNode c)
+  {
+    return ( (c.getName() == null) ? "" : nodeName(c.getName())) +
+        ( (HasBootstrap)
+         ? ( (c.getBootstrap() > -1) ? (" " + c.getBootstrap()) : "") : "") +
+        ( (HasDistances) ? (":" + c.dist) : "");
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param root DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  private String printRootField(SequenceNode root)
+  {
+    return (printRootInfo)
+        ? ( ( (root.getName() == null) ? "" : nodeName(root.getName())) +
+           ( (HasBootstrap)
+            ? ( (root.getBootstrap() > -1) ? (" " + root.getBootstrap()) : "") :
+            "") +
+           ( (RootHasDistance) ? (":" + root.dist) : "")) : "";
+  }
+
+  // Non recursive call deals with root node properties
+  public void print(StringBuffer tf, SequenceNode root)
+  {
+    if (root != null)
     {
-        if (NodeSafeName[0].search(name))
+      if (root.isLeaf() && printRootInfo)
+      {
+        tf.append(printRootField(root));
+      }
+      else
+      {
+        if (root.isDummy())
         {
-            return QuoteChar + NodeSafeName[1].replaceAll(name) + QuoteChar;
+          _print(tf, (SequenceNode) root.right());
+          _print(tf, (SequenceNode) root.left());
         }
         else
         {
-            return NodeSafeName[2].replaceAll(name);
-        }
-    }
+          tf.append("(");
+          _print(tf, (SequenceNode) root.right());
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param c DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    private String printNodeField(SequenceNode c)
-    {
-        return ((c.getName() == null) ? "" : nodeName(c.getName())) +
-        ((HasBootstrap)
-        ? ((c.getBootstrap() > -1) ? (" " + c.getBootstrap()) : "") : "") +
-        ((HasDistances) ? (":" + c.dist) : "");
-    }
+          if (root.left() != null)
+          {
+            tf.append(",");
+          }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param root DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    private String printRootField(SequenceNode root)
-    {
-        return (printRootInfo)
-        ? (((root.getName() == null) ? "" : nodeName(root.getName())) +
-        ((HasBootstrap)
-        ? ((root.getBootstrap() > -1) ? (" " + root.getBootstrap()) : "") : "") +
-        ((RootHasDistance) ? (":" + root.dist) : "")) : "";
+          _print(tf, (SequenceNode) root.left());
+          tf.append(")" + printRootField(root));
+        }
+      }
     }
+  }
 
-    // Non recursive call deals with root node properties
-    public void print(StringBuffer tf, SequenceNode root)
+  // Recursive call for non-root nodes
+  public void _print(StringBuffer tf, SequenceNode c)
+  {
+    if (c != null)
     {
-        if (root != null)
+      if (c.isLeaf())
+      {
+        tf.append(printNodeField(c));
+      }
+      else
+      {
+        if (c.isDummy())
         {
-            if (root.isLeaf() && printRootInfo)
-            {
-                tf.append(printRootField(root));
-            }
-            else
-            {
-                if (root.isDummy())
-                {
-                    _print(tf, (SequenceNode) root.right());
-                    _print(tf, (SequenceNode) root.left());
-                }
-                else
-                {
-                    tf.append("(");
-                    _print(tf, (SequenceNode) root.right());
-
-                    if (root.left() != null)
-                    {
-                        tf.append(",");
-                    }
-
-                    _print(tf, (SequenceNode) root.left());
-                    tf.append(")" + printRootField(root));
-                }
-            }
+          _print(tf, (SequenceNode) c.left());
+          if (c.left() != null)
+          {
+            tf.append(",");
+          }
+          _print(tf, (SequenceNode) c.right());
         }
-    }
-
-    // Recursive call for non-root nodes
-    public void _print(StringBuffer tf, SequenceNode c)
-    {
-        if (c != null)
+        else
         {
-            if (c.isLeaf())
-            {
-                tf.append(printNodeField(c));
-            }
-            else
-            {
-                if (c.isDummy())
-                {
-                    _print(tf, (SequenceNode) c.left());
-                    if (c.left() != null)
-                    {
-                      tf.append(",");
-                    }
-                    _print(tf, (SequenceNode) c.right());
-                }
-                else
-                {
-                    tf.append("(");
-                    _print(tf, (SequenceNode) c.right());
+          tf.append("(");
+          _print(tf, (SequenceNode) c.right());
 
-                    if (c.left() != null)
-                    {
-                        tf.append(",");
-                    }
+          if (c.left() != null)
+          {
+            tf.append(",");
+          }
 
-                    _print(tf, (SequenceNode) c.left());
-                    tf.append(")" + printNodeField(c));
-                }
-            }
+          _print(tf, (SequenceNode) c.left());
+          tf.append(")" + printNodeField(c));
         }
+      }
     }
+  }
 
-    // Test
-    public static void main(String[] args)
+  // Test
+  public static void main(String[] args)
+  {
+    try
     {
-        try
-        {
-            if (args==null || args.length!=1) {
-              System.err.println("Takes one argument - file name of a newick tree file.");
-              System.exit(0);
-            }
-
-            File fn = new File(args[0]);
-
-            StringBuffer newickfile = new StringBuffer();
-            BufferedReader treefile = new BufferedReader(new FileReader(fn));
-            String l;
-
-            while ((l = treefile.readLine()) != null)
-            {
-                newickfile.append(l);
-            }
-
-            treefile.close();
-            System.out.println("Read file :\n");
-
-            NewickFile trf = new NewickFile(args[0], "File");
-            trf.parse();
-            System.out.println("Original file :\n");
-
-            com.stevesoft.pat.Regex nonl = new com.stevesoft.pat.Regex("\n+", "");
-            System.out.println(nonl.replaceAll(newickfile.toString()) + "\n");
-
-            System.out.println("Parsed file.\n");
-            System.out.println("Default output type for original input.\n");
-            System.out.println(trf.print());
-            System.out.println("Without bootstraps.\n");
-            System.out.println(trf.print(false));
-            System.out.println("Without distances.\n");
-            System.out.println(trf.print(true, false));
-            System.out.println("Without bootstraps but with distanecs.\n");
-            System.out.println(trf.print(false, true));
-            System.out.println("Without bootstraps or distanecs.\n");
-            System.out.println(trf.print(false, false));
-            System.out.println("With bootstraps and with distances.\n");
-            System.out.println(trf.print(true, true));
-        }
-        catch (java.io.IOException e)
-        {
-            System.err.println("Exception\n" + e);
-            e.printStackTrace();
-        }
+      if (args == null || args.length != 1)
+      {
+        System.err.println(
+            "Takes one argument - file name of a newick tree file.");
+        System.exit(0);
+      }
+
+      File fn = new File(args[0]);
+
+      StringBuffer newickfile = new StringBuffer();
+      BufferedReader treefile = new BufferedReader(new FileReader(fn));
+      String l;
+
+      while ( (l = treefile.readLine()) != null)
+      {
+        newickfile.append(l);
+      }
+
+      treefile.close();
+      System.out.println("Read file :\n");
+
+      NewickFile trf = new NewickFile(args[0], "File");
+      trf.parse();
+      System.out.println("Original file :\n");
+
+      com.stevesoft.pat.Regex nonl = new com.stevesoft.pat.Regex("\n+", "");
+      System.out.println(nonl.replaceAll(newickfile.toString()) + "\n");
+
+      System.out.println("Parsed file.\n");
+      System.out.println("Default output type for original input.\n");
+      System.out.println(trf.print());
+      System.out.println("Without bootstraps.\n");
+      System.out.println(trf.print(false));
+      System.out.println("Without distances.\n");
+      System.out.println(trf.print(true, false));
+      System.out.println("Without bootstraps but with distanecs.\n");
+      System.out.println(trf.print(false, true));
+      System.out.println("Without bootstraps or distanecs.\n");
+      System.out.println(trf.print(false, false));
+      System.out.println("With bootstraps and with distances.\n");
+      System.out.println(trf.print(true, true));
+    }
+    catch (java.io.IOException e)
+    {
+      System.err.println("Exception\n" + e);
+      e.printStackTrace();
     }
+  }
 }
diff --git a/src/jalview/io/PIRFile.java b/src/jalview/io/PIRFile.java
index a33e118..910d189 100755
--- a/src/jalview/io/PIRFile.java
+++ b/src/jalview/io/PIRFile.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -40,57 +40,60 @@ public class PIRFile
     super(inFile, type);
   }
 
-  public void parse() throws IOException
+  public void parse()
+      throws IOException
   {
-      StringBuffer sequence;
-      String line = null;
-      ModellerDescription md;
+    StringBuffer sequence;
+    String line = null;
+    ModellerDescription md;
 
-      while ( (line = nextLine()) != null)
+    while ( (line = nextLine()) != null)
+    {
+      if (line.length() == 0)
       {
-        if (line.length() == 0)
-        {
-          //System.out.println("blank line");
-          continue;
-        }
-        if (line.indexOf("C;") == 0 || line.indexOf("#") == 0)
-        {
-          continue;
-        }
-        Sequence newSeq = parseId(line.substring(line.indexOf(";") + 1));
-
-        sequence = new StringBuffer();
+        //System.out.println("blank line");
+        continue;
+      }
+      if (line.indexOf("C;") == 0 || line.indexOf("#") == 0)
+      {
+        continue;
+      }
+      Sequence newSeq = parseId(line.substring(line.indexOf(";") + 1));
 
-        newSeq.setDescription(nextLine()); // this is the title line
+      sequence = new StringBuffer();
 
-        boolean starFound = false;
+      newSeq.setDescription(nextLine()); // this is the title line
 
-        while(!starFound)
-        {
-          line = nextLine();
-          sequence.append(line);
+      boolean starFound = false;
 
-          if (line == null)
-            break;
+      while (!starFound)
+      {
+        line = nextLine();
+        sequence.append(line);
 
-          if (line.indexOf("*") > -1)
-          {
-            starFound = true;
-          }
+        if (line == null)
+        {
+          break;
         }
 
-        if (sequence.length() > 0)
+        if (line.indexOf("*") > -1)
         {
-          sequence.setLength(sequence.length() - 1);
-          newSeq.setSequence(sequence.toString());
+          starFound = true;
+        }
+      }
 
-          seqs.addElement(newSeq);
+      if (sequence.length() > 0)
+      {
+        sequence.setLength(sequence.length() - 1);
+        newSeq.setSequence(sequence.toString());
 
-          md = new ModellerDescription(newSeq.
-                getDescription());
-          md.updateSequenceI(newSeq);
-        }
+        seqs.addElement(newSeq);
+
+        md = new ModellerDescription(newSeq.
+                                     getDescription());
+        md.updateSequenceI(newSeq);
       }
+    }
   }
 
   public String print()
@@ -111,19 +114,18 @@ public class PIRFile
       String seq = s[i].getSequenceAsString();
       seq = seq + "*";
 
-
       if (is_NA)
       {
-          // modeller doesn't really do nucleotides, so we don't do anything fancy
-          // Official tags area as follows, for now we'll use P1 and DL
-          // Protein (complete) P1
-          // Protein (fragment) F1
-          // DNA (linear) Dl
-          // DNA (circular) DC
-          // RNA (linear) RL
-          // RNA (circular) RC
-          // tRNA N3
-          // other functional RNA N1
+        // modeller doesn't really do nucleotides, so we don't do anything fancy
+        // Official tags area as follows, for now we'll use P1 and DL
+        // Protein (complete) P1
+        // Protein (fragment) F1
+        // DNA (linear) Dl
+        // DNA (circular) DC
+        // RNA (linear) RL
+        // RNA (circular) RC
+        // tRNA N3
+        // other functional RNA N1
 
         out.append(">N1;" + s[i].getName() + "\n");
         if (s[i].getDescription() == null)
@@ -134,28 +136,32 @@ public class PIRFile
         }
         else
         {
-          out.append(s[i].getDescription()+"\n");
+          out.append(s[i].getDescription() + "\n");
         }
       }
       else
       {
 
-       if(useModellerOutput)
-       {
-         out.append(">P1;" + s[i].getName() + "\n");
-         md = new ModellerDescription(s[i]);
-         out.append(md.getDescriptionLine() + "\n");
-       }
-       else
-       {
-         out.append(">P1;" + printId(s[i]) + "\n");
-         if (s[i].getDescription() != null)
-           out.append(s[i].getDescription() + "\n");
-         else
-           out.append(s[i].getName() + " "
-                      + (s[i].getEnd() - s[i].getStart() + 1)
-                      + " residues\n");
-       }
+        if (useModellerOutput)
+        {
+          out.append(">P1;" + s[i].getName() + "\n");
+          md = new ModellerDescription(s[i]);
+          out.append(md.getDescriptionLine() + "\n");
+        }
+        else
+        {
+          out.append(">P1;" + printId(s[i]) + "\n");
+          if (s[i].getDescription() != null)
+          {
+            out.append(s[i].getDescription() + "\n");
+          }
+          else
+          {
+            out.append(s[i].getName() + " "
+                       + (s[i].getEnd() - s[i].getStart() + 1)
+                       + " residues\n");
+          }
+        }
       }
       int nochunks = (seq.length() / len) + 1;
 
diff --git a/src/jalview/io/PfamFile.java b/src/jalview/io/PfamFile.java
index d84dc70..4c90bca 100755
--- a/src/jalview/io/PfamFile.java
+++ b/src/jalview/io/PfamFile.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -43,7 +43,8 @@ public class PfamFile
     super.initData();
   }
 
-  public void parse() throws IOException
+  public void parse()
+      throws IOException
   {
     int i = 0;
     String line;
@@ -105,11 +106,11 @@ public class PfamFile
               .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 " +
@@ -153,7 +154,7 @@ public class PfamFile
 
     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]) + " "));
 
       out.append(s[j].getSequenceAsString() + "\n");
       j++;
diff --git a/src/jalview/io/PileUpfile.java b/src/jalview/io/PileUpfile.java
index be16169..4715d9c 100755
--- a/src/jalview/io/PileUpfile.java
+++ b/src/jalview/io/PileUpfile.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -34,41 +34,42 @@ import java.io.*;
 import jalview.datamodel.*;
 import jalview.util.*;
 
-public class PileUpfile  extends MSFfile
+public class PileUpfile
+    extends MSFfile
 {
 
-    /**
-     * Creates a new MSFfile object.
-     */
-    public PileUpfile()
-    {
-    }
+  /**
+   * Creates a new MSFfile object.
+   */
+  public PileUpfile()
+  {
+  }
 
+  /**
+   * Creates a new MSFfile object.
+   *
+   * @param inFile DOCUMENT ME!
+   * @param type DOCUMENT ME!
+   *
+   * @throws IOException DOCUMENT ME!
+   */
+  public PileUpfile(String inFile, String type)
+      throws IOException
+  {
+    super(inFile, type);
+  }
 
-    /**
-     * Creates a new MSFfile object.
-     *
-     * @param inFile DOCUMENT ME!
-     * @param type DOCUMENT ME!
-     *
-     * @throws IOException DOCUMENT ME!
-     */
-    public PileUpfile(String inFile, String type) throws IOException
-    {
-        super(inFile, type);
-    }
-   /**
+  /**
    * DOCUMENT ME!
    *
    * @return DOCUMENT ME!
    */
   public String print()
   {
-      return print(getSeqsAsArray());
+    return print(getSeqsAsArray());
   }
 
-
-  public  String print(SequenceI[] s)
+  public String print(SequenceI[] s)
   {
     StringBuffer out = new StringBuffer("PileUp\n\n");
 
@@ -86,9 +87,9 @@ public class PileUpfile  extends MSFfile
     }
 
     out.append("   MSF: " + s[0].getSequence().length +
-               "   Type: P    Check:  " + bigChecksum%10000 + "   ..\n\n\n");
+               "   Type: P    Check:  " + bigChecksum % 10000 + "   ..\n\n\n");
 
-    i=0;
+    i = 0;
     while ( (i < s.length) && (s[i] != null))
     {
       String seq = s[i].getSequenceAsString();
@@ -135,7 +136,7 @@ public class PileUpfile  extends MSFfile
       {
         String name = printId(s[j]);
 
-         out.append(new Format("%-" + maxid + "s").form(name + " "));
+        out.append(new Format("%-" + maxid + "s").form(name + " "));
 
         for (int k = 0; k < 5; k++)
         {
diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index fd5fd44..10ddf53 100644
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -20,10 +20,13 @@
  * This extension was written by Benjamin Schuster-Boeckler at sanger.ac.uk
  */
 package jalview.io;
+
 import java.io.*;
 import java.util.*;
-import jalview.datamodel.*;
+
 import com.stevesoft.pat.*;
+import jalview.datamodel.*;
+
 //import org.apache.log4j.*;
 
 /**
@@ -31,379 +34,440 @@ import com.stevesoft.pat.*;
  * @author bsb at sanger.ac.uk
  * @version 0.3
  */
-public class StockholmFile extends AlignFile
+public class StockholmFile
+    extends AlignFile
 {
-        //static Logger logger = Logger.getLogger("jalview.io.StockholmFile");
-
-    public StockholmFile()
+  //static Logger logger = Logger.getLogger("jalview.io.StockholmFile");
+
+  public StockholmFile()
+  {
+  }
+
+  public StockholmFile(String inFile, String type)
+      throws IOException
+  {
+    super(inFile, type);
+  }
+
+  public void initData()
+  {
+    super.initData();
+  }
+
+  /**
+   * Parse a file in Stockholm format into Jalview's data model. The file has
+   * to be passed at construction time
+   * @throws IOException If there is an error with the input file
+   */
+  public void parse()
+      throws IOException
+  {
+    // --------------- Variable Definitions -------------------
+    String line;
+    String version;
+    //  String id;
+    Hashtable alAnn = new Hashtable(); // Alignment wide annotations
+    Hashtable seqAnn = new Hashtable(); // Sequence related annotations
+    Hashtable seqs = new Hashtable();
+    Regex p, r, rend, s, x;
+
+    // ------------------ Parsing File ----------------------
+    // First, we have to check that this file has STOCKHOLM format, i.e. the first line must match
+    r = new Regex("# STOCKHOLM ([\\d\\.]+)");
+    if (!r.search(nextLine()))
     {
+      throw new IOException("This file is not in valid STOCKHOLM format: First line does not contain '# STOCKHOLM'");
     }
-
-
-    public StockholmFile(String inFile, String type) throws IOException
+    else
     {
-        super(inFile, type);
+      version = r.stringMatched(1);
+      //logger.debug("Stockholm version: " + version);
     }
 
-    public void initData()
+//      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
+    s = new Regex("(\\S+)\\s+(\\w{2})\\s+(.*)"); // Parses annotation subtype
+    r = new Regex("#=(G[FSRC]?)\\s+(.*)"); // Finds any annotation line
+    x = new Regex("(\\S+)\\s+(\\S+)"); //split id from sequence
+
+    rend.optimize();
+    p.optimize();
+    s.optimize();
+    r.optimize();
+    x.optimize();
+
+    while ( (line = nextLine()) != null)
     {
-         super.initData();
-    }
+      if (line.length() == 0)
+      {
+        continue;
+      }
+      if (rend.search(line))
+      {
+//              End of the alignment, pass stuff back
 
-    /**
-     * Parse a file in Stockholm format into Jalview's data model. The file has
-     * to be passed at construction time
-     * @throws IOException If there is an error with the input file
-     */
-    public void parse() throws IOException
-    {
-        // --------------- Variable Definitions -------------------
-        String line;
-        String version;
-      //  String id;
-        Hashtable alAnn = new Hashtable(); // Alignment wide annotations
-        Hashtable seqAnn = new Hashtable(); // Sequence related annotations
-        Hashtable seqs = new Hashtable();
-        Regex p, r, rend, s, x;
-
-        // ------------------ Parsing File ----------------------
-        // First, we have to check that this file has STOCKHOLM format, i.e. the first line must match
-        r = new Regex("# STOCKHOLM ([\\d\\.]+)");
-        if(!r.search(nextLine()))
+        this.noSeqs = seqs.size();
+        //logger.debug("Number of sequences: " + this.noSeqs);
+        Enumeration accs = seqs.keys();
+        while (accs.hasMoreElements())
         {
-            throw new IOException("This file is not in valid STOCKHOLM format: First line does not contain '# STOCKHOLM'");
+          String acc = (String) accs.nextElement();
+          //logger.debug("Processing sequence " + acc);
+          String seq = (String) seqs.get(acc);
+          if (maxLength < seq.length())
+          {
+            maxLength = seq.length();
+          }
+          int start = 1;
+          int end = -1;
+          String sid = acc;
+          // Split accession in id and from/to
+          if (p.search(acc))
+          {
+            sid = p.stringMatched(1);
+            start = Integer.parseInt(p.stringMatched(2));
+            end = Integer.parseInt(p.stringMatched(3));
+          }
+          //logger.debug(sid + ", " + start + ", " + end);
+
+          Sequence seqO = new Sequence(sid, seq, start, end);
+          Hashtable features = null;
+          // We need to adjust the positions of all features to account for gaps
+          try
+          {
+            features = (Hashtable) ( (Hashtable) seqAnn.get(acc)).get(
+                "features");
+          }
+          catch (java.lang.NullPointerException e)
+          {
+            //loggerwarn("Getting Features for " + acc + ": " + e.getMessage());
+            //continue;
+          }
+          // if we have features
+          if (features != null)
+          {
+            Enumeration i = features.keys();
+            while (i.hasMoreElements())
+            {
+              String type = i.nextElement().toString();
+              Hashtable content = (Hashtable) features.get(type);
+
+              Enumeration j = content.keys();
+              while (j.hasMoreElements())
+              {
+                String desc = j.nextElement().toString();
+                String ns = content.get(desc).toString();
+                char[] byChar = ns.toCharArray();
+                for (int k = 0; k < byChar.length; k++)
+                {
+                  char c = byChar[k];
+                  if (! (c == ' ' || c == '_' ||
+                         c == '-'))
+                  {
+                    int new_pos = seqO.findPosition(k);
+                    SequenceFeature feat =
+                        new SequenceFeature(type,
+                                            desc, new_pos, new_pos, 0f, null);
+
+                    seqO.addSequenceFeature(feat);
+                  }
+                }
+              }
+
+            }
+
+          }
+          //logger.debug("Adding seq " + acc + " from "  + start + " to " + end + ": " + seq);
+          this.seqs.addElement(seqO);
         }
-        else
+      }
+      else if (!r.search(line))
+      {
+        //System.err.println("Found sequence line: " + line);
+
+        // Split sequence in sequence and accession parts
+        if (!x.search(line))
+        {
+          //logger.error("Could not parse sequence line: " + line);
+          throw new IOException("Could not parse sequence line: " + line);
+        }
+        String ns = (String) seqs.get(x.stringMatched(1));
+        if (ns == null)
         {
-            version = r.stringMatched(1);
-            //logger.debug("Stockholm version: " + version);
+          ns = "";
         }
+        ns += x.stringMatched(2);
 
-//      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
-        s = new Regex("(\\S+)\\s+(\\w{2})\\s+(.*)"); // Parses annotation subtype
-        r = new Regex("#=(G[FSRC]?)\\s+(.*)"); // Finds any annotation line
-        x = new Regex("(\\S+)\\s+(\\S+)"); //split id from sequence
-
-        rend.optimize();
-        p.optimize();
-        s.optimize();
-        r.optimize();
-        x.optimize();
-
-        while ( (line = nextLine()) != null)
+        seqs.put(x.stringMatched(1), ns);
+      }
+      else
+      {
+        String annType = r.stringMatched(1);
+        String annContent = r.stringMatched(2);
+
+        //System.err.println("type:" + annType + " content: " + annContent);
+
+        if (annType.equals("GF"))
+        {
+          /* Generic per-File annotation, free text
+           * Magic features:
+           * #=GF NH <tree in New Hampshire eXtended format>
+           * #=GF TN <Unique identifier for the next tree>
+           * Pfam descriptions:
+              7. DESCRIPTION OF FIELDS
+
+                 Compulsory fields:
+                 ------------------
+
+                 AC   Accession number:           Accession number in form PFxxxxx.version or PBxxxxxx.
+                 ID   Identification:             One word name for family.
+                 DE   Definition:                 Short description of family.
+                 AU   Author:                     Authors of the entry.
+                 SE   Source of seed:             The source suggesting the seed members belong to one family.
+           GA   Gathering method:           Search threshold to build the full alignment.
+                 TC   Trusted Cutoff:             Lowest sequence score and domain score of match in the full alignment.
+                 NC   Noise Cutoff:               Highest sequence score and domain score of match not in full alignment.
+                 TP   Type:                       Type of family -- presently Family, Domain, Motif or Repeat.
+           SQ   Sequence:                   Number of sequences in alignment.
+                 AM   Alignment Method        The order ls and fs hits are aligned to the model to build the full align.
+                 //                               End of alignment.
+
+                 Optional fields:
+                 ----------------
+
+           DC   Database Comment:           Comment about database reference.
+           DR   Database Reference:         Reference to external database.
+           RC   Reference Comment:          Comment about literature reference.
+                 RN   Reference Number:           Reference Number.
+           RM   Reference Medline:          Eight digit medline UI number.
+                 RT   Reference Title:            Reference Title.
+                 RA   Reference Author:           Reference Author
+                 RL   Reference Location:         Journal location.
+           PI   Previous identifier:        Record of all previous ID lines.
+                 KW   Keywords:                   Keywords.
+                 CC   Comment:                    Comments.
+                 NE   Pfam accession:         Indicates a nested domain.
+                 NL   Location:                   Location of nested domains - sequence ID, start and end of insert.
+
+                 Obsolete fields:
+                 -----------
+           AL   Alignment method of seed:   The method used to align the seed members.
+           */
+          // Let's save the annotations, maybe we'll be able to do something with them later...
+          Regex an = new Regex("(\\w+)\\s*(.*)");
+          if (an.search(annContent))
+          {
+            alAnn.put(an.stringMatched(1), an.stringMatched(2));
+          }
+        }
+        else if (annType.equals("GS"))
         {
-            if (line.length() == 0) continue;
-            if(rend.search(line))
+          // Generic per-Sequence annotation, free text
+          /* Pfam uses these features:
+              Feature                    Description
+              ---------------------      -----------
+              AC <accession>             ACcession number
+              DE <freetext>              DEscription
+              DR <db>; <accession>;      Database Reference
+              OS <organism>              OrganiSm (species)
+              OC <clade>                 Organism Classification (clade, etc.)
+              LO <look>                  Look (Color, etc.)
+           */
+          if (s.search(annContent))
+          {
+            String acc = s.stringMatched(1);
+            String type = s.stringMatched(2);
+            String content = s.stringMatched(3);
+
+            Hashtable ann;
+            if (seqAnn.containsKey(acc))
             {
-//              End of the alignment, pass stuff back
-
-                 this.noSeqs = seqs.size();
-                //logger.debug("Number of sequences: " + this.noSeqs);
-                Enumeration accs = seqs.keys();
-                while (accs.hasMoreElements())
-                {
-                    String acc = (String) accs.nextElement();
-                    //logger.debug("Processing sequence " + acc);
-                    String seq = (String) seqs.get(acc);
-                    if (maxLength < seq.length())
-                    {
-                        maxLength = seq.length();
-                    }
-                    int start = 1;
-                    int end = -1;
-                    String sid = acc;
-                    // Split accession in id and from/to
-                    if (p.search(acc))
-                    {
-                        sid = p.stringMatched(1);
-                        start = Integer.parseInt(p.stringMatched(2));
-                        end = Integer.parseInt(p.stringMatched(3));
-                    }
-                    //logger.debug(sid + ", " + start + ", " + end);
-
-                    Sequence seqO = new Sequence(sid, seq, start, end);
-                    Hashtable features = null;
-                    // We need to adjust the positions of all features to account for gaps
-                    try
-                    {
-                         features = (Hashtable) ((Hashtable) seqAnn.get(acc)).get("features");
-                    }
-                    catch (java.lang.NullPointerException e)
-                    {
-                       //loggerwarn("Getting Features for " + acc + ": " + e.getMessage());
-                       //continue;
-                    }
-                    // if we have features
-                    if (features != null)
-                    {
-                        Enumeration i = features.keys();
-                        while(i.hasMoreElements())
-                        {
-                            String type = i.nextElement().toString();
-                            Hashtable content = (Hashtable) features.get(type);
-
-                            Enumeration j = content.keys();
-                            while(j.hasMoreElements())
-                            {
-                                        String desc = j.nextElement().toString();
-                                        String ns = content.get(desc).toString();
-                                        char[] byChar = ns.toCharArray();
-                                        for (int k = 0; k < byChar.length; k++)
-                                        {
-                                                char c = byChar[k];
-                                                if (! (c == ' ' || c == '_' ||
-                                                       c == '-'))
-                                                {
-                                                  int new_pos = seqO.findPosition(k);
-                                                  SequenceFeature feat =
-                                                      new SequenceFeature(type,
-                                                      desc, new_pos, new_pos, 0f, null);
-
-                                                  seqO.addSequenceFeature(feat);
-                                                }
-                                        }
-                                }
-
-                        }
-
-                    }
-                    //logger.debug("Adding seq " + acc + " from "  + start + " to " + end + ": " + seq);
-                    this.seqs.addElement(seqO);
-                }
+              ann = (Hashtable) seqAnn.get(acc);
             }
-            else if (!r.search(line))
+            else
             {
-                //System.err.println("Found sequence line: " + line);
-
-                // Split sequence in sequence and accession parts
-                if(!x.search(line))
-                {
-                                //logger.error("Could not parse sequence line: " + line);
-                                throw new IOException("Could not parse sequence line: " + line);
-                }
-                String ns  = (String) seqs.get(x.stringMatched(1));
-                if (ns == null) ns = "";
-                ns += x.stringMatched(2);
+              ann = new Hashtable();
+            }
+            ann.put(type, content);
+            seqAnn.put(acc, ann);
+          }
+          else
+          {
+            throw new IOException("Error parsing " + line);
+          }
+        }
+        else if (annType.equals("GC"))
+        {
+          System.out.println(annContent);
+          // Generic per-Column annotation, exactly 1 char per column
+        }
+        else if (annType.equals("GR"))
+        {
+          // Generic per-Sequence AND per-Column markup, exactly 1 char per column
+          /*
+              Feature   Description            Markup letters
+              -------   -----------            --------------
+              SS        Secondary Structure    [HGIEBTSCX]
+              SA        Surface Accessibility  [0-9X]
+                            (0=0%-10%; ...; 9=90%-100%)
+              TM        TransMembrane          [Mio]
+              PP        Posterior Probability  [0-9*]
+                            (0=0.00-0.05; 1=0.05-0.15; *=0.95-1.00)
+              LI        LIgand binding         [*]
+              AS        Active Site            [*]
+              IN        INtron (in or after)   [0-2]
+           */
+          if (s.search(annContent))
+          {
+            String acc = s.stringMatched(1);
+            String type = s.stringMatched(2);
+            String seq = s.stringMatched(3);
+            String description = new String();
+
+            // Check for additional information about the current annotation
+            if (x.search(seq))
+            {
+              description = x.stringMatched(1);
+              seq = x.stringMatched(2);
+            }
+            // sequence id with from-to fields
 
-                seqs.put(x.stringMatched(1), ns);
+            Hashtable ann;
+            // Get an object with all the annotations for this sequence
+            if (seqAnn.containsKey(acc))
+            {
+              //logger.debug("Found annotations for " + acc);
+              ann = (Hashtable) seqAnn.get(acc);
             }
             else
             {
-                String annType = r.stringMatched(1);
-                String annContent = r.stringMatched(2);
+              //logger.debug("Creating new annotations holder for " + acc);
+              ann = new Hashtable();
+              seqAnn.put(acc, ann);
+            }
 
-                //System.err.println("type:" + annType + " content: " + annContent);
+            Hashtable features;
+            // Get an object with all the content for an annotation
+            if (ann.containsKey("features"))
+            {
+              //logger.debug("Found features for " + acc);
+              features = (Hashtable) ann.get("features");
+            }
+            else
+            {
+              //logger.debug("Creating new features holder for " + acc);
+              features = new Hashtable();
+              ann.put("features", features);
+            }
 
-                if (annType.equals("GF"))
-                {
-                    /* Generic per-File annotation, free text
-                     * Magic features:
-                     * #=GF NH <tree in New Hampshire eXtended format>
-                     * #=GF TN <Unique identifier for the next tree>
-                     * Pfam descriptions:
-                        7. DESCRIPTION OF FIELDS
-
-                           Compulsory fields:
-                           ------------------
-
-                           AC   Accession number:           Accession number in form PFxxxxx.version or PBxxxxxx.
-                           ID   Identification:             One word name for family.
-                           DE   Definition:                 Short description of family.
-                           AU   Author:                     Authors of the entry.
-                           SE   Source of seed:             The source suggesting the seed members belong to one family.
-                           GA   Gathering method:           Search threshold to build the full alignment.
-                           TC   Trusted Cutoff:             Lowest sequence score and domain score of match in the full alignment.
-                           NC   Noise Cutoff:               Highest sequence score and domain score of match not in full alignment.
-                           TP   Type:                       Type of family -- presently Family, Domain, Motif or Repeat.
-                           SQ   Sequence:                   Number of sequences in alignment.
-                           AM   Alignment Method        The order ls and fs hits are aligned to the model to build the full align.
-                           //                               End of alignment.
-
-                           Optional fields:
-                           ----------------
-
-                           DC   Database Comment:           Comment about database reference.
-                           DR   Database Reference:         Reference to external database.
-                           RC   Reference Comment:          Comment about literature reference.
-                           RN   Reference Number:           Reference Number.
-                           RM   Reference Medline:          Eight digit medline UI number.
-                           RT   Reference Title:            Reference Title.
-                           RA   Reference Author:           Reference Author
-                           RL   Reference Location:         Journal location.
-                           PI   Previous identifier:        Record of all previous ID lines.
-                           KW   Keywords:                   Keywords.
-                           CC   Comment:                    Comments.
-                           NE   Pfam accession:         Indicates a nested domain.
-                           NL   Location:                   Location of nested domains - sequence ID, start and end of insert.
-
-                           Obsolete fields:
-                           -----------
-                           AL   Alignment method of seed:   The method used to align the seed members.
-                     */
-                    // Let's save the annotations, maybe we'll be able to do something with them later...
-                    Regex an = new Regex("(\\w+)\\s*(.*)");
-                    if (an.search(annContent)) alAnn.put(an.stringMatched(1), an.stringMatched(2));
-                }
-                else if(annType.equals("GS"))
-                {
-                    // Generic per-Sequence annotation, free text
-                    /* Pfam uses these features:
-                        Feature                    Description
-                        ---------------------      -----------
-                        AC <accession>             ACcession number
-                        DE <freetext>              DEscription
-                        DR <db>; <accession>;      Database Reference
-                        OS <organism>              OrganiSm (species)
-                        OC <clade>                 Organism Classification (clade, etc.)
-                        LO <look>                  Look (Color, etc.)
-                    */
-                    if (s.search(annContent))
-                    {
-                        String acc = s.stringMatched(1);
-                        String type = s.stringMatched(2);
-                        String content = s.stringMatched(3);
-
-                        Hashtable ann;
-                        if (seqAnn.containsKey(acc))
-                        {
-                            ann = (Hashtable) seqAnn.get(acc);
-                        }
-                        else
-                        {
-                            ann = new Hashtable();
-                        }
-                        ann.put(type, content);
-                        seqAnn.put(acc, ann);
-                    }
-                    else
-                    {
-                        throw new IOException("Error parsing " + line);
-                    }
-                }
-                else if(annType.equals("GC"))
-                {
-                  System.out.println(annContent);
-                    // Generic per-Column annotation, exactly 1 char per column
-                }
-                else if(annType.equals("GR"))
-                {
-                    // Generic per-Sequence AND per-Column markup, exactly 1 char per column
-                    /*
-                        Feature   Description            Markup letters
-                        -------   -----------            --------------
-                        SS        Secondary Structure    [HGIEBTSCX]
-                        SA        Surface Accessibility  [0-9X]
-                                      (0=0%-10%; ...; 9=90%-100%)
-                        TM        TransMembrane          [Mio]
-                        PP        Posterior Probability  [0-9*]
-                                      (0=0.00-0.05; 1=0.05-0.15; *=0.95-1.00)
-                        LI        LIgand binding         [*]
-                        AS        Active Site            [*]
-                        IN        INtron (in or after)   [0-2]
-                     */
-                    if (s.search(annContent))
-                    {
-                        String acc = s.stringMatched(1);
-                        String type = s.stringMatched(2);
-                        String seq = s.stringMatched(3);
-                        String description = new String();
-
-                        // Check for additional information about the current annotation
-                        if (x.search(seq))
-                        {
-                            description = x.stringMatched(1);
-                            seq = x.stringMatched(2);
-                        }
-                        // sequence id with from-to fields
-
-                        Hashtable ann;
-                        // Get an object with all the annotations for this sequence
-                        if (seqAnn.containsKey(acc))
-                        {
-                            //logger.debug("Found annotations for " + acc);
-                            ann = (Hashtable) seqAnn.get(acc);
-                        }
-                        else
-                        {
-                            //logger.debug("Creating new annotations holder for " + acc);
-                            ann = new Hashtable();
-                            seqAnn.put(acc, ann);
-                        }
-
-                        Hashtable features;
-                        // Get an object with all the content for an annotation
-                        if (ann.containsKey("features"))
-                        {
-                            //logger.debug("Found features for " + acc);
-                            features = (Hashtable) ann.get("features");
-                        }
-                        else
-                        {
-                            //logger.debug("Creating new features holder for " + acc);
-                            features = new Hashtable();
-                            ann.put("features", features);
-                        }
-
-                        Hashtable content;
-                        if (features.containsKey(this.id2type(type)))
-                        {
-                            //logger.debug("Found content for " + this.id2type(type));
-                            content = (Hashtable) features.get(this.id2type(type));
-                        }
-                        else
-                        {
-                            //logger.debug("Creating new content holder for " + this.id2type(type));
-                            content = new Hashtable();
-                            features.put(this.id2type(type), content);
-                        }
-                        String ns = (String) content.get(description);
-                        if (ns == null) ns = "";
-                        ns += seq;
-                        content.put(description, seq);
-                    }
-                    else
-                    {
-                        throw new IOException("Error parsing " + line);
-                    }
-                }
-                else
-                {
-                    throw new IOException("Unknown annotation detected: " + annType + " " + annContent);
-                }
+            Hashtable content;
+            if (features.containsKey(this.id2type(type)))
+            {
+              //logger.debug("Found content for " + this.id2type(type));
+              content = (Hashtable) features.get(this.id2type(type));
             }
+            else
+            {
+              //logger.debug("Creating new content holder for " + this.id2type(type));
+              content = new Hashtable();
+              features.put(this.id2type(type), content);
+            }
+            String ns = (String) content.get(description);
+            if (ns == null)
+            {
+              ns = "";
+            }
+            ns += seq;
+            content.put(description, seq);
+          }
+          else
+          {
+            throw new IOException("Error parsing " + line);
+          }
+        }
+        else
+        {
+          throw new IOException("Unknown annotation detected: " + annType + " " +
+                                annContent);
         }
+      }
     }
-
-    public static String print(SequenceI[] s)
+  }
+
+  public static String print(SequenceI[] s)
+  {
+    return "not yet implemented";
+  }
+
+  public String print()
+  {
+    return print(getSeqsAsArray());
+  }
+
+  private String id2type(String id)
+  {
+    // GR ids
+    if (id.equals("SS"))
     {
-        return "not yet implemented";
+      return "secondary structure";
     }
-
-    public String print()
+    else if (id.equals("SA"))
     {
-        return print(getSeqsAsArray());
+      return "surface accessibility";
     }
-
-    private String id2type(String id)
+    else if (id.equals("TM"))
+    {
+      return "transmembrane";
+    }
+    else if (id.equals("PP"))
+    {
+      return "posterior probability";
+    }
+    else if (id.equals("LI"))
+    {
+      return "ligand binding";
+    }
+    else if (id.equals("AS"))
+    {
+      return "active site";
+    }
+    else if (id.equals("IN"))
+    {
+      return "intron";
+    }
+    else if (id.equals("IR"))
+    {
+      return "interacting residue";
+    }
+    // GS ids
+    else if (id.equals("AC"))
+    {
+      return "accession";
+    }
+    else if (id.equals("OS"))
+    {
+      return "organism";
+    }
+    else if (id.equals("CL"))
+    {
+      return "class";
+    }
+    else if (id.equals("DE"))
+    {
+      return "description";
+    }
+    else if (id.equals("DR"))
+    {
+      return "reference";
+    }
+    else if (id.equals("LO"))
+    {
+      return "look";
+    }
+    else
     {
-        // GR ids
-        if (id.equals("SS")) return "secondary structure";
-        else if (id.equals("SA")) return "surface accessibility";
-        else if (id.equals("TM")) return "transmembrane";
-        else if (id.equals("PP")) return "posterior probability";
-        else if (id.equals("LI")) return "ligand binding";
-        else if (id.equals("AS")) return "active site";
-        else if (id.equals("IN")) return "intron";
-        else if (id.equals("IR")) return "interacting residue";
-        // GS ids
-        else if (id.equals("AC")) return "accession";
-        else if (id.equals("OS")) return "organism";
-        else if (id.equals("CL")) return "class";
-        else if (id.equals("DE")) return "description";
-        else if (id.equals("DR")) return "reference";
-        else if (id.equals("LO")) return "look";
-        else return null;
+      return null;
     }
+  }
 }
diff --git a/src/jalview/io/VamsasDatastore.java b/src/jalview/io/VamsasDatastore.java
index 6869169..f1cba4f 100755
--- a/src/jalview/io/VamsasDatastore.java
+++ b/src/jalview/io/VamsasDatastore.java
@@ -69,7 +69,8 @@ import org.vamsas.test.simpleclient.ClientDoc;
  *
  */
 
-public class VamsasDatastore {
+public class VamsasDatastore
+{
   Entry provEntry = null;
 
   // AlignViewport av;
@@ -84,8 +85,9 @@ public class VamsasDatastore {
   IdentityHashMap jv2vobj;
 
   public VamsasDatastore(ClientDoc cdoc, Hashtable vobj2jv,
-      IdentityHashMap jv2vobj, Entry provEntry) {
-      this.cdoc = cdoc;
+                         IdentityHashMap jv2vobj, Entry provEntry)
+  {
+    this.cdoc = cdoc;
     this.vobj2jv = vobj2jv;
     this.jv2vobj = jv2vobj;
     this.provEntry = provEntry;
@@ -110,9 +112,12 @@ public class VamsasDatastore {
   /**
    * @return the Vobject bound to Jalview datamodel object
    */
-  protected Vobject getjv2vObj(Object jvobj) {
+  protected Vobject getjv2vObj(Object jvobj)
+  {
     if (jv2vobj.containsKey(jvobj))
-      return cdoc.getObject((VorbaId) jv2vobj.get(jvobj));
+    {
+      return cdoc.getObject( (VorbaId) jv2vobj.get(jvobj));
+    }
     return null;
   }
 
@@ -121,38 +126,53 @@ public class VamsasDatastore {
    * @param vobj
    * @return Jalview datamodel object bound to the vamsas document object
    */
-  protected Object getvObj2jv(org.vamsas.client.Vobject vobj) {
+  protected Object getvObj2jv(org.vamsas.client.Vobject vobj)
+  {
     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()))
+    {
       return vobj2jv.get(vobj.getVorbaId());
+    }
     return null;
   }
 
-  protected void bindjvvobj(Object jvobj, org.vamsas.client.Vobject vobj) {
+  protected void bindjvvobj(Object jvobj, org.vamsas.client.Vobject vobj)
+  {
     VorbaId id = vobj.getVorbaId();
     if (id == null)
     {
       id = cdoc.registerObject(vobj);
-      if (id==null || vobj.getVorbaId()==null)
-        Cache.log.error("Failed to get id for "+(vobj.isRegisterable() ? "registerable" : "unregisterable") +" object "+vobj);
+      if (id == null || vobj.getVorbaId() == null)
+      {
+        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)) {
-      Cache.log.debug("Warning? Overwriting existing vamsas id binding for "+vobj.getVorbaId(), new Exception("Overwriting vamsas id binding."));
+    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."));
     }
-    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."));
+      Cache.log.debug(
+          "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"));
-    }*/
+         }*/
     // we just update the hash's regardless!
     vobj2jv.put(vobj.getVorbaId(), jvobj);
     // JBPNote - better implementing a hybrid invertible hash.
@@ -165,7 +185,8 @@ public class VamsasDatastore {
    * @param av alignViewport to be stored
    * @param aFtitle title for alignment
    */
-  public void storeVAMSAS(AlignViewport av, String aFtitle) {
+  public void storeVAMSAS(AlignViewport av, String aFtitle)
+  {
     try
     {
       jalview.datamodel.AlignmentI jal = av.getAlignment();
@@ -200,7 +221,8 @@ public class VamsasDatastore {
       // flag.
       // this *will* break when alignment contains both nucleotide and amino
       // acid sequences.
-      String dict = jal.isNucleotide() ? org.vamsas.objects.utils.SymbolDictionary.STANDARD_NA
+      String dict = jal.isNucleotide() ?
+          org.vamsas.objects.utils.SymbolDictionary.STANDARD_NA
           : org.vamsas.objects.utils.SymbolDictionary.STANDARD_AA;
       for (int i = 0; i < jal.getHeight(); i++)
       {
@@ -233,8 +255,9 @@ public class VamsasDatastore {
 
           for (int sf = 0; sf < sfSize; sf++)
           {
-            jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) sq
-            .getSequenceFeatures()[sf];
+            jalview.datamodel.SequenceFeature feature = (jalview.datamodel.
+                SequenceFeature) sq
+                .getSequenceFeatures()[sf];
 
             DataSetAnnotations dsa = (DataSetAnnotations) getjv2vObj(feature);
             if (dsa == null)
@@ -287,7 +310,7 @@ public class VamsasDatastore {
               // contain more residues than were originally referenced - we must
               // then make a number of dataset sequence entries
               System.out
-              .println("update dataset sequence database references.");
+                  .println("update dataset sequence database references.");
             }
           }
 
@@ -305,7 +328,9 @@ public class VamsasDatastore {
         alignment = new Alignment();
         bindjvvobj(av, alignment);
         if (alignment.getProvenance() == null)
+        {
           alignment.setProvenance(new Provenance());
+        }
         addProvenance(alignment.getProvenance(), "added"); // TODO: insert some
         // sensible source
         // here
@@ -342,30 +367,33 @@ public class VamsasDatastore {
         else
         {
           System.out
-          .println("update edited alignment to new alignment in document.");
+              .println("update edited alignment to new alignment in document.");
         }
       }
       // ////////////////////////////////////////////
       // SAVE Alignment Sequence Features
-      for (int i = 0, iSize = alignment.getAlignmentSequenceCount(); i < iSize; i++)
+      for (int i = 0, iSize = alignment.getAlignmentSequenceCount(); i < iSize;
+           i++)
       {
         AlignmentSequence valseq;
         SequenceI alseq = (SequenceI) getvObj2jv(valseq = alignment
-            .getAlignmentSequence(i));
+                                                 .getAlignmentSequence(i));
         if (alseq != null && alseq.getSequenceFeatures() != null)
         {
           jalview.datamodel.SequenceFeature[] features = alseq
-          .getSequenceFeatures();
+              .getSequenceFeatures();
           for (int f = 0; f < features.length; f++)
           {
             if (features[f] != null)
             {
-              AlignmentSequenceAnnotation valseqf = (AlignmentSequenceAnnotation) getjv2vObj(features[i]);
+              AlignmentSequenceAnnotation valseqf = (
+                  AlignmentSequenceAnnotation) getjv2vObj(features[i]);
               if (valseqf == null)
               {
 
-                valseqf = (AlignmentSequenceAnnotation) getDSAnnotationFromJalview(
-                    new AlignmentSequenceAnnotation(), features[i]);
+                valseqf = (AlignmentSequenceAnnotation)
+                    getDSAnnotationFromJalview(
+                        new AlignmentSequenceAnnotation(), features[i]);
                 if (valseqf.getProvenance() == null)
                 {
                   valseqf.setProvenance(new Provenance());
@@ -387,7 +415,7 @@ public class VamsasDatastore {
       if (jal.getAlignmentAnnotation() != null)
       {
         jalview.datamodel.AlignmentAnnotation[] aa = jal
-        .getAlignmentAnnotation();
+            .getAlignmentAnnotation();
         java.util.HashMap AlSeqMaps = new HashMap(); // stores int maps from
         // alignment columns to
         // sequence positions.
@@ -399,8 +427,11 @@ public class VamsasDatastore {
           }
           if (aa[i].sequenceRef != null)
           {
-            org.vamsas.objects.core.AlignmentSequence alsref = (org.vamsas.objects.core.AlignmentSequence) getjv2vObj(aa[i].sequenceRef);
-            org.vamsas.objects.core.AlignmentSequenceAnnotation an = (org.vamsas.objects.core.AlignmentSequenceAnnotation) getjv2vObj(aa[i]);
+            org.vamsas.objects.core.AlignmentSequence alsref = (org.vamsas.
+                objects.core.AlignmentSequence) getjv2vObj(aa[i].sequenceRef);
+            org.vamsas.objects.core.AlignmentSequenceAnnotation an = (org.
+                vamsas.objects.core.AlignmentSequenceAnnotation) getjv2vObj(aa[
+                i]);
             int[] gapMap = null;
             if (AlSeqMaps.containsKey(aa[i].sequenceRef))
             {
@@ -412,7 +443,9 @@ public class VamsasDatastore {
               // map from alignment position to sequence position.
               int[] sgapMap = aa[i].sequenceRef.gapMap();
               for (int a = 0; a < sgapMap.length; a++)
+              {
                 gapMap[sgapMap[a]] = a;
+              }
             }
             if (an == null)
             {
@@ -422,17 +455,21 @@ public class VamsasDatastore {
               vSeg.setInclusive(true);
               vSeg.setEnd(gapMap.length);
               an.addSeg(vSeg);
-              an.setType("jalview:SecondaryStructurePrediction");// TODO: better fix this rough guess ;)
+              an.setType("jalview:SecondaryStructurePrediction"); // TODO: better fix this rough guess ;)
               alsref.addAlignmentSequenceAnnotation(an);
-              bindjvvobj(aa[i],an);
+              bindjvvobj(aa[i], an);
               // LATER: much of this is verbatim from the alignmentAnnotation
               // method below. suggests refactoring to make rangeAnnotation the
               // base class
               an.setDescription(aa[i].description);
               if (aa[i].graph > 0)
+              {
                 an.setGraph(true); // aa[i].graph);
+              }
               else
+              {
                 an.setGraph(false);
+              }
               an.setLabel(aa[i].label);
               an.setProvenance(dummyProvenance()); // get provenance as user
               // created, or jnet, or
@@ -457,25 +494,30 @@ public class VamsasDatastore {
                 ae.setDescription(aa[i].annotations[a].description);
                 ae.addGlyph(new Glyph());
                 ae.getGlyph(0)
-                .setContent(aa[i].annotations[a].displayCharacter); // assume
+                    .setContent(aa[i].annotations[a].displayCharacter); // assume
                 // jax-b
                 // takes
                 // care
                 // of
                 // utf8
                 // translation
-                if (aa[i].graph!=jalview.datamodel.AlignmentAnnotation.NO_GRAPH)
+                if (aa[i].graph !=
+                    jalview.datamodel.AlignmentAnnotation.NO_GRAPH)
+                {
                   ae.addValue(aa[i].annotations[a].value);
-                ae.setPosition(gapMap[a]+1); // position w.r.t. AlignmentSequence
+                }
+                ae.setPosition(gapMap[a] + 1); // position w.r.t. AlignmentSequence
                 // symbols
                 if (aa[i].annotations[a].secondaryStructure != ' ')
                 {
                   // we only write an annotation where it really exists.
                   Glyph ss = new Glyph();
                   ss
-                  .setDict(org.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE);
+                      .setDict(org.vamsas.objects.utils.GlyphDictionary.
+                               PROTEIN_SS_3STATE);
                   ss.setContent(String
-                      .valueOf(aa[i].annotations[a].secondaryStructure));
+                                .valueOf(aa[i].annotations[a].
+                                         secondaryStructure));
                   ae.addGlyph(ss);
                 }
                 an.addAnnotationElement(ae);
@@ -493,14 +535,16 @@ public class VamsasDatastore {
               {
                 // verify existing alignment sequence annotation is up to date
                 System.out
-                .println("make new alignment sequence annotation if modification has happened.");
+                    .println(
+                    "make new alignment sequence annotation if modification has happened.");
               }
             }
           }
           else
           {
             // add Alignment Annotation
-            org.vamsas.objects.core.AlignmentAnnotation an = (org.vamsas.objects.core.AlignmentAnnotation) getjv2vObj(aa[i]);
+            org.vamsas.objects.core.AlignmentAnnotation an = (org.vamsas.
+                objects.core.AlignmentAnnotation) getjv2vObj(aa[i]);
             if (an == null)
             {
               an = new org.vamsas.objects.core.AlignmentAnnotation();
@@ -513,27 +557,32 @@ public class VamsasDatastore {
               vSeg.setEnd(jal.getWidth());
               an.addSeg(vSeg);
               if (aa[i].graph > 0)
+              {
                 an.setGraph(true); // aa[i].graph);
+              }
               an.setLabel(aa[i].label);
               an.setProvenance(dummyProvenance());
-              if (aa[i].graph!=aa[i].NO_GRAPH) {
+              if (aa[i].graph != aa[i].NO_GRAPH)
+              {
                 an.setGroup(Integer.toString(aa[i].graphGroup)); // // JBPNote -
                 // originally we
-              // were going to
-              // store
-              // graphGroup in
-              // the Jalview
-              // specific
-              // bits.
+                // were going to
+                // store
+                // graphGroup in
+                // the Jalview
+                // specific
+                // bits.
                 an.setGraph(true);
-              } else {
+              }
+              else
+              {
                 an.setGraph(false);
               }
               AnnotationElement ae;
 
               for (int a = 0; a < aa[i].annotations.length; a++)
               {
-                if ((aa[i] == null) || (aa[i].annotations[a] == null))
+                if ( (aa[i] == null) || (aa[i].annotations[a] == null))
                 {
                   continue;
                 }
@@ -542,7 +591,7 @@ public class VamsasDatastore {
                 ae.setDescription(aa[i].annotations[a].description);
                 ae.addGlyph(new Glyph());
                 ae.getGlyph(0)
-                .setContent(aa[i].annotations[a].displayCharacter); // assume
+                    .setContent(aa[i].annotations[a].displayCharacter); // assume
                 // jax-b
                 // takes
                 // care
@@ -550,27 +599,34 @@ public class VamsasDatastore {
                 // utf8
                 // translation
                 ae.addValue(aa[i].annotations[a].value);
-                ae.setPosition(a+1);
+                ae.setPosition(a + 1);
                 if (aa[i].annotations[a].secondaryStructure != ' ')
                 {
                   Glyph ss = new Glyph();
                   ss
-                  .setDict(org.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE);
+                      .setDict(org.vamsas.objects.utils.GlyphDictionary.
+                               PROTEIN_SS_3STATE);
                   ss.setContent(String
-                      .valueOf(aa[i].annotations[a].secondaryStructure));
+                                .valueOf(aa[i].annotations[a].
+                                         secondaryStructure));
                   ae.addGlyph(ss);
                 }
                 an.addAnnotationElement(ae);
               }
-              if (aa[i].editable) {
+              if (aa[i].editable)
+              {
                 //an.addProperty(newProperty("jalview:editable", null, "true"));
                 an.setModifiable(true);
               }
-              if (aa[i].graph!=jalview.datamodel.AlignmentAnnotation.NO_GRAPH) {
+              if (aa[i].graph != jalview.datamodel.AlignmentAnnotation.NO_GRAPH)
+              {
                 an.setGraph(true);
                 an.setGroup(Integer.toString(aa[i].graphGroup));
-                an.addProperty(newProperty("jalview:graphType",null,
-                    ((aa[i].graph==jalview.datamodel.AlignmentAnnotation.BAR_GRAPH) ? "BAR_GRAPH" : "LINE_GRAPH")));
+                an.addProperty(newProperty("jalview:graphType", null,
+                                           ( (aa[i].graph ==
+                                              jalview.datamodel.AlignmentAnnotation.
+                                              BAR_GRAPH) ? "BAR_GRAPH" :
+                                            "LINE_GRAPH")));
 
                 /** and on and on..
                  vProperty=new Property();
@@ -585,7 +641,8 @@ public class VamsasDatastore {
               if (an.getModifiable())
               {
                 // verify annotation - update (perhaps)
-                Cache.log.info("update alignment sequence annotation. not yet implemented.");
+                Cache.log.info(
+                    "update alignment sequence annotation. not yet implemented.");
               }
               else
               {
@@ -639,7 +696,7 @@ public class VamsasDatastore {
                 else
                 {
                   System.out
-                  .println("Add modified tree as new tree in document.");
+                      .println("Add modified tree as new tree in document.");
                 }
               }
             }
@@ -657,13 +714,18 @@ public class VamsasDatastore {
 
   }
 
-  private Property newProperty(String name, String type, String content) {
-    Property vProperty=new Property();
+  private Property newProperty(String name, String type, String content)
+  {
+    Property vProperty = new Property();
     vProperty.setName(name);
-    if (type!=null)
+    if (type != null)
+    {
       vProperty.setType(type);
+    }
     else
+    {
       vProperty.setType("String");
+    }
     vProperty.setContent(content);
     return vProperty;
   }
@@ -678,7 +740,8 @@ public class VamsasDatastore {
    * @return
    */
   private RangeAnnotation getDSAnnotationFromJalview(RangeAnnotation dsa,
-      SequenceFeature feature) {
+      SequenceFeature feature)
+  {
     dsa.setType(feature.getType());
     Seg vSeg = new Seg();
     vSeg.setStart(feature.getBegin());
@@ -697,9 +760,13 @@ public class VamsasDatastore {
         {
           Link vLink = new Link();
           if (sep > 0)
+          {
             vLink.setContent(link.substring(0, sep - 1));
+          }
           else
+          {
             vLink.setContent("");
+          }
           vLink.setHref(link.substring(sep + 1)); // TODO: validate href.
           dsa.addLink(vLink);
         }
@@ -717,10 +784,11 @@ public class VamsasDatastore {
    * @param tp
    * @return
    */
-  private Provenance makeTreeProvenance(AlignmentI jal, TreePanel tp) {
+  private Provenance makeTreeProvenance(AlignmentI jal, TreePanel tp)
+  {
     Provenance prov = new Provenance();
     prov.addEntry(new Entry());
-    prov.getEntry(0).setAction("imported "+tp.getTitle());
+    prov.getEntry(0).setAction("imported " + tp.getTitle());
     prov.getEntry(0).setUser(provEntry.getUser());
     prov.getEntry(0).setApp(provEntry.getApp());
     prov.getEntry(0).setDate(provEntry.getDate());
@@ -732,7 +800,7 @@ public class VamsasDatastore {
       // the document.
       // vInput.setObjRef(getjv2vObj(jal));
       vInput.setObjRef(getjv2vObj(tp.getViewPort()));
-      prov.getEntry(0).setAction("created "+tp.getTitle());
+      prov.getEntry(0).setAction("created " + tp.getTitle());
       prov.getEntry(0).addInput(vInput);
       vInput.setName("jalview:seqdist");
       prov.getEntry(0).addParam(new Param());
@@ -742,12 +810,12 @@ public class VamsasDatastore {
 
       int ranges[] = tp.getTree().seqData.getVisibleContigs();
       // VisibleContigs are with respect to alignment coordinates. Still need offsets
-      int start= tp.getTree().seqData.getAlignmentOrigin();
+      int start = tp.getTree().seqData.getAlignmentOrigin();
       for (int r = 0; r < ranges.length; r += 2)
       {
         Seg visSeg = new Seg();
-        visSeg.setStart(1+start+ranges[r]);
-        visSeg.setEnd(start+ranges[r + 1]);
+        visSeg.setStart(1 + start + ranges[r]);
+        visSeg.setEnd(start + ranges[r + 1]);
         visSeg.setInclusive(true);
         vInput.addSeg(visSeg);
       }
@@ -761,47 +829,56 @@ public class VamsasDatastore {
    * @return Object[] { AlignmentView, AlignmentI - reference alignment for
    *         input }
    */
-  private Object[] recoverInputData(Provenance tp) {
+  private Object[] recoverInputData(Provenance tp)
+  {
     for (int pe = 0; pe < tp.getEntryCount(); pe++)
     {
       if (tp.getEntry(pe).getInputCount() > 0)
       {
         if (tp.getEntry(pe).getInputCount() > 1)
+        {
           Cache.log.warn("Ignoring additional input spec in provenance entry "
-              + tp.getEntry(pe).toString());
+                         + tp.getEntry(pe).toString());
+        }
         // LATER: deal sensibly with multiple inputs.
         Input vInput = tp.getEntry(pe).getInput(0);
         if (vInput.getObjRef() instanceof org.vamsas.objects.core.Alignment)
         {
           // recover an AlignmentView for the input data
-          AlignViewport javport = (AlignViewport) getvObj2jv((org.vamsas.client.Vobject) vInput
+          AlignViewport javport = (AlignViewport) getvObj2jv( (org.vamsas.
+              client.Vobject) vInput
               .getObjRef());
           jalview.datamodel.AlignmentI jal = javport.getAlignment();
-          jalview.datamodel.CigarArray view = javport.getAlignment().getCompactAlignment();
+          jalview.datamodel.CigarArray view = javport.getAlignment().
+              getCompactAlignment();
           int from = 1, to = jal.getWidth();
-          int offset=0; // deleteRange modifies its frame of reference
+          int offset = 0; // deleteRange modifies its frame of reference
           for (int r = 0, s = vInput.getSegCount(); r < s; r++)
           {
             Seg visSeg = vInput.getSeg(r);
-            int se[] = getSegRange(visSeg,true); // jalview doesn't do bidirection alignments yet.
+            int se[] = getSegRange(visSeg, true); // jalview doesn't do bidirection alignments yet.
             if (to < se[1])
+            {
               Cache.log.warn("Ignoring invalid segment in InputData spec.");
+            }
             else
             {
               if (se[0] > from)
               {
-                view.deleteRange(offset+from-1, offset+se[0] - 2);
-                offset-=se[0]-from;
+                view.deleteRange(offset + from - 1, offset + se[0] - 2);
+                offset -= se[0] - from;
               }
               from = se[1] + 1;
             }
           }
           if (from < to)
           {
-            view.deleteRange(offset+from-1, offset+to-1); // final deletion - TODO: check off by
+            view.deleteRange(offset + from - 1, offset + to - 1); // final deletion - TODO: check off by
             // one for to
           }
-          return new Object[] { new AlignmentView(view), jal };
+          return new Object[]
+              {
+              new AlignmentView(view), jal};
         }
       }
     }
@@ -817,21 +894,24 @@ public class VamsasDatastore {
    * @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.
    */
-  private int[] getSegRange(Seg visSeg, boolean ensureDirection) {
+  private int[] getSegRange(Seg visSeg, boolean ensureDirection)
+  {
     boolean incl = visSeg.getInclusive();
     // adjust for inclusive flag.
     int pol = (visSeg.getStart() <= visSeg.getEnd()) ? 1 : -1; // polarity of
     // region.
     int start = visSeg.getStart() + (incl ? 0 : pol);
     int end = visSeg.getEnd() + (incl ? 0 : -pol);
-    if (ensureDirection && pol==-1)
+    if (ensureDirection && pol == -1)
     {
       // jalview doesn't deal with inverted ranges, yet.
       int t = end;
       end = start;
       start = t;
     }
-    return new int[] { start, end, pol<0 ? 1 : 0 };
+    return new int[]
+        {
+        start, end, pol < 0 ? 1 : 0};
   }
 
   /**
@@ -839,11 +919,13 @@ public class VamsasDatastore {
    * @param annotation
    * @return true if annotation is not to be stored in document
    */
-  private boolean isJalviewOnly(AlignmentAnnotation annotation) {
+  private boolean isJalviewOnly(AlignmentAnnotation annotation)
+  {
     return annotation.label.equals("Quality")
-    || annotation.label.equals("Conservation")
-    || annotation.label.equals("Consensus");
+        || annotation.label.equals("Conservation")
+        || annotation.label.equals("Consensus");
   }
+
   /**
    * This will return the first AlignFrame viewing AlignViewport av.
    * It will break if there are more than one AlignFrames viewing a particular av.
@@ -851,89 +933,112 @@ public class VamsasDatastore {
    * @param av
    * @return alignFrame for av
    */
-  public AlignFrame getAlignFrameFor(AlignViewport av) {
+  public AlignFrame getAlignFrameFor(AlignViewport av)
+  {
     if (Desktop.desktop != null)
     {
       javax.swing.JInternalFrame[] frames = Desktop.desktop.getAllFrames();
 
       for (int t = 0; t < frames.length; t++)
       {
-        if (frames[t] instanceof AlignFrame) {
-          if (((AlignFrame) frames[t]).getViewport()==av)
+        if (frames[t] instanceof AlignFrame)
+        {
+          if ( ( (AlignFrame) frames[t]).getViewport() == av)
+          {
             return (AlignFrame) frames[t];
+          }
         }
       }
     }
     return null;
   }
-  public void updateToJalview() {
+
+  public void updateToJalview()
+  {
     VAMSAS _roots[] = cdoc.getVamsasRoots();
 
-    for (int _root = 0; _root<_roots.length; _root++) {
+    for (int _root = 0; _root < _roots.length; _root++)
+    {
       VAMSAS root = _roots[_root];
-      boolean newds=false;
-      for (int _ds=0,_nds=root.getDataSetCount(); _ds<_nds; _ds++) {
+      boolean newds = false;
+      for (int _ds = 0, _nds = root.getDataSetCount(); _ds < _nds; _ds++)
+      {
         // ///////////////////////////////////
         // ///LOAD DATASET
         DataSet dataset = root.getDataSet(_ds);
         int i, iSize = dataset.getSequenceCount();
         Vector dsseqs;
-        jalview.datamodel.Alignment jdataset = (jalview.datamodel.Alignment) getvObj2jv(dataset);
-        int jremain=0;
-        if (jdataset==null) {
+        jalview.datamodel.Alignment jdataset = (jalview.datamodel.Alignment)
+            getvObj2jv(dataset);
+        int jremain = 0;
+        if (jdataset == null)
+        {
           Cache.log.debug("Initialising new jalview dataset fields");
-          newds=true;
-          dsseqs=new Vector();
-        } else {
+          newds = true;
+          dsseqs = new Vector();
+        }
+        else
+        {
           Cache.log.debug("Update jalview dataset from vamsas.");
-          jremain=jdataset.getHeight();
-          dsseqs=jdataset.getSequences();
+          jremain = jdataset.getHeight();
+          dsseqs = jdataset.getSequences();
         }
 
         // TODO: test sequence merging - we preserve existing non vamsas
         // sequences but add in any new vamsas ones, and don't yet update any
         // sequence attributes
-        for (i = 0; i < iSize ; i++)
+        for (i = 0; i < iSize; i++)
         {
           Sequence vdseq = dataset.getSequence(i);
           jalview.datamodel.SequenceI dsseq = (SequenceI) getvObj2jv(vdseq);
-          if (dsseq!=null) {
+          if (dsseq != null)
+          {
             if (!dsseq.getSequence().equals(vdseq.getSequence()))
-              throw new Error("Broken! - mismatch of dataset sequence and jalview internal dataset sequence.");
+            {
+              throw new Error(
+                  "Broken! - mismatch of dataset sequence and jalview internal dataset sequence.");
+            }
             jremain--;
-          } else {
+          }
+          else
+          {
             dsseq = new jalview.datamodel.Sequence(
                 dataset.getSequence(i).getName(),
                 dataset.getSequence(i).getSequence(),
                 dataset.getSequence(i).getStart(),
-                dataset.getSequence(i).getEnd()  );
+                dataset.getSequence(i).getEnd());
             dsseq.setDescription(dataset.getSequence(i).getDescription());
             bindjvvobj(dsseq, dataset.getSequence(i));
             dsseq.setVamsasId(dataset.getSequence(i).getVorbaId().getId());
             dsseqs.add(dsseq);
           }
-          if (vdseq.getDbRefCount()>0) {
-            DbRef [] dbref = vdseq.getDbRef();
-            for(int db=0; db<dbref.length; db++)
+          if (vdseq.getDbRefCount() > 0)
+          {
+            DbRef[] dbref = vdseq.getDbRef();
+            for (int db = 0; db < dbref.length; db++)
             {
-              jalview.datamodel.DBRefEntry dbr=(jalview.datamodel.DBRefEntry) getvObj2jv(dbref[db]);
-              if (dbr==null) {
+              jalview.datamodel.DBRefEntry dbr = (jalview.datamodel.DBRefEntry)
+                  getvObj2jv(dbref[db]);
+              if (dbr == null)
+              {
                 // add new dbref
-                dsseq.addDBRef(dbr= new jalview.datamodel.DBRefEntry
-                    (
-                        dbref[db].getSource().toString(),
-                        dbref[db].getVersion().toString(),
-                        dbref[db].getAccessionId().toString()));
+                dsseq.addDBRef(dbr = new jalview.datamodel.DBRefEntry
+                               (
+                                   dbref[db].getSource().toString(),
+                                   dbref[db].getVersion().toString(),
+                                   dbref[db].getAccessionId().toString()));
                 bindjvvobj(dbr, dbref[db]);
               }
             }
           }
         }
 
-        if (newds) {
+        if (newds)
+        {
           SequenceI[] seqs = new SequenceI[dsseqs.size()];
-          for (i=0,iSize=dsseqs.size(); i<iSize; i++) {
-            seqs[i]=(SequenceI) dsseqs.elementAt(i);
+          for (i = 0, iSize = dsseqs.size(); i < iSize; i++)
+          {
+            seqs[i] = (SequenceI) dsseqs.elementAt(i);
             dsseqs.setElementAt(null, i);
           }
           jdataset = new jalview.datamodel.Alignment(seqs);
@@ -942,20 +1047,33 @@ public class VamsasDatastore {
         }
         // ////////
         // add any new dataset sequence feature annotations
-        if (dataset.getDataSetAnnotations() != null) {
-          for (int dsa = 0; dsa < dataset.getDataSetAnnotationsCount(); dsa++) {
-            DataSetAnnotations dseta=dataset.getDataSetAnnotations(dsa);
-            SequenceI dsSeq=(SequenceI) getvObj2jv((Vobject) dseta.getSeqRef());
-            if (dsSeq==null) {
-              jalview.bin.Cache.log.warn("Couldn't resolve jalview sequenceI for dataset object reference "+((Vobject)dataset.getDataSetAnnotations(dsa).getSeqRef()).getVorbaId().getId());
-            } else {
-              if (dseta.getAnnotationElementCount()==0) {
-                jalview.datamodel.SequenceFeature sf=(jalview.datamodel.SequenceFeature) getvObj2jv(dseta);
-                if (sf==null) {
-                  dsSeq.addSequenceFeature(sf=getJalviewSeqFeature(dseta));
+        if (dataset.getDataSetAnnotations() != null)
+        {
+          for (int dsa = 0; dsa < dataset.getDataSetAnnotationsCount(); dsa++)
+          {
+            DataSetAnnotations dseta = dataset.getDataSetAnnotations(dsa);
+            SequenceI dsSeq = (SequenceI) getvObj2jv( (Vobject) dseta.getSeqRef());
+            if (dsSeq == null)
+            {
+              jalview.bin.Cache.log.warn(
+                  "Couldn't resolve jalview sequenceI for dataset object reference " +
+                  ( (Vobject) dataset.getDataSetAnnotations(dsa).getSeqRef()).
+                  getVorbaId().getId());
+            }
+            else
+            {
+              if (dseta.getAnnotationElementCount() == 0)
+              {
+                jalview.datamodel.SequenceFeature sf = (jalview.datamodel.
+                    SequenceFeature) getvObj2jv(dseta);
+                if (sf == null)
+                {
+                  dsSeq.addSequenceFeature(sf = getJalviewSeqFeature(dseta));
                   bindjvvobj(sf, dseta);
                 }
-              } else {
+              }
+              else
+              {
                 // TODO: deal with alignmentAnnotation style annotation
                 // appearing on dataset sequences.
                 // JBPNote: we could just add them to all alignments but
@@ -967,71 +1085,100 @@ public class VamsasDatastore {
           }
         }
 
-        if (dataset.getAlignmentCount()>0) {
+        if (dataset.getAlignmentCount() > 0)
+        {
           // LOAD ALIGNMENTS from DATASET
 
-          for (int al=0,nal=dataset.getAlignmentCount(); al<nal; al++) {
-            org.vamsas.objects.core.Alignment alignment = dataset.getAlignment(al);
+          for (int al = 0, nal = dataset.getAlignmentCount(); al < nal; al++)
+          {
+            org.vamsas.objects.core.Alignment alignment = dataset.getAlignment(
+                al);
             AlignViewport av = (AlignViewport) getvObj2jv(alignment);
-            jalview.datamodel.AlignmentI jal=null;
-            if (av!=null)
+            jalview.datamodel.AlignmentI jal = null;
+            if (av != null)
+            {
               jal = av.getAlignment();
+            }
             iSize = alignment.getAlignmentSequenceCount();
-            boolean newal=(jal==null) ? true : false;
-            Vector newasAnnots=new Vector();
-            char gapChar=' '; // default for new alignments read in from the document
-            if (jal!=null) {
-              dsseqs=jal.getSequences(); // for merge/update
-              gapChar=jal.getGapCharacter();
-            } else {
-              dsseqs=new Vector();
+            boolean newal = (jal == null) ? true : false;
+            Vector newasAnnots = new Vector();
+            char gapChar = ' '; // default for new alignments read in from the document
+            if (jal != null)
+            {
+              dsseqs = jal.getSequences(); // for merge/update
+              gapChar = jal.getGapCharacter();
             }
-            char valGapchar=alignment.getGapChar().charAt(0);
+            else
+            {
+              dsseqs = new Vector();
+            }
+            char valGapchar = alignment.getGapChar().charAt(0);
             for (i = 0; i < iSize; i++)
             {
               AlignmentSequence valseq = alignment.getAlignmentSequence(i);
               jalview.datamodel.SequenceI alseq = (SequenceI) getvObj2jv(valseq);
-              if (alseq!=null) {
+              if (alseq != null)
+              {
                 //TODO: upperCase/LowerCase situation here ? do we allow it ?
                 //if (!alseq.getSequence().equals(valseq.getSequence())) {
                 // throw new Error("Broken! - mismatch of dataset sequence and jalview internal dataset sequence.");
                 if (Cache.log.isDebugEnabled())
-                  Cache.log.debug("Updating apparently edited sequence "+alseq.getName());
+                {
+                  Cache.log.debug("Updating apparently edited sequence " +
+                                  alseq.getName());
+                }
                 // this might go *horribly* wrong
-                alseq.setSequence(new String(valseq.getSequence()).replace(valGapchar, gapChar));
+                alseq.setSequence(new String(valseq.getSequence()).replace(
+                    valGapchar, gapChar));
                 jremain--;
-              } else {
+              }
+              else
+              {
                 alseq = new jalview.datamodel.Sequence(
                     valseq.getName(),
                     valseq.getSequence().replace(valGapchar, gapChar),
                     valseq.getStart(),
-                    valseq.getEnd()  );
+                    valseq.getEnd());
 
-                Vobject datsetseq = (Vobject)valseq.getRefid();
-                if (datsetseq!=null) {
-                  alseq.setDatasetSequence((SequenceI)getvObj2jv(datsetseq)); // exceptions if AlignemntSequence reference isn't a simple SequenceI
-                } else {
-                  Cache.log.error("Invalid dataset sequence id (null) for alignment sequence "+valseq.getVorbaId());
+                Vobject datsetseq = (Vobject) valseq.getRefid();
+                if (datsetseq != null)
+                {
+                  alseq.setDatasetSequence( (SequenceI) getvObj2jv(datsetseq)); // exceptions if AlignemntSequence reference isn't a simple SequenceI
+                }
+                else
+                {
+                  Cache.log.error(
+                      "Invalid dataset sequence id (null) for alignment sequence " +
+                      valseq.getVorbaId());
                 }
                 bindjvvobj(alseq, valseq);
                 alseq.setVamsasId(valseq.getVorbaId().getId());
                 dsseqs.add(alseq);
               }
-              if (valseq.getAlignmentSequenceAnnotationCount()>0) {
-                AlignmentSequenceAnnotation[] vasannot=valseq.getAlignmentSequenceAnnotation();
-                for (int a=0; a<vasannot.length; a++) {
-                  jalview.datamodel.AlignmentAnnotation asa = (jalview.datamodel.AlignmentAnnotation) getvObj2jv(vasannot[a]); // TODO: 1:many jalview alignment sequence annotations
-                  if (asa==null) {
+              if (valseq.getAlignmentSequenceAnnotationCount() > 0)
+              {
+                AlignmentSequenceAnnotation[] vasannot = valseq.
+                    getAlignmentSequenceAnnotation();
+                for (int a = 0; a < vasannot.length; a++)
+                {
+                  jalview.datamodel.AlignmentAnnotation asa = (jalview.
+                      datamodel.AlignmentAnnotation) getvObj2jv(vasannot[a]); // TODO: 1:many jalview alignment sequence annotations
+                  if (asa == null)
+                  {
                     int se[] = getBounds(vasannot[a]);
                     asa = getjAlignmentAnnotation(jal, vasannot[a]);
-                    asa.sequenceRef=alseq;
-                    asa.createSequenceMapping(alseq, alseq.getStart()+se[0], false); // TODO: verify that positions in alseqAnnotation correspond to ungapped residue positions.
+                    asa.sequenceRef = alseq;
+                    asa.createSequenceMapping(alseq, alseq.getStart() + se[0], false); // TODO: verify that positions in alseqAnnotation correspond to ungapped residue positions.
                     bindjvvobj(asa, vasannot[a]);
                     newasAnnots.add(asa);
-                  } else {
+                  }
+                  else
+                  {
                     // update existing annotation - can do this in place
-                    if (vasannot[a].getModifiable()) {
-                      Cache.log.info("UNIMPLEMENTED: not recovering user modifiable sequence alignment annotation");
+                    if (vasannot[a].getModifiable())
+                    {
+                      Cache.log.info(
+                          "UNIMPLEMENTED: not recovering user modifiable sequence alignment annotation");
                       // TODO: should at least replace with new one - otherwise things will break
                       // basically do this:
                       // int se[] = getBounds(vasannot[a]);
@@ -1043,49 +1190,62 @@ public class VamsasDatastore {
                 }
               }
             }
-            if (jal==null) {
+            if (jal == null)
+            {
               SequenceI[] seqs = new SequenceI[dsseqs.size()];
-              for (i=0,iSize=dsseqs.size(); i<iSize; i++) {
-                seqs[i]=(SequenceI) dsseqs.elementAt(i);
+              for (i = 0, iSize = dsseqs.size(); i < iSize; i++)
+              {
+                seqs[i] = (SequenceI) dsseqs.elementAt(i);
                 dsseqs.setElementAt(null, i);
               }
               jal = new jalview.datamodel.Alignment(seqs);
-              Cache.log.debug("New vamsas alignment imported into jalview "+alignment.getVorbaId().getId());
+              Cache.log.debug("New vamsas alignment imported into jalview " +
+                              alignment.getVorbaId().getId());
               jal.setDataset(jdataset);
             }
-            if (newasAnnots!=null && newasAnnots.size()>0) {
+            if (newasAnnots != null && newasAnnots.size() > 0)
+            {
               // Add the new sequence annotations in to the alignment.
-              for (int an=0,anSize=newasAnnots.size(); an<anSize; an++) {
-                jal.addAnnotation((AlignmentAnnotation) newasAnnots.elementAt(an));
+              for (int an = 0, anSize = newasAnnots.size(); an < anSize; an++)
+              {
+                jal.addAnnotation( (AlignmentAnnotation) newasAnnots.elementAt(
+                    an));
                 // TODO: check if anything has to be done - like calling adjustForAlignment or something.
                 newasAnnots.setElementAt(null, an);
               }
-              newasAnnots=null;
+              newasAnnots = null;
             }
             // //////////////////////////////////////////
             // //LOAD ANNOTATIONS FOR THE ALIGNMENT
             // ////////////////////////////////////
-            if (alignment.getAlignmentAnnotationCount()>0)
+            if (alignment.getAlignmentAnnotationCount() > 0)
             {
-              org.vamsas.objects.core.AlignmentAnnotation[] an = alignment.getAlignmentAnnotation();
+              org.vamsas.objects.core.AlignmentAnnotation[] an = alignment.
+                  getAlignmentAnnotation();
 
               for (int j = 0; j < an.length; j++)
               {
-                jalview.datamodel.AlignmentAnnotation jan=(jalview.datamodel.AlignmentAnnotation) getvObj2jv(an[j]);
-                if (jan!=null) {
+                jalview.datamodel.AlignmentAnnotation jan = (jalview.datamodel.
+                    AlignmentAnnotation) getvObj2jv(an[j]);
+                if (jan != null)
+                {
                   // update or stay the same.
                   // TODO: should at least replace with a new one - otherwise things will break
                   // basically do this:
                   // jan.update(getjAlignmentAnnotation(jal, an[a])); //  update from another annotation object in place.
 
                   Cache.log.debug("update from vamsas alignment annotation to existing jalview alignment annotation.");
-                  if (an[j].getModifiable()) {
+                  if (an[j].getModifiable())
+                  {
                     // TODO: user defined annotation is totally mutable... - so load it up or throw away if locally edited.
-                    Cache.log.info("NOT IMPLEMENTED - Recovering user-modifiable annotation - yet...");
+                    Cache.log.info(
+                        "NOT IMPLEMENTED - Recovering user-modifiable annotation - yet...");
                   }
                   // TODO: compare annotation element rows
                   // TODO: compare props.
-                } else {
+                }
+                else
+                {
                   jan = getjAlignmentAnnotation(jal, an[j]);
                   jal.addAnnotation(jan);
                   bindjvvobj(jan, an[j]);
@@ -1093,29 +1253,40 @@ public class VamsasDatastore {
               }
             }
             AlignFrame alignFrame;
-            if (av==null) {
-              Cache.log.debug("New alignframe for alignment "+alignment.getVorbaId());
+            if (av == null)
+            {
+              Cache.log.debug("New alignframe for alignment " +
+                              alignment.getVorbaId());
               // ///////////////////////////////
               // construct alignment view
-              alignFrame = new AlignFrame(jal, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
-              av=alignFrame.getViewport();
-              String title = alignment.getProvenance().getEntry(alignment.getProvenance().getEntryCount()-1).getAction();
-              if (alignment.getPropertyCount()>0) {
-                for (int p=0,pe=alignment.getPropertyCount(); p<pe; p++) {
-                  if (alignment.getProperty(p).getName().equals("jalview:AlTitle")) {
+              alignFrame = new AlignFrame(jal, AlignFrame.DEFAULT_WIDTH,
+                                          AlignFrame.DEFAULT_HEIGHT);
+              av = alignFrame.getViewport();
+              String title = alignment.getProvenance().getEntry(alignment.
+                  getProvenance().getEntryCount() - 1).getAction();
+              if (alignment.getPropertyCount() > 0)
+              {
+                for (int p = 0, pe = alignment.getPropertyCount(); p < pe; p++)
+                {
+                  if (alignment.getProperty(p).getName().equals(
+                      "jalview:AlTitle"))
+                  {
                     title = alignment.getProperty(p).getContent();
                   }
                 }
               }
               // TODO: automatically create meaningful title for a vamsas alignment using its provenance.
-              jalview.gui.Desktop.addInternalFrame(alignFrame, title + "("+alignment.getVorbaId()+")",
+              jalview.gui.Desktop.addInternalFrame(alignFrame,
+                  title + "(" + alignment.getVorbaId() + ")",
                   AlignFrame.DEFAULT_WIDTH,
                   AlignFrame.DEFAULT_HEIGHT);
               bindjvvobj(av, alignment);
-            } else {
+            }
+            else
+            {
               // find the alignFrame for jal.
               // TODO: fix this so we retrieve the alignFrame handing av *directly*
-              alignFrame=getAlignFrameFor(av);
+              alignFrame = getAlignFrameFor(av);
             }
             // LOAD TREES
             // /////////////////////////////////////
@@ -1125,24 +1296,35 @@ public class VamsasDatastore {
               for (int t = 0; t < alignment.getTreeCount(); t++)
               {
                 Tree tree = alignment.getTree(t);
-                TreePanel tp=(TreePanel) getvObj2jv(tree);
-                if (tp!=null) {
-                  Cache.log.info("Update from vamsas document to alignment associated tree not implemented yet.");
-                } else {
+                TreePanel tp = (TreePanel) getvObj2jv(tree);
+                if (tp != null)
+                {
+                  Cache.log.info(
+                      "Update from vamsas document to alignment associated tree not implemented yet.");
+                }
+                else
+                {
                   // make a new tree
                   Object[] idata = this.recoverInputData(tree.getProvenance());
-                  try {
-                    AlignmentView inputData=null;
-                    if (idata!=null && idata[0]!=null)
+                  try
+                  {
+                    AlignmentView inputData = null;
+                    if (idata != null && idata[0] != null)
+                    {
                       inputData = (AlignmentView) idata[0];
+                    }
                     tp = alignFrame.ShowNewickTree(
                         new jalview.io.NewickFile(tree.getNewick(0).getContent()),
-                        tree.getNewick(0).getTitle()+" ("+tree.getVorbaId()+")",inputData,
+                        tree.getNewick(0).getTitle() + " (" + tree.getVorbaId() +
+                        ")", inputData,
                         600, 500,
                         t * 20 + 50, t * 20 + 50);
                     bindjvvobj(tp, tree);
-                  } catch (Exception e) {
-                    Cache.log.warn("Problems parsing treefile '"+tree.getNewick(0).getContent()+"'",e);
+                  }
+                  catch (Exception e)
+                  {
+                    Cache.log.warn("Problems parsing treefile '" +
+                                   tree.getNewick(0).getContent() + "'", e);
                   }
                 }
               }
@@ -1153,219 +1335,334 @@ public class VamsasDatastore {
       }
     }
   }
+
   // bitfields - should be a template in j1.5
-  private static int HASSECSTR=0;
-  private static int HASVALS=1;
-  private static int HASHPHOB=2;
-  private static int HASDC=3;
-  private static int HASDESCSTR=4;
-  private static int HASTWOSTATE=5; // not used yet.
+  private static int HASSECSTR = 0;
+  private static int HASVALS = 1;
+  private static int HASHPHOB = 2;
+  private static int HASDC = 3;
+  private static int HASDESCSTR = 4;
+  private static int HASTWOSTATE = 5; // not used yet.
   /**
    * parses the AnnotationElements - if they exist - into jalview.datamodel.Annotation[] rows
    * Two annotation rows are made if there are distinct annotation for both at 'pos' and 'after pos' at any particular site.
    * @param annotation
    * @return { boolean[static int constants ], int[ae.length] - map to annotated object frame, jalview.datamodel.Annotation[], jalview.datamodel.Annotation[] (after)}
    */
-  private Object[] parseRangeAnnotation(org.vamsas.objects.core.RangeAnnotation annotation) {
+  private Object[] parseRangeAnnotation(org.vamsas.objects.core.RangeAnnotation
+                                        annotation)
+  {
     // set these attributes by looking in the annotation to decide what kind of alignment annotation rows will be made
     // TODO: potentially we might make several annotation rows from one vamsas alignment annotation. the jv2Vobj binding mechanism
     // may not quite cope with this (without binding an array of annotations to a vamsas alignment annotation)
     // summary flags saying what we found over the set of annotation rows.
-    boolean[] AeContent = new boolean[] { false, false, false, false, false};
+    boolean[] AeContent = new boolean[]
+        {
+        false, false, false, false, false};
     int[] rangeMap = getMapping(annotation);
-    jalview.datamodel.Annotation[][] anot=new jalview.datamodel.Annotation[][] {
+    jalview.datamodel.Annotation[][] anot = new jalview.datamodel.Annotation[][]
+        {
         new jalview.datamodel.Annotation[rangeMap.length],
         new jalview.datamodel.Annotation[rangeMap.length]
     };
-    boolean mergeable=true; //false  if 'after positions cant be placed on same annotation row as positions.
+    boolean mergeable = true; //false  if 'after positions cant be placed on same annotation row as positions.
 
-    if (annotation.getAnnotationElementCount()>0) {
+    if (annotation.getAnnotationElementCount() > 0)
+    {
       AnnotationElement ae[] = annotation.getAnnotationElement();
       for (int aa = 0; aa < ae.length; aa++)
       {
-        int pos = ae[aa].getPosition()-1;// pos counts from 1 to (|seg.start-seg.end|+1)
-        if (pos>=0 && pos<rangeMap.length) {
-          int row=ae[aa].getAfter()?1:0;
-          if (anot[row][pos]!=null) {
+        int pos = ae[aa].getPosition() - 1; // pos counts from 1 to (|seg.start-seg.end|+1)
+        if (pos >= 0 && pos < rangeMap.length)
+        {
+          int row = ae[aa].getAfter() ? 1 : 0;
+          if (anot[row][pos] != null)
+          {
             // only time this should happen is if the After flag is set.
-            Cache.log.debug("Ignoring duplicate annotation site at "+pos);
+            Cache.log.debug("Ignoring duplicate annotation site at " + pos);
             continue;
           }
-          if (anot[1-row][pos]!=null)
-            mergeable=false;
+          if (anot[1 - row][pos] != null)
+          {
+            mergeable = false;
+          }
           String desc = "";
-          if (ae[aa].getDescription()!=null) {
+          if (ae[aa].getDescription() != null)
+          {
             desc = ae[aa].getDescription();
-            if (desc.length()>0) {
+            if (desc.length() > 0)
+            {
               // have imported valid description string
-              AeContent[HASDESCSTR]=true;
+              AeContent[HASDESCSTR] = true;
             }
           }
-          String dc = null;//ae[aa].getDisplayCharacter()==null ? "dc" : ae[aa].getDisplayCharacter();
-          String ss = null;//ae[aa].getSecondaryStructure()==null ? "ss" : ae[aa].getSecondaryStructure();
+          String dc = null; //ae[aa].getDisplayCharacter()==null ? "dc" : ae[aa].getDisplayCharacter();
+          String ss = null; //ae[aa].getSecondaryStructure()==null ? "ss" : ae[aa].getSecondaryStructure();
           java.awt.Color colour = null;
-          if (ae[aa].getGlyphCount()>0) {
+          if (ae[aa].getGlyphCount() > 0)
+          {
             Glyph[] glyphs = ae[aa].getGlyph();
-            for (int g=0; g<glyphs.length; g++) {
-              if (glyphs[g].getDict().equals(org.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE)) {
-                ss=glyphs[g].getContent();
-                AeContent[HASSECSTR]=true;
-              } else if (glyphs[g].getDict().equals(org.vamsas.objects.utils.GlyphDictionary.PROTEIN_HD_HYDRO)) {
+            for (int g = 0; g < glyphs.length; g++)
+            {
+              if (glyphs[g].getDict().equals(org.vamsas.objects.utils.
+                                             GlyphDictionary.PROTEIN_SS_3STATE))
+              {
+                ss = glyphs[g].getContent();
+                AeContent[HASSECSTR] = true;
+              }
+              else if (glyphs[g].getDict().equals(org.vamsas.objects.utils.
+                                                  GlyphDictionary.
+                                                  PROTEIN_HD_HYDRO))
+              {
                 Cache.log.debug("ignoring hydrophobicity glyph marker.");
-                AeContent[HASHPHOB]=true;
-                char c=(dc=glyphs[g].getContent()).charAt(0);
+                AeContent[HASHPHOB] = true;
+                char c = (dc = glyphs[g].getContent()).charAt(0);
                 // dc may get overwritten - but we still set the colour.
-                colour = new java.awt.Color(c=='+'?255:0,c=='.'?255:0,c=='-'?255:0);
+                colour = new java.awt.Color(c == '+' ? 255 : 0,
+                                            c == '.' ? 255 : 0,
+                                            c == '-' ? 255 : 0);
 
-              } else if (glyphs[g].getDict().equals(org.vamsas.objects.utils.GlyphDictionary.DEFAULT)) {
+              }
+              else if (glyphs[g].getDict().equals(org.vamsas.objects.utils.
+                                                  GlyphDictionary.DEFAULT))
+              {
                 dc = glyphs[g].getContent();
-                AeContent[HASDC]=true;
-              } else {
-                Cache.log.debug("Ignoring unknown glyph type "+glyphs[g].getDict());
+                AeContent[HASDC] = true;
+              }
+              else
+              {
+                Cache.log.debug("Ignoring unknown glyph type " +
+                                glyphs[g].getDict());
               }
             }
           }
-          float val=0;
-          if (ae[aa].getValueCount()>0) {
-            AeContent[HASVALS]=true;
-            if (ae[aa].getValueCount()>1) {
-              Cache.log.warn("ignoring additional "+(ae[aa].getValueCount()-1)+"values in annotation element.");
+          float val = 0;
+          if (ae[aa].getValueCount() > 0)
+          {
+            AeContent[HASVALS] = true;
+            if (ae[aa].getValueCount() > 1)
+            {
+              Cache.log.warn("ignoring additional " +
+                             (ae[aa].getValueCount() - 1) +
+                             "values in annotation element.");
             }
             val = ae[aa].getValue(0);
           }
-          if (colour==null) {
-            anot[row][pos]=new jalview.datamodel.Annotation((dc!=null) ? dc : "", desc, (ss!=null)?ss.charAt(0):' ', val);
-          } else {
-            anot[row][pos]=new jalview.datamodel.Annotation((dc!=null) ? dc : "", desc, (ss!=null)?ss.charAt(0):' ', val, colour);
+          if (colour == null)
+          {
+            anot[row][pos] = new jalview.datamodel.Annotation( (dc != null) ?
+                dc : "", desc, (ss != null) ? ss.charAt(0) : ' ', val);
           }
-        } else {
-          Cache.log.warn("Ignoring out of bound annotation element "+aa+" in "+annotation.getVorbaId().getId());
+          else
+          {
+            anot[row][pos] = new jalview.datamodel.Annotation( (dc != null) ?
+                dc : "", desc, (ss != null) ? ss.charAt(0) : ' ', val, colour);
+          }
+        }
+        else
+        {
+          Cache.log.warn("Ignoring out of bound annotation element " + aa +
+                         " in " + annotation.getVorbaId().getId());
         }
       }
       // decide on how many annotation rows are needed.
-      if (mergeable) {
-        for (int i=0; i<anot[0].length;i++) {
-          if (anot[1][i]!=null) {
+      if (mergeable)
+      {
+        for (int i = 0; i < anot[0].length; i++)
+        {
+          if (anot[1][i] != null)
+          {
             anot[0][i] = anot[1][i];
-            anot[0][i].description = anot[0][i].description+" (after)";
-            AeContent[HASDESCSTR]=true; // we have valid description string data
+            anot[0][i].description = anot[0][i].description + " (after)";
+            AeContent[HASDESCSTR] = true; // we have valid description string data
             anot[1][i] = null;
           }
         }
         anot[1] = null;
-      } else {
-        for (int i=0; i<anot[0].length;i++) {
-          anot[1][i].description = anot[1][i].description+" (after)";
+      }
+      else
+      {
+        for (int i = 0; i < anot[0].length; i++)
+        {
+          anot[1][i].description = anot[1][i].description + " (after)";
         }
       }
-      return new Object[] { AeContent, rangeMap, anot[0], anot[1] };
-    } else {
+      return new Object[]
+          {
+          AeContent, rangeMap, anot[0], anot[1]};
+    }
+    else
+    {
       // no annotations to parse. Just return an empty annotationElement[] array.
-      return new Object[] { AeContent, rangeMap, anot[0], anot[1] };
+      return new Object[]
+          {
+          AeContent, rangeMap, anot[0], anot[1]};
     }
     // return null;
   }
+
   /**
    * @param jal the jalview alignment to which the annotation will be attached (ideally - freshly updated from corresponding vamsas alignment)
    * @param annotation
    * @return unbound jalview alignment annotation object.
    */
-  private jalview.datamodel.AlignmentAnnotation getjAlignmentAnnotation(jalview.datamodel.AlignmentI jal, org.vamsas.objects.core.RangeAnnotation annotation) {
-    jalview.datamodel.AlignmentAnnotation jan =null;
-    if (annotation==null)
+  private jalview.datamodel.AlignmentAnnotation getjAlignmentAnnotation(jalview.
+      datamodel.AlignmentI jal,
+      org.vamsas.objects.core.RangeAnnotation annotation)
+  {
+    jalview.datamodel.AlignmentAnnotation jan = null;
+    if (annotation == null)
+    {
       return null;
+    }
     // boolean hasSequenceRef=annotation.getClass().equals(org.vamsas.objects.core.AlignmentSequenceAnnotation.class);
     //boolean hasProvenance=hasSequenceRef || (annotation.getClass().equals(org.vamsas.objects.core.AlignmentAnnotation.class));
     /*int se[] = getBounds(annotation);
-    if (se==null)
+         if (se==null)
       se=new int[] {0,jal.getWidth()-1};
      */
     Object[] parsedRangeAnnotation = parseRangeAnnotation(annotation);
-    String a_label=annotation.getLabel();
-    String a_descr=annotation.getDescription();
-    if (a_label==null || a_label.length()==0) {
+    String a_label = annotation.getLabel();
+    String a_descr = annotation.getDescription();
+    if (a_label == null || a_label.length() == 0)
+    {
       a_label = annotation.getType();
-      if (a_label.length()==0)
+      if (a_label.length() == 0)
+      {
         a_label = "Unamed annotation";
+      }
     }
-    if (a_descr==null || a_descr.length()==0) {
-      a_descr = "Annotation of type '"+annotation.getType()+"'";
+    if (a_descr == null || a_descr.length() == 0)
+    {
+      a_descr = "Annotation of type '" + annotation.getType() + "'";
     }
-    if (parsedRangeAnnotation==null) {
-      Cache.log.debug("Inserting empty annotation row elements for a whole-alignment annotation.");
-
+    if (parsedRangeAnnotation == null)
+    {
+      Cache.log.debug(
+          "Inserting empty annotation row elements for a whole-alignment annotation.");
 
-    } else {
-      if (parsedRangeAnnotation[3]!=null) {
-        Cache.log.warn("Ignoring 'After' annotation row in "+annotation.getVorbaId());
+    }
+    else
+    {
+      if (parsedRangeAnnotation[3] != null)
+      {
+        Cache.log.warn("Ignoring 'After' annotation row in " +
+                       annotation.getVorbaId());
       }
-      jalview.datamodel.Annotation[] arow = (jalview.datamodel.Annotation[]) parsedRangeAnnotation[2];
-      boolean[] has=(boolean[])parsedRangeAnnotation[0];
+      jalview.datamodel.Annotation[] arow = (jalview.datamodel.Annotation[])
+          parsedRangeAnnotation[2];
+      boolean[] has = (boolean[]) parsedRangeAnnotation[0];
       // VAMSAS: getGraph is only on derived annotation for alignments - in this way its 'odd' - there is already an existing TODO about removing this flag as being redundant
       /*if ((annotation.getClass().equals(org.vamsas.objects.core.AlignmentAnnotation.class) && ((org.vamsas.objects.core.AlignmentAnnotation)annotation).getGraph())
           || (hasSequenceRef=true && ((org.vamsas.objects.core.AlignmentSequenceAnnotation)annotation).getGraph())) {
-      */
-      if (has[HASVALS]) {
+       */
+      if (has[HASVALS])
+      {
         // make bounds and automatic description strings for jalview user's benefit (these shouldn't be written back to vamsas document)
-        boolean first=true;
-        float min=0,max=1;
-        int lastval=0;
-        for (int i=0;i<arow.length; i++) {
-          if (arow[i]!=null) {
-            if (i-lastval>1) {
+        boolean first = true;
+        float min = 0, max = 1;
+        int lastval = 0;
+        for (int i = 0; i < arow.length; i++)
+        {
+          if (arow[i] != null)
+          {
+            if (i - lastval > 1)
+            {
               // do some interpolation *between* points
-              if (arow[lastval]!=null) {
-                float interval = arow[i].value-arow[lastval].value;
-                interval/=i-lastval;
+              if (arow[lastval] != null)
+              {
+                float interval = arow[i].value - arow[lastval].value;
+                interval /= i - lastval;
                 float base = arow[lastval].value;
-                for (int ip=lastval+1,np=0; ip<i; np++,ip++) {
-                  arow[ip] = new jalview.datamodel.Annotation("","",' ', interval*np+base);
+                for (int ip = lastval + 1, np = 0; ip < i; np++, ip++)
+                {
+                  arow[ip] = new jalview.datamodel.Annotation("", "", ' ',
+                      interval * np + base);
                   // NB - Interpolated points don't get a tooltip and description.
                 }
               }
             }
-            lastval=i;
+            lastval = i;
             // check range - shouldn't we have a min and max property in the annotation object ?
-            if (first) { min=max=arow[i].value; first=false;}
-            else { if (arow[i].value<min) { min=arow[i].value; }
-            else if (arow[i].value>max) { max=arow[i].value; }
+            if (first)
+            {
+              min = max = arow[i].value;
+              first = false;
+            }
+            else
+            {
+              if (arow[i].value < min)
+              {
+                min = arow[i].value;
+              }
+              else if (arow[i].value > max)
+              {
+                max = arow[i].value;
+              }
             }
             // make tooltip and display char value
-            if (!has[HASDESCSTR]) arow[i].description = arow[i].value + "";
-            if (!has[HASDC]) arow[i].displayCharacter=arow[i].value+"";
+            if (!has[HASDESCSTR])
+            {
+              arow[i].description = arow[i].value + "";
+            }
+            if (!has[HASDC])
+            {
+              arow[i].displayCharacter = arow[i].value + "";
+            }
           }
         }
-        int type=jalview.datamodel.AlignmentAnnotation.LINE_GRAPH;
-        if (has[HASHPHOB]) {
+        int type = jalview.datamodel.AlignmentAnnotation.LINE_GRAPH;
+        if (has[HASHPHOB])
+        {
           type = jalview.datamodel.AlignmentAnnotation.BAR_GRAPH;
         }
-        jan = new jalview.datamodel.AlignmentAnnotation(a_label, a_descr, arow, min, max, type);
-      } else {
+        jan = new jalview.datamodel.AlignmentAnnotation(a_label, a_descr, arow,
+            min, max, type);
+      }
+      else
+      {
         jan = new jalview.datamodel.AlignmentAnnotation(a_label, a_descr, arow);
         jan.setThreshold(null);
       }
-      if (annotation.getLinkCount()>0) {
-        Cache.log.warn("Ignoring "+annotation.getLinkCount()+"links added to AlignmentAnnotation.");
+      if (annotation.getLinkCount() > 0)
+      {
+        Cache.log.warn("Ignoring " + annotation.getLinkCount() +
+                       "links added to AlignmentAnnotation.");
       }
-      if (annotation.getModifiable()) {
-        jan.editable=true;
+      if (annotation.getModifiable())
+      {
+        jan.editable = true;
       }
 
-      if (annotation.getPropertyCount()>0) {
+      if (annotation.getPropertyCount() > 0)
+      {
         // look for special jalview properties
-        org.vamsas.objects.core.Property[] props=annotation.getProperty();
-        for (int p=0;p<props.length; p++) {
-          if (props[p].getName().equalsIgnoreCase("jalview:graphType")) {
-            try {
+        org.vamsas.objects.core.Property[] props = annotation.getProperty();
+        for (int p = 0; p < props.length; p++)
+        {
+          if (props[p].getName().equalsIgnoreCase("jalview:graphType"))
+          {
+            try
+            {
               // probably a jalview annotation graph so recover the visualization hints.
-              jan.graph = jalview.datamodel.AlignmentAnnotation.getGraphValueFromString(props[p].getContent());
-            } catch (Exception e) {
-              Cache.log.debug("Invalid graph type value in jalview:graphType property.");
+              jan.graph = jalview.datamodel.AlignmentAnnotation.
+                  getGraphValueFromString(props[p].getContent());
             }
-            try {
-              if (annotation.getGroup()!=null && annotation.getGroup().length()>0)
+            catch (Exception e)
+            {
+              Cache.log.debug(
+                  "Invalid graph type value in jalview:graphType property.");
+            }
+            try
+            {
+              if (annotation.getGroup() != null &&
+                  annotation.getGroup().length() > 0)
+              {
                 jan.graphGroup = Integer.parseInt(annotation.getGroup());
-            } catch (Exception e) {
+              }
+            }
+            catch (Exception e)
+            {
               Cache.log.info("UNIMPLEMENTED : Couldn't parse non-integer group value for setting graphGroup correctly.");
             }
           }
@@ -1379,7 +1676,8 @@ public class VamsasDatastore {
     return null;
   }
 
-  private SequenceFeature getJalviewSeqFeature(RangeAnnotation dseta) {
+  private SequenceFeature getJalviewSeqFeature(RangeAnnotation dseta)
+  {
     int[] se = getBounds(dseta);
     SequenceFeature sf = new jalview.datamodel.SequenceFeature(dseta.getType(),
         dseta.getDescription(), dseta.getStatus(), se[0], se[1], dseta
@@ -1402,61 +1700,79 @@ public class VamsasDatastore {
    * @param dseta
    * @return int[] { start, end}
    */
-  private int[] getBounds(RangeType dseta) {
+  private int[] getBounds(RangeType dseta)
+  {
     if (dseta != null)
     {
       int[] se = null;
-      if (dseta.getSegCount()>0 && dseta.getPosCount()>0)
+      if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
+      {
         throw new Error("Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");
+      }
       if (dseta.getSegCount() > 0)
       {
-        se = getSegRange(dseta.getSeg(0),true);
+        se = getSegRange(dseta.getSeg(0), true);
         for (int s = 1, sSize = dseta.getSegCount(); s < sSize; s++)
         {
           int nse[] = getSegRange(dseta.getSeg(s), true);
           if (se[0] > nse[0])
+          {
             se[0] = nse[0];
+          }
           if (se[1] < nse[1])
+          {
             se[1] = nse[1];
+          }
         }
       }
       if (dseta.getPosCount() > 0)
       {
         // 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 };
+        se = new int[]
+            {
+            pos, pos};
         for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)
         {
           pos = dseta.getPos(p).getI();
           if (se[0] > pos)
+          {
             se[0] = pos;
+          }
           if (se[1] < pos)
+          {
             se[1] = pos;
+          }
         }
       }
       return se;
     }
     return null;
   }
+
   /**
    * 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.
    */
-  private int[] getMapping(RangeType dseta) {
-    Vector posList=new Vector();
+  private int[] getMapping(RangeType dseta)
+  {
+    Vector posList = new Vector();
     if (dseta != null)
     {
       int[] se = null;
-      if (dseta.getSegCount()>0 && dseta.getPosCount()>0)
+      if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
+      {
         throw new Error("Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");
+      }
       if (dseta.getSegCount() > 0)
       {
         for (int s = 0, sSize = dseta.getSegCount(); s < sSize; s++)
         {
           se = getSegRange(dseta.getSeg(s), false);
-          int se_end=se[1-se[2]]+(se[2]==0 ? 1 : -1);
-          for (int p=se[se[2]]; p!=se_end; p+=se[2]==0 ? 1 : -1 ) {
+          int se_end = se[1 - se[2]] + (se[2] == 0 ? 1 : -1);
+          for (int p = se[se[2]]; p != se_end; p += se[2] == 0 ? 1 : -1)
+          {
             posList.add(new Integer(p));
           }
         }
@@ -1472,15 +1788,19 @@ public class VamsasDatastore {
         }
       }
     }
-    if (posList!=null && posList.size()>0) {
-      int[] range=new int[posList.size()];
-      for (int i=0; i<range.length; i++)
-        range[i] = ((Integer)posList.elementAt(i)).intValue();
+    if (posList != null && posList.size() > 0)
+    {
+      int[] range = new int[posList.size()];
+      for (int i = 0; i < range.length; i++)
+      {
+        range[i] = ( (Integer) posList.elementAt(i)).intValue();
+      }
       posList.clear();
       return range;
     }
     return null;
   }
+
   /* not needed now.
    * Provenance getVamsasProvenance(jalview.datamodel.Provenance jprov) {
     jalview.datamodel.ProvenanceEntry[] entries = null;
@@ -1522,15 +1842,17 @@ public class VamsasDatastore {
     }
 
     return prov;
-  }
+     }
    */
-  jalview.datamodel.Provenance getJalviewProvenance(Provenance prov) {
+  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().toDate(), prov.getEntry(i).getId());
+                     prov.getEntry(i).getDate().toDate(),
+                     prov.getEntry(i).getId());
     }
 
     return jprov;
@@ -1541,29 +1863,37 @@ public class VamsasDatastore {
    * @return default initial provenance list for a Jalview created vamsas
    *         object.
    */
-  Provenance dummyProvenance() {
+  Provenance dummyProvenance()
+  {
     return dummyProvenance(null);
   }
 
-  Entry dummyPEntry(String action) {
+  Entry dummyPEntry(String action)
+  {
     Entry entry = new Entry();
     entry.setApp(this.provEntry.getApp());
     if (action != null)
+    {
       entry.setAction(action);
+    }
     else
+    {
       entry.setAction("created.");
+    }
     entry.setDate(new org.exolab.castor.types.Date(new java.util.Date()));
     entry.setUser(this.provEntry.getUser());
     return entry;
   }
 
-  Provenance dummyProvenance(String action) {
+  Provenance dummyProvenance(String action)
+  {
     Provenance prov = new Provenance();
     prov.addEntry(dummyPEntry(action));
     return prov;
   }
 
-  void addProvenance(Provenance p, String action) {
+  void addProvenance(Provenance p, String action)
+  {
     p.addEntry(dummyPEntry(action));
   }
 
diff --git a/src/jalview/io/WSWUBlastClient.java b/src/jalview/io/WSWUBlastClient.java
index e2910ee..e1798e3 100755
--- a/src/jalview/io/WSWUBlastClient.java
+++ b/src/jalview/io/WSWUBlastClient.java
@@ -1,36 +1,30 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 jalview.io;
 
-import jalview.datamodel.*;
-
-import jalview.gui.*;
-
-import org.apache.axis.client.*;
-
 import java.util.*;
 
 import javax.swing.*;
 
-import javax.xml.namespace.QName;
-import jalview.analysis.AlignSeq;
-
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.gui.*;
 import uk.ac.ebi.www.*;
 
 /**
@@ -41,265 +35,269 @@ import uk.ac.ebi.www.*;
  */
 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)
+  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++)
     {
-        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++;
-        }
+      Sequence sequence = (Sequence) ids.get(i);
+      System.out.println(sequence.getName());
 
-        ImageTwirler thread = new ImageTwirler();
-        thread.start();
+      BlastThread thread = new BlastThread(sequence);
+      thread.start();
+      jobsRunning++;
     }
 
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param id1 DOCUMENT ME!
-     * @param res DOCUMENT ME!
-     */
-    void parseResult(Sequence seq, String res)
+    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())
     {
-        StringTokenizer st = new StringTokenizer(res, "\n");
-        String data;
-        String id2;
-        int maxFound = 90;
-        StringBuffer buffer = new StringBuffer("\n\n" + seq.getName() + " :");
+      data = st.nextToken();
 
-        while (st.hasMoreTokens())
+      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();
+          data = st.nextToken();
+
+          if (data.indexOf("Identities") > -1)
+          {
+            identitiesFound = true;
 
-            if (data.indexOf(">UNIPROT") > -1)
+            int value = Integer.parseInt(data.substring(data.indexOf(
+                "(") + 1,
+                data.indexOf("%")));
+
+            if (value >= maxFound)
             {
-                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});
-                        }
-                    }
-                }
+              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);
+    output.appendText(buffer.toString());
+  }
 
-      if (reply == JOptionPane.YES_OPTION)
+  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())
       {
-        Enumeration keys = suggestedIds.elements();
-        while(keys.hasMoreElements())
-        {
-          Object [] object = (Object[])keys.nextElement();
+        Object[] object = (Object[]) keys.nextElement();
 
-          Sequence oldseq = (Sequence)object[0];
+        Sequence oldseq = (Sequence) object[0];
 
-          oldseq.setName( object[1].toString() );
+        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++)
+        // 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)
           {
-            if (al.getSequenceAt(i).getDatasetSequence() == oldseq)
-            {
-              al.getSequenceAt(i).setName(oldseq.getName());
-              break;
-            }
+            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()));
-          }
+        DBRefEntry[] entries = oldseq.getDBRef();
+        if (entries != null)
+        {
+          oldseq.addDBRef(new jalview.datamodel.
+                          DBRefEntry(jalview.datamodel.DBRefSource.UNIPROT,
+                                     "0",
+                                     entries[0].getAccessionId()));
         }
       }
-      ap.repaint();
-
     }
+    ap.repaint();
 
-    class ImageTwirler extends Thread
-    {
-        ImageIcon[] imageIcon;
-        int imageIndex = 0;
+  }
 
-        public ImageTwirler()
-        {
-            imageIcon = new ImageIcon[9];
+  class ImageTwirler
+      extends Thread
+  {
+    ImageIcon[] imageIcon;
+    int imageIndex = 0;
 
-            for (int i = 0; i < 9; i++)
-            {
-                java.net.URL url = getClass().getResource("/images/dna" +
-                        (i + 1) + ".gif");
+    public ImageTwirler()
+    {
+      imageIcon = new ImageIcon[9];
 
-                if (url != null)
-                {
-                    imageIcon[i] = new ImageIcon(url);
-                }
-            }
-        }
+      for (int i = 0; i < 9; i++)
+      {
+        java.net.URL url = getClass().getResource("/images/dna" +
+                                                  (i + 1) + ".gif");
 
-        public void run()
+        if (url != null)
         {
-            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();
-            }
+          imageIcon[i] = new ImageIcon(url);
         }
+      }
     }
 
-    class BlastThread extends Thread
+    public void run()
     {
-        Sequence sequence;
-        String jobid;
-        boolean jobComplete = false;
-
-        BlastThread(Sequence sequence)
+      while (jobsRunning > 0)
+      {
+        try
         {
-          System.out.println("blasting for: "+sequence.getName());
-          this.sequence = sequence;
+          Thread.sleep(100);
+          imageIndex++;
+          imageIndex %= 9;
+          output.setFrameIcon(imageIcon[imageIndex]);
+          output.setTitle("BLASTing for unidentified sequences - " +
+                          jobsRunning + " jobs running.");
         }
+        catch (Exception ex)
+        {
+        }
+      }
 
-        public void run()
+      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
         {
-            StartJob();
+          WSWUBlastService service = new WSWUBlastServiceLocator();
+          WSWUBlast wublast = service.getWSWUBlast();
+          WSFile[] results = wublast.getResults(jobid);
 
-            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)
-                {
-                }
-            }
+          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
+          }
         }
-
-        void StartJob()
+        catch (Exception ex)
         {
-          InputParams params = new InputParams();
+        }
+      }
+    }
 
-          params.setProgram("blastp");
-          params.setDatabase("uniprot");
-          params.setMatrix("pam10");
+    void StartJob()
+    {
+      InputParams params = new InputParams();
 
-          params.setNumal(5);
-          params.setSensitivity("low");
-          params.setSort("totalscore");
-          params.setOutformat("txt");
-          params.setAsync(true);
+      params.setProgram("blastp");
+      params.setDatabase("uniprot");
+      params.setMatrix("pam10");
 
-            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();
-            }
-        }
+      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/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 47d4137..1b89d71 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -24,10 +24,6 @@ import javax.swing.*;
 import javax.swing.event.*;
 
 import jalview.schemes.*;
-import java.awt.BorderLayout;
-
-
-
 
 public class GAlignFrame
     extends JInternalFrame
@@ -159,7 +155,8 @@ 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()
         {
@@ -188,45 +185,49 @@ public class GAlignFrame
       reload.setMnemonic('R');
     }
 
-
-    if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)
+    if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
     {
       java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
           getUserColourSchemes().keys();
 
       while (userColours.hasMoreElements())
       {
-        final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
+        final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
+            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)
+              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)
               {
-                if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
+                jalview.gui.UserDefinedColours.removeColourFromDefaults(
+                    radioItem.getText());
+                colourMenu.remove(radioItem);
+              }
+              else
+              {
+                radioItem.addActionListener(new ActionListener()
                 {
-                  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)
+                  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)
@@ -254,7 +255,6 @@ public class GAlignFrame
 
     setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));
 
-
   }
 
   public void setColourSelected(String defaultColour)
@@ -267,8 +267,8 @@ public class GAlignFrame
       switch (index)
       {
         case ColourSchemeProperty.NONE:
-              noColourmenuItem.setSelected(true);
-              break;
+          noColourmenuItem.setSelected(true);
+          break;
         case ColourSchemeProperty.CLUSTAL:
           clustalColour.setSelected(true);
 
@@ -339,7 +339,8 @@ public class GAlignFrame
     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));
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() |
+        java.awt.event.KeyEvent.SHIFT_MASK, false));
     saveAs.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -399,7 +400,8 @@ public class GAlignFrame
     });
     remove2LeftMenuItem.setText("Remove Left");
     remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
-        awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+        awt.event.KeyEvent.VK_L,
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
     remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -409,7 +411,8 @@ public class GAlignFrame
     });
     remove2RightMenuItem.setText("Remove Right");
     remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
-        awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+        awt.event.KeyEvent.VK_R,
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
     remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -432,7 +435,8 @@ public class GAlignFrame
     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));
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() |
+        java.awt.event.KeyEvent.SHIFT_MASK, false));
     removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -484,7 +488,8 @@ public class GAlignFrame
     });
     removeRedundancyMenuItem.setText("Remove Redundancy...");
     removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-        java.awt.event.KeyEvent.VK_D, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+        java.awt.event.KeyEvent.VK_D,
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
     removeRedundancyMenuItem.addActionListener(new java.awt.event.
                                                ActionListener()
     {
@@ -644,7 +649,8 @@ public class GAlignFrame
     });
     annotationPanelMenuItem.setActionCommand("");
     annotationPanelMenuItem.setText("Show Annotations");
-    annotationPanelMenuItem.setState( jalview.bin.Cache.getDefault("SHOW_ANNOTATIONS",true));
+    annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
+        "SHOW_ANNOTATIONS", true));
     annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -824,7 +830,8 @@ public class GAlignFrame
     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));
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() |
+        java.awt.event.KeyEvent.SHIFT_MASK, false));
     pasteNew.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -870,7 +877,7 @@ public class GAlignFrame
     });
 
     seqLimits.setText("Show Sequence Limits");
-    seqLimits.setState( jalview.bin.Cache.getDefault("SHOW_JVSUFFIX",true));
+    seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
     seqLimits.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -961,7 +968,7 @@ public class GAlignFrame
 
     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)
@@ -987,7 +994,6 @@ public class GAlignFrame
       }
     });
 
-
     featureSettings.setText("Feature Settings...");
     featureSettings.addActionListener(new ActionListener()
     {
@@ -1022,7 +1028,7 @@ 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)
@@ -1118,7 +1124,7 @@ public class GAlignFrame
     invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
         event.KeyEvent.VK_I,
         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
-        |java.awt.event.KeyEvent.ALT_MASK,
+        | java.awt.event.KeyEvent.ALT_MASK,
         false));
     invertColSel.addActionListener(new ActionListener()
     {
@@ -1129,12 +1135,12 @@ public class GAlignFrame
     });
     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
     {
-        public void stateChanged(ChangeEvent evt)
-        {
-            JTabbedPane pane = (JTabbedPane)evt.getSource();
-            int sel = pane.getSelectedIndex();
-            tabSelectionChanged(sel);
-        }
+      public void stateChanged(ChangeEvent evt)
+      {
+        JTabbedPane pane = (JTabbedPane) evt.getSource();
+        int sel = pane.getSelectedIndex();
+        tabSelectionChanged(sel);
+      }
     });
     tabbedPane.addMouseListener(new MouseAdapter()
     {
@@ -1180,7 +1186,8 @@ 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("Text Colour");
     textColour.addActionListener(new ActionListener()
     {
@@ -1313,8 +1320,9 @@ public class GAlignFrame
     calculateMenu.addSeparator();
     calculateMenu.add(showTranslation);
     calculateMenu.add(autoCalculate);
-    webServiceNoServices=new JMenuItem("<No Services>");
-    webService.add(webServiceNoServices);pasteMenu.add(pasteNew);
+    webServiceNoServices = new JMenuItem("<No Services>");
+    webService.add(webServiceNoServices);
+    pasteMenu.add(pasteNew);
     pasteMenu.add(pasteThis);
     sort.add(sortIDMenuItem);
     sort.add(sortGroupMenuItem);
@@ -1617,7 +1625,6 @@ public class GAlignFrame
 
   }
 
-
   public void createEPS(java.io.File f)
   {
   }
@@ -1650,8 +1657,6 @@ public class GAlignFrame
   {
   }
 
-
-
   protected void saveAs_actionPerformed(ActionEvent e)
   {
   }
@@ -1660,7 +1665,6 @@ public class GAlignFrame
   {
   }
 
-
   public void vamsasStore_actionPerformed(ActionEvent e)
   {
 
@@ -1696,7 +1700,6 @@ public class GAlignFrame
 
   }
 
-
   public void associatedData_actionPerformed(ActionEvent e)
   {
 
diff --git a/src/jalview/jbgui/GAlignmentPanel.java b/src/jalview/jbgui/GAlignmentPanel.java
index d560d5d..f8b91c4 100755
--- a/src/jalview/jbgui/GAlignmentPanel.java
+++ b/src/jalview/jbgui/GAlignmentPanel.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
diff --git a/src/jalview/jbgui/GCutAndPasteTransfer.java b/src/jalview/jbgui/GCutAndPasteTransfer.java
index 487f712..c19db0e 100755
--- a/src/jalview/jbgui/GCutAndPasteTransfer.java
+++ b/src/jalview/jbgui/GCutAndPasteTransfer.java
@@ -1,94 +1,94 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 jalview.jbgui;
 
 import java.awt.*;
 import java.awt.event.*;
-
 import javax.swing.*;
 
-
 /**
  * DOCUMENT ME!
  *
  * @author $author$
  * @version $Revision$
  */
-public class GCutAndPasteTransfer extends JInternalFrame
+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();
+  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()
+   * Creates a new GCutAndPasteTransfer object.
+   */
+  public GCutAndPasteTransfer()
+  {
+    try
+    {
+      setJMenuBar(editMenubar);
+      jbInit();
+    }
+    catch (Exception e)
     {
-        try
-        {
-            setJMenuBar(editMenubar);
-            jbInit();
-        }
-        catch (Exception e)
-        {
-            e.printStackTrace();
-        }
+      e.printStackTrace();
     }
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @throws Exception DOCUMENT ME!
-     */
-    private void jbInit() throws Exception
+  /**
+   * 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()
     {
-        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);
+      public void actionPerformed(ActionEvent e)
+      {
+        cancel_actionPerformed(e);
+      }
+    });
+    textarea.setBorder(null);
 
     selectAll.setText("Select All");
     selectAll.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
@@ -117,94 +117,93 @@ public class GCutAndPasteTransfer extends JInternalFrame
         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);
+    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);
+    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 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 copyItem_actionPerformed(ActionEvent e)
+  {
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void ok_actionPerformed(ActionEvent e)
-    {
-    }
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void pasteMenu_actionPerformed(ActionEvent e)
+  {
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void cancel_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 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 a3493d8..d4f6d1d 100755
--- a/src/jalview/jbgui/GDasSourceBrowser.java
+++ b/src/jalview/jbgui/GDasSourceBrowser.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,17 +18,11 @@
  */
 package jalview.jbgui;
 
-import javax.swing.*;
-import javax.swing.border.TitledBorder;
-import java.awt.event.ActionListener;
-import java.awt.event.ActionEvent;
 import java.awt.*;
-import javax.swing.BorderFactory;
-import javax.swing.event.HyperlinkListener;
-import javax.swing.event.HyperlinkEvent;
-import java.awt.Dimension;
-import java.awt.Font;
-import java.awt.Insets;
+import java.awt.event.*;
+import javax.swing.*;
+import javax.swing.border.*;
+import javax.swing.event.*;
 
 public class GDasSourceBrowser
     extends JPanel
@@ -185,12 +179,15 @@ public class GDasSourceBrowser
 
   public void fullDetails_hyperlinkUpdate(HyperlinkEvent e)
   {
-    try{
+    try
+    {
 
       if (e.getEventType() == HyperlinkEvent.EventType.ACTIVATED)
+      {
         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 daea610..722a408 100755
--- a/src/jalview/jbgui/GDesktop.java
+++ b/src/jalview/jbgui/GDesktop.java
@@ -1,54 +1,53 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 jalview.jbgui;
 
 import java.awt.*;
 import java.awt.event.*;
-
 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();
-    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();
-    JMenu toolsMenu = new JMenu();
-    JMenuItem preferences = new JMenuItem();
-    JMenuItem saveState = new JMenuItem();
-    JMenuItem loadState = new JMenuItem();
-    JMenu inputMenu = new JMenu();
+  protected static JMenu windowMenu = new JMenu();
+  JMenuBar desktopMenubar = new JMenuBar();
+  JMenu FileMenu = new JMenu();
+  JMenu HelpMenu = new JMenu();
+  protected JMenu VamsasMenu = 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();
+  JMenu toolsMenu = new JMenu();
+  JMenuItem preferences = new JMenuItem();
+  JMenuItem saveState = new JMenuItem();
+  JMenuItem loadState = new JMenuItem();
+  JMenu inputMenu = new JMenu();
   protected JMenuItem vamsasLoad = new JMenuItem();
   JMenuItem inputSequence = new JMenuItem();
   protected JMenuItem vamsasStop = new JMenuItem();
@@ -57,125 +56,127 @@ public class GDesktop extends JFrame
   JMenuItem minimizeAssociated = new JMenuItem();
 
   /**
-     * Creates a new GDesktop object.
-     */
-    public GDesktop()
+   * Creates a new GDesktop object.
+   */
+  public GDesktop()
+  {
+    try
     {
-        try
-        {
-            jbInit();
-            this.setJMenuBar(desktopMenubar);
-        }
-        catch (Exception e)
-        {
-            e.printStackTrace();
-        }
-
-        if (!System.getProperty("os.name").startsWith("Mac"))
-        {
-          FileMenu.setMnemonic('F');
-          inputLocalFileMenuItem.setMnemonic('L');
-          VamsasMenu.setMnemonic('V');
-          inputURLMenuItem.setMnemonic('U');
-          inputTextboxMenuItem.setMnemonic('C');
-          quit.setMnemonic('Q');
-          saveState.setMnemonic('S');
-          loadState.setMnemonic('L');
-          inputMenu.setMnemonic('I');
-        }
+      jbInit();
+      this.setJMenuBar(desktopMenubar);
+    }
+    catch (Exception e)
+    {
+      e.printStackTrace();
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @throws Exception DOCUMENT ME!
-     */
-    private void jbInit() throws Exception
+    if (!System.getProperty("os.name").startsWith("Mac"))
     {
-        FileMenu.setText("File");
-        HelpMenu.setText("Help");
-        VamsasMenu.setText("Vamsas");
-        VamsasMenu.setToolTipText("Share data with other vamsas applications.");
-        inputLocalFileMenuItem.setText("from File");
+      FileMenu.setMnemonic('F');
+      inputLocalFileMenuItem.setMnemonic('L');
+      VamsasMenu.setMnemonic('V');
+      inputURLMenuItem.setMnemonic('U');
+      inputTextboxMenuItem.setMnemonic('C');
+      quit.setMnemonic('Q');
+      saveState.setMnemonic('S');
+      loadState.setMnemonic('L');
+      inputMenu.setMnemonic('I');
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @throws Exception DOCUMENT ME!
+   */
+  private void jbInit()
+      throws Exception
+  {
+    FileMenu.setText("File");
+    HelpMenu.setText("Help");
+    VamsasMenu.setText("Vamsas");
+    VamsasMenu.setToolTipText("Share data with other vamsas applications.");
+    inputLocalFileMenuItem.setText("from File");
     inputLocalFileMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-        java.awt.event.KeyEvent.VK_O, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+        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()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    inputURLMenuItem_actionPerformed(null);
-                }
-            });
-        inputTextboxMenuItem.setText("from Textbox");
-        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()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    quit();
-                }
-            });
-        aboutMenuItem.setText("About");
-        aboutMenuItem.addActionListener(new java.awt.event.ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    aboutMenuItem_actionPerformed(e);
-                }
-            });
-        documentationMenuItem.setText("Documentation");
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        inputLocalFileMenuItem_actionPerformed(null);
+      }
+    });
+    inputURLMenuItem.setText("from URL");
+    inputURLMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        inputURLMenuItem_actionPerformed(null);
+      }
+    });
+    inputTextboxMenuItem.setText("from Textbox");
+    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()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        quit();
+      }
+    });
+    aboutMenuItem.setText("About");
+    aboutMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        aboutMenuItem_actionPerformed(e);
+      }
+    });
+    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);
-                }
-            });
-        this.getContentPane().setLayout(flowLayout1);
-        windowMenu.setText("Window");
-        preferences.setText("Preferences...");
-        preferences.addActionListener(new ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    preferences_actionPerformed(e);
-                }
-            });
-        toolsMenu.setText("Tools");
-        saveState.setText("Save Project");
-        saveState.addActionListener(new ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    saveState_actionPerformed(e);
-                }
-            });
-        loadState.setText("Load Project");
-        loadState.addActionListener(new ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    loadState_actionPerformed(e);
-                }
-            });
-        inputMenu.setText("Input Alignment");
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        documentationMenuItem_actionPerformed(e);
+      }
+    });
+    this.getContentPane().setLayout(flowLayout1);
+    windowMenu.setText("Window");
+    preferences.setText("Preferences...");
+    preferences.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        preferences_actionPerformed(e);
+      }
+    });
+    toolsMenu.setText("Tools");
+    saveState.setText("Save Project");
+    saveState.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        saveState_actionPerformed(e);
+      }
+    });
+    loadState.setText("Load Project");
+    loadState.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        loadState_actionPerformed(e);
+      }
+    });
+    inputMenu.setText("Input Alignment");
     vamsasLoad.setText("Start Vamsas Session...");
     vamsasLoad.setVisible(false);
     vamsasLoad.addActionListener(new ActionListener()
@@ -254,102 +255,104 @@ public class GDesktop extends JFrame
     //    inputMenu.add(vamsasLoad);
   }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void inputLocalFileMenuItem_actionPerformed(jalview.gui.AlignViewport av)
-    {
-    }
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void inputLocalFileMenuItem_actionPerformed(jalview.gui.
+      AlignViewport av)
+  {
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void inputURLMenuItem_actionPerformed(jalview.gui.AlignViewport av)
-    {
-    }
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void inputURLMenuItem_actionPerformed(jalview.gui.AlignViewport av)
+  {
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void inputTextboxMenuItem_actionPerformed(jalview.gui.AlignViewport av)
-    {
-    }
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void inputTextboxMenuItem_actionPerformed(jalview.gui.AlignViewport
+      av)
+  {
+  }
 
-    /**
-     * DOCUMENT ME!
-     */
-    protected void quit()
-    {
-    }
+  /**
+   * DOCUMENT ME!
+   */
+  protected void quit()
+  {
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void aboutMenuItem_actionPerformed(ActionEvent e)
-    {
-    }
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void aboutMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void documentationMenuItem_actionPerformed(ActionEvent e)
-    {
-    }
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void documentationMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void SaveState_actionPerformed(ActionEvent e)
-    {
-    }
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void SaveState_actionPerformed(ActionEvent e)
+  {
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void preferences_actionPerformed(ActionEvent e)
-    {
-    }
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void preferences_actionPerformed(ActionEvent e)
+  {
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void saveState_actionPerformed(ActionEvent e)
-    {
-    }
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void saveState_actionPerformed(ActionEvent e)
+  {
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void loadState_actionPerformed(ActionEvent e)
-    {
-    }
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void loadState_actionPerformed(ActionEvent e)
+  {
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void loadJalviewAlign_actionPerformed(ActionEvent e)
-    {
-    }
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void loadJalviewAlign_actionPerformed(ActionEvent e)
+  {
+  }
 
   public void vamsasLoad_actionPerformed(ActionEvent e)
   {
@@ -360,6 +363,7 @@ public class GDesktop extends JFrame
   {
 
   }
+
   public void vamsasStop_actionPerformed(ActionEvent e)
   {
 
diff --git a/src/jalview/jbgui/GFinder.java b/src/jalview/jbgui/GFinder.java
index b8dcad3..9d72d26 100755
--- a/src/jalview/jbgui/GFinder.java
+++ b/src/jalview/jbgui/GFinder.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -22,9 +22,9 @@ import java.awt.*;
 import java.awt.event.*;
 import javax.swing.*;
 import javax.swing.event.*;
-import jalview.io.FormatAdapter;
-import jalview.datamodel.Alignment;
-import java.awt.BorderLayout;
+
+import jalview.datamodel.*;
+import jalview.io.*;
 
 public class GFinder
     extends JPanel
@@ -105,10 +105,12 @@ public class GFinder
         textfield_caretUpdate(e);
       }
     });
-    textfield.addKeyListener(new java.awt.event.KeyAdapter() {
-        public void keyPressed(KeyEvent e) {
-            textfield_keyPressed(e);
-        }
+    textfield.addKeyListener(new java.awt.event.KeyAdapter()
+    {
+      public void keyPressed(KeyEvent e)
+      {
+        textfield_keyPressed(e);
+      }
     });
 
     borderLayout1.setHgap(5);
@@ -140,10 +142,9 @@ public class GFinder
   {
   }
 
-
   protected void textfield_keyPressed(KeyEvent e)
   {
-    if(e.getKeyCode()==KeyEvent.VK_ENTER)
+    if (e.getKeyCode() == KeyEvent.VK_ENTER)
     {
       e.consume();
       findNext_actionPerformed(null);
@@ -164,9 +165,13 @@ public class GFinder
         {
           String str = textfield.getText();
           Alignment al = null;
-          try{al = new FormatAdapter().readFile(str, "Paste", "FASTA");}
-          catch(Exception ex){}
-          if(al!=null && al.getHeight()>0)
+          try
+          {
+            al = new FormatAdapter().readFile(str, "Paste", "FASTA");
+          }
+          catch (Exception ex)
+          {}
+          if (al != null && al.getHeight() > 0)
           {
             str = jalview.analysis.AlignSeq.extractGaps(
                 jalview.util.Comparison.GapChars,
diff --git a/src/jalview/jbgui/GFontChooser.java b/src/jalview/jbgui/GFontChooser.java
index abc6b71..6c04561 100755
--- a/src/jalview/jbgui/GFontChooser.java
+++ b/src/jalview/jbgui/GFontChooser.java
@@ -1,30 +1,26 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 jalview.jbgui;
 
 import java.awt.*;
 import java.awt.event.*;
-
 import javax.swing.*;
-import java.awt.BorderLayout;
-import java.awt.Font;
-import java.awt.Rectangle;
 
 /**
  * DOCUMENT ME!
@@ -32,132 +28,134 @@ import java.awt.Rectangle;
  * @author $author$
  * @version $Revision$
  */
-public class GFontChooser extends JPanel
+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();
+  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();
+  protected JCheckBox smoothFont = new JCheckBox();
   BorderLayout borderLayout4 = new BorderLayout();
- protected JCheckBox monospaced = new JCheckBox();
+  protected JCheckBox monospaced = new JCheckBox();
   JPanel jPanel4 = new JPanel();
 
   /**
-     * Creates a new GFontChooser object.
-     */
-    public GFontChooser()
+   * Creates a new GFontChooser object.
+   */
+  public GFontChooser()
+  {
+    try
     {
-        try
-        {
-            jbInit();
-        }
-        catch (Exception e)
-        {
-            e.printStackTrace();
-        }
+      jbInit();
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @throws Exception DOCUMENT ME!
-     */
-    private void jbInit() throws Exception
+    catch (Exception e)
     {
-        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));
+      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));
+    {
+      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);
+    {
+      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);
+    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);
-                }
-            });
+    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);
-                }
-            });
+    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);
+    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.setOpaque(false);
     jPanel2.setBounds(new Rectangle(5, 37, 128, 21));
     jPanel2.setLayout(borderLayout3);
-        jPanel3.setOpaque(false);
+    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);
-                }
-            });
+    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)");
@@ -177,7 +175,7 @@ public class GFontChooser extends JPanel
     jPanel4.setOpaque(false);
     jPanel4.setBounds(new Rectangle(24, 92, 259, 35));
     jPanel1.add(jLabel1, BorderLayout.WEST);
-        jPanel1.add(fontName, BorderLayout.CENTER);
+    jPanel1.add(fontName, BorderLayout.CENTER);
     jPanel1.add(monospaced, java.awt.BorderLayout.EAST);
     this.add(jPanel3, null);
     this.add(jPanel2, null);
@@ -193,62 +191,62 @@ public class GFontChooser extends JPanel
     this.add(jPanel1, null);
   }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void ok_actionPerformed(ActionEvent e)
-    {
-    }
+  /**
+   * 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 cancel_actionPerformed(ActionEvent e)
+  {
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void fontName_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 fontSize_actionPerformed(ActionEvent e)
+  {
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void fontStyle_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)
-    {
-    }
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void defaultButton_actionPerformed(ActionEvent e)
+  {
+  }
 
-    public void smoothFont_actionPerformed(ActionEvent e)
-    {
+  public void smoothFont_actionPerformed(ActionEvent e)
+  {
 
-    }
+  }
 }
diff --git a/src/jalview/jbgui/GPCAPanel.java b/src/jalview/jbgui/GPCAPanel.java
index 74182f3..5c17ba7 100755
--- a/src/jalview/jbgui/GPCAPanel.java
+++ b/src/jalview/jbgui/GPCAPanel.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -21,8 +21,7 @@ package jalview.jbgui;
 import java.awt.*;
 import java.awt.event.*;
 import javax.swing.*;
-import javax.swing.event.MenuListener;
-import javax.swing.event.MenuEvent;
+import javax.swing.event.*;
 
 public class GPCAPanel
     extends JInternalFrame
@@ -67,7 +66,6 @@ public class GPCAPanel
       zCombobox.addItem("dim " + i);
     }
 
-
     setJMenuBar(jMenuBar1);
   }
 
diff --git a/src/jalview/jbgui/GPairwiseAlignPanel.java b/src/jalview/jbgui/GPairwiseAlignPanel.java
index ab4eb54..f690a21 100755
--- a/src/jalview/jbgui/GPairwiseAlignPanel.java
+++ b/src/jalview/jbgui/GPairwiseAlignPanel.java
@@ -1,90 +1,90 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 jalview.jbgui;
 
 import java.awt.*;
 import java.awt.event.*;
-
 import javax.swing.*;
 
-
 /**
  * DOCUMENT ME!
  *
  * @author $author$
  * @version $Revision$
  */
-public class GPairwiseAlignPanel extends JPanel
+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();
+  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()
+  /**
+   * Creates a new GPairwiseAlignPanel object.
+   */
+  public GPairwiseAlignPanel()
+  {
+    try
     {
-        try
-        {
-            jbInit();
-        }
-        catch (Exception e)
-        {
-            e.printStackTrace();
-        }
+      jbInit();
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @throws Exception DOCUMENT ME!
-     */
-    private void jbInit() throws Exception
+    catch (Exception e)
     {
-        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);
+      e.printStackTrace();
     }
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void viewInEditorButton_actionPerformed(ActionEvent e)
+  /**
+   * 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 2b194bf..f5e6604 100755
--- a/src/jalview/jbgui/GPreferences.java
+++ b/src/jalview/jbgui/GPreferences.java
@@ -1,32 +1,28 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 jalview.jbgui;
 
 import java.awt.*;
-
-import javax.swing.*;
-import javax.swing.border.TitledBorder;
 import java.awt.event.*;
+import javax.swing.*;
+import javax.swing.border.*;
 import javax.swing.event.*;
-import java.awt.Font;
-import java.awt.Rectangle;
-import java.awt.Insets;
 
 /**
  * DOCUMENT ME!
@@ -34,30 +30,31 @@ import java.awt.Insets;
  * @author $author$
  * @version $Revision$
  */
-public class GPreferences extends JPanel
+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();
+  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();
+  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();
@@ -93,14 +90,14 @@ public class GPreferences extends 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();
+  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();
+  protected JCheckBox pirjv = new JCheckBox();
   JPanel jPanel11 = new JPanel();
   Font verdana11 = new java.awt.Font("Verdana", Font.PLAIN, 11);
   protected JCheckBox seqLimit = new JCheckBox();
@@ -116,118 +113,119 @@ public class GPreferences extends JPanel
   protected JCheckBox rightAlign = new JCheckBox();
   protected JCheckBox idItalics = new JCheckBox();
   /**
-     * Creates a new GPreferences object.
-     */
-    public GPreferences()
+   * Creates a new GPreferences object.
+   */
+  public GPreferences()
+  {
+    try
     {
-        try
-        {
-            jbInit();
-        }
-        catch (Exception ex)
-        {
-            ex.printStackTrace();
-        }
+      jbInit();
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
     }
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @throws Exception DOCUMENT ME!
-     */
-    private void jbInit() throws Exception
+  /**
+   * DOCUMENT ME!
+   *
+   * @throws Exception DOCUMENT ME!
+   */
+  private void jbInit()
+      throws Exception
+  {
+    this.setLayout(borderLayout1);
+    ok.setText("OK");
+    ok.addActionListener(new ActionListener()
     {
-        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");
+      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.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");
+    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");
+    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.setHorizontalAlignment(SwingConstants.RIGHT);
+    annotations.setHorizontalTextPosition(SwingConstants.LEFT);
     annotations.setSelected(true);
-        annotations.setText("Show Annotations");
+    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 ");
+    {
+      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 ");
+    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 ");
+    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");
+    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();
-                    }
-                }
-            });
+    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);
+    connectTab.setLayout(gridBagLayout3);
     serverLabel.setText("Address");
     serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
     serverLabel.setFont(verdana11);
@@ -242,41 +240,47 @@ public class GPreferences extends JPanel
     defaultBrowser.setFont(verdana11);
     defaultBrowser.setText("");
     newLink.setText("New");
-    newLink.addActionListener(new java.awt.event.ActionListener() {
-      public void actionPerformed(ActionEvent e) {
+    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.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.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);
-            }
-         });
+    {
+      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);
-          }
-        });
+    {
+      public void valueChanged(ListSelectionEvent e)
+      {
+        int index = linkNameList.getSelectedIndex();
+        linkURLList.setSelectedIndex(index);
+      }
+    });
 
     linkScrollPane.setBorder(null);
     linkPanel.setBorder(new TitledBorder("URL link from Sequence ID"));
@@ -294,9 +298,9 @@ public class GPreferences extends JPanel
       public void mouseClicked(MouseEvent e)
       {
         if (e.getClickCount() > 1)
-            {
-              defaultBrowser_mouseClicked(e);
-            }
+        {
+          defaultBrowser_mouseClicked(e);
+        }
       }
     });
     useProxy.setFont(verdana11);
@@ -422,11 +426,11 @@ public class GPreferences extends JPanel
     linkScrollPane.getViewport().add(linkPanel2, null);
     linkPanel2.add(linkURLList, BorderLayout.CENTER);
     linkPanel2.add(linkNameList, BorderLayout.WEST);
-        okCancelPanel.add(ok);
-        okCancelPanel.add(cancel);
+    okCancelPanel.add(ok);
+    okCancelPanel.add(cancel);
     this.add(tabbedPane, java.awt.BorderLayout.CENTER);
 
-        this.add(okCancelPanel, java.awt.BorderLayout.SOUTH);
+    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));
@@ -453,18 +457,17 @@ public class GPreferences extends JPanel
         , 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);
+    dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
+    gapSymbolCB.setRenderer(dlcr);
 
     tabbedPane.add(visualTab, "Visual");
-    tabbedPane.add(connectTab,"Connections");
+    tabbedPane.add(connectTab, "Connections");
     tabbedPane.add(exportTab, "Output");
     jPanel11.add(jLabel1);
     jPanel11.add(blcjv);
@@ -485,51 +488,52 @@ public class GPreferences extends JPanel
     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!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void ok_actionPerformed(ActionEvent e)
+  {
+  }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void cancel_actionPerformed(ActionEvent e)
+  {
+  }
 
-    /**
-     * DOCUMENT ME!
-     */
-    public void startupFileTextfield_mouseClicked()
-    {
-    }
+  /**
+   * 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 newLink_actionPerformed(ActionEvent e)
+  {
 
   }
 
-  public void editLink_actionPerformed(ActionEvent e) {
+  public void editLink_actionPerformed(ActionEvent e)
+  {
 
   }
 
-  public void deleteLink_actionPerformed(ActionEvent e) {
+  public void deleteLink_actionPerformed(ActionEvent e)
+  {
 
   }
 
@@ -545,8 +549,8 @@ public class GPreferences extends JPanel
 
   public void useProxy_actionPerformed()
   {
-      proxyServerTB.setEnabled(useProxy.isSelected());
-      proxyPortTB.setEnabled(useProxy.isSelected());
+    proxyServerTB.setEnabled(useProxy.isSelected());
+    proxyPortTB.setEnabled(useProxy.isSelected());
   }
 
 }
diff --git a/src/jalview/jbgui/GSequenceLink.java b/src/jalview/jbgui/GSequenceLink.java
index 2c688ce..19740fa 100755
--- a/src/jalview/jbgui/GSequenceLink.java
+++ b/src/jalview/jbgui/GSequenceLink.java
@@ -1,29 +1,26 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 jalview.jbgui;
 
 import java.awt.*;
-import javax.swing.JTextField;
-import javax.swing.JLabel;
+import java.awt.event.*;
 import javax.swing.*;
-import java.awt.event.KeyAdapter;
-import java.awt.event.KeyEvent;
 
 public class GSequenceLink
     extends Panel
@@ -109,18 +106,17 @@ public class GSequenceLink
 
   public boolean checkValid()
   {
-    if(urlTB.getText().indexOf("$SEQUENCE_ID$")==-1)
+    if (urlTB.getText().indexOf("$SEQUENCE_ID$") == -1)
     {
       JOptionPane.showInternalMessageDialog(jalview.gui.Desktop.desktop,
                                             "Sequence URL must contain $SEQUENCE_ID$",
-           "URL not valid", JOptionPane.WARNING_MESSAGE);
+                                            "URL not valid",
+                                            JOptionPane.WARNING_MESSAGE);
       return false;
     }
     return true;
   }
 
-
-
   JTextField nameTB = new JTextField();
   JTextField urlTB = new JTextField();
   JLabel jLabel1 = new JLabel();
@@ -130,19 +126,18 @@ public class GSequenceLink
   GridBagLayout gridBagLayout1 = new GridBagLayout();
   public void nameTB_keyTyped(KeyEvent e)
   {
-    if(e.getKeyChar()=='|')
-     {
-       e.consume();
-     }
+    if (e.getKeyChar() == '|')
+    {
+      e.consume();
+    }
   }
 
   public void urlTB_keyTyped(KeyEvent e)
   {
-    if (e.getKeyChar() == '|' || e.getKeyChar()==' ')
+    if (e.getKeyChar() == '|' || e.getKeyChar() == ' ')
     {
       e.consume();
     }
 
   }
 }
-
diff --git a/src/jalview/jbgui/GSliderPanel.java b/src/jalview/jbgui/GSliderPanel.java
index 198c479..568c66a 100755
--- a/src/jalview/jbgui/GSliderPanel.java
+++ b/src/jalview/jbgui/GSliderPanel.java
@@ -1,28 +1,26 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 jalview.jbgui;
 
 import java.awt.*;
 import java.awt.event.*;
-
 import javax.swing.*;
-import java.awt.BorderLayout;
 
 /**
  * DOCUMENT ME!
@@ -30,52 +28,54 @@ import java.awt.BorderLayout;
  * @author $author$
  * @version $Revision$
  */
-public class GSliderPanel extends JPanel
+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();
+  // 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()
+   * Creates a new GSliderPanel object.
+   */
+  public GSliderPanel()
+  {
+    try
     {
-        try
-        {
-            jbInit();
-        }
-        catch (Exception e)
-        {
-            e.printStackTrace();
-        }
+      jbInit();
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @throws Exception DOCUMENT ME!
-     */
-    private void jbInit() throws Exception
+    catch (Exception e)
     {
-        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);
+      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)
@@ -84,111 +84,111 @@ public class GSliderPanel extends JPanel
       }
     });
     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");
+    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);
+    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);
+    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 valueField_actionPerformed(ActionEvent e)
+  {
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void applyButton_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 undoButton_actionPerformed(ActionEvent e)
+  {
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void allGroupsCheck_actionPerformed(ActionEvent e)
-    {
-    }
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void allGroupsCheck_actionPerformed(ActionEvent e)
+  {
+  }
 
-    public void slider_mouseReleased(MouseEvent e)
-    {
+  public void slider_mouseReleased(MouseEvent e)
+  {
 
-    }
   }
+}
diff --git a/src/jalview/jbgui/GTreePanel.java b/src/jalview/jbgui/GTreePanel.java
index 9b125de..5d3b8b8 100755
--- a/src/jalview/jbgui/GTreePanel.java
+++ b/src/jalview/jbgui/GTreePanel.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -21,8 +21,7 @@ package jalview.jbgui;
 import java.awt.*;
 import java.awt.event.*;
 import javax.swing.*;
-import javax.swing.event.MenuListener;
-import javax.swing.event.MenuEvent;
+import javax.swing.event.*;
 
 public class GTreePanel
     extends JInternalFrame
diff --git a/src/jalview/jbgui/GUserDefinedColours.java b/src/jalview/jbgui/GUserDefinedColours.java
index 9b685b5..1801152 100755
--- a/src/jalview/jbgui/GUserDefinedColours.java
+++ b/src/jalview/jbgui/GUserDefinedColours.java
@@ -1,28 +1,26 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 jalview.jbgui;
 
 import java.awt.*;
 import java.awt.event.*;
-
 import javax.swing.*;
-import java.awt.Dimension;
 
 /**
  * DOCUMENT ME!
@@ -30,17 +28,18 @@ import java.awt.Dimension;
  * @author $author$
  * @version $Revision$
  */
-public class GUserDefinedColours extends JPanel
+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();
+  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();
@@ -60,78 +59,79 @@ public class GUserDefinedColours extends JPanel
   protected JCheckBox caseSensitive = new JCheckBox();
   protected JButton lcaseColour = new JButton();
   /**
-     * Creates a new GUserDefinedColours object.
-     */
-    public GUserDefinedColours()
+   * Creates a new GUserDefinedColours object.
+   */
+  public GUserDefinedColours()
+  {
+    try
     {
-        try
-        {
-            jbInit();
-        }
-        catch (Exception e)
-        {
-            e.printStackTrace();
-        }
-
+      jbInit();
+    }
+    catch (Exception e)
+    {
+      e.printStackTrace();
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @throws Exception DOCUMENT ME!
-     */
-    private void jbInit() throws Exception
+  }
+
+  /**
+   * 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()
     {
-        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));
+      public void actionPerformed(ActionEvent e)
+      {
+        cancelButton_actionPerformed(e);
+      }
+    });
+    this.setBackground(new Color(212, 208, 223));
     lowerPanel.setOpaque(false);
     lowerPanel.setLayout(borderLayout3);
     colorChooser.setOpaque(false);
@@ -196,58 +196,58 @@ public class GUserDefinedColours extends JPanel
     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 okButton_actionPerformed(ActionEvent e)
+  {
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void applyButton_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 loadbutton_actionPerformed(ActionEvent e)
+  {
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void savebutton_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)
-    {
-    }
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void cancelButton_actionPerformed(ActionEvent e)
+  {
+  }
 
-    public void caseSensitive_actionPerformed(ActionEvent e)
-    {
+  public void caseSensitive_actionPerformed(ActionEvent e)
+  {
 
-    }
+  }
 
-    public void lcaseColour_actionPerformed(ActionEvent e)
-    {
+  public void lcaseColour_actionPerformed(ActionEvent e)
+  {
 
-    }
+  }
 }
diff --git a/src/jalview/jbgui/GWebserviceInfo.java b/src/jalview/jbgui/GWebserviceInfo.java
index 8f21f63..ca68115 100755
--- a/src/jalview/jbgui/GWebserviceInfo.java
+++ b/src/jalview/jbgui/GWebserviceInfo.java
@@ -1,26 +1,25 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 jalview.jbgui;
 
 import java.awt.*;
 import java.awt.event.*;
-
 import javax.swing.*;
 
 /**
@@ -29,86 +28,88 @@ import javax.swing.*;
  * @author $author$
  * @version $Revision$
  */
-public class GWebserviceInfo extends JPanel
+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();
+  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()
+   * Creates a new GWebserviceInfo object.
+   */
+  public GWebserviceInfo()
+  {
+    try
+    {
+      jbInit();
+    }
+    catch (Exception e)
     {
-        try
-        {
-            jbInit();
-        }
-        catch (Exception e)
-        {
-            e.printStackTrace();
-        }
+      e.printStackTrace();
     }
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @throws Exception DOCUMENT ME!
-     */
-    private void jbInit() throws Exception
+  /**
+   * 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()
     {
-        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);
-                }
-            });
+      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);
+    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));
+        , GridBagConstraints.CENTER,
+        GridBagConstraints.NONE,
+        new Insets(19, 6, 16, 4), 0, 0));
   }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void cancel_actionPerformed(ActionEvent e)
-    {
-    }
+  /**
+   * 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 06177f5..2f79875 100755
--- a/src/jalview/math/Matrix.java
+++ b/src/jalview/math/Matrix.java
@@ -1,27 +1,26 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 jalview.math;
 
-import jalview.util.*;
-
 import java.io.*;
 
+import jalview.util.*;
 
 /**
  * DOCUMENT ME!
@@ -31,822 +30,822 @@ import java.io.*;
  */
 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)
+  /**
+   * 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++)
     {
-        this.rows = rows;
-        this.cols = cols;
-        this.value = value;
+      for (int j = 0; j < rows; j++)
+      {
+        out[i][j] = value[j][i];
+      }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Matrix transpose()
+    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++)
     {
-        double[][] out = new double[cols][rows];
+      for (int j = 0; j < this.cols; j++)
+      {
+        tmp[i][j] = 0.0;
 
-        for (int i = 0; i < cols; i++)
+        for (int k = 0; k < in.cols; k++)
         {
-            for (int j = 0; j < rows; j++)
-            {
-                out[i][j] = value[j][i];
-            }
+          tmp[i][j] += (in.value[i][k] * this.value[k][j]);
         }
-
-        return new Matrix(out, cols, rows);
+      }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param ps DOCUMENT ME!
-     */
-    public void print(PrintStream ps)
+    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++)
     {
-        for (int i = 0; i < rows; i++)
-        {
-            for (int j = 0; j < cols; j++)
-            {
-                Format.print(ps, "%8.2f", value[i][j]);
-            }
+      out[i] = 0.0;
 
-            ps.println();
-        }
+      for (int k = 0; k < in.length; k++)
+      {
+        out[i] += (value[i][k] * in[k]);
+      }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param in DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Matrix preMultiply(Matrix in)
+    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++)
     {
-        double[][] tmp = new double[in.rows][this.cols];
+      for (int j = 0; j < in.cols; j++)
+      {
+        out[i][j] = 0.0;
 
-        for (int i = 0; i < in.rows; i++)
+        for (int k = 0; k < rows; k++)
         {
-            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]);
-                }
-            }
+          out[i][j] = out[i][j] + (value[i][k] * in.value[k][j]);
         }
+      }
+    }
+
+    return new Matrix(out, this.cols, in.rows);
+  }
 
-        return new Matrix(tmp, in.rows, this.cols);
+  /**
+   * 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];
+      }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param in DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public double[] vectorPostMultiply(double[] in)
+    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--)
     {
-        double[] out = new double[in.length];
+      l = i - 1;
+      h = 0.0;
+      scale = 0.0;
 
-        for (int i = 0; i < in.length; i++)
+      if (l > 1)
+      {
+        for (k = 1; k <= l; k++)
         {
-            out[i] = 0.0;
+          scale += Math.abs(value[i - 1][k - 1]);
+        }
 
-            for (int k = 0; k < in.length; k++)
+        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++)
             {
-                out[i] += (value[i][k] * in[k]);
+              g += (value[j - 1][k - 1] * value[i - 1][k - 1]);
             }
-        }
 
-        return out;
-    }
+            for (k = j + 1; k <= l; k++)
+            {
+              g += (value[k - 1][j - 1] * value[i - 1][k - 1]);
+            }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param in DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Matrix postMultiply(Matrix in)
-    {
-        double[][] out = new double[this.rows][in.cols];
+            e[j - 1] = g / h;
+            f += (e[j - 1] * value[i - 1][j - 1]);
+          }
 
-        for (int i = 0; i < this.rows; i++)
-        {
-            for (int j = 0; j < in.cols; j++)
-            {
-                out[i][j] = 0.0;
+          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 (int k = 0; k < rows; k++)
-                {
-                    out[i][j] = out[i][j] + (value[i][k] * in.value[k][j]);
-                }
+            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];
+      }
 
-        return new Matrix(out, this.cols, in.rows);
+      d[i - 1] = h;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Matrix copy()
+    d[0] = 0.0;
+    e[0] = 0.0;
+
+    for (i = 1; i <= n; i++)
     {
-        double[][] newmat = new double[rows][cols];
+      l = i - 1;
 
-        for (int i = 0; i < rows; i++)
+      if (d[i - 1] != 0.0)
+      {
+        for (j = 1; j <= l; j++)
         {
-            for (int j = 0; j < cols; j++)
-            {
-                newmat[i][j] = value[i][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]);
+          }
         }
+      }
 
-        return new Matrix(newmat, rows, cols);
+      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];
     }
 
-    /**
-     * DOCUMENT ME!
-     */
-    public void tred()
+    e[n - 1] = 0.0;
+
+    for (l = 1; l <= n; l++)
     {
-        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--)
+      iter = 0;
+
+      do
+      {
+        for (m = l; m <= (n - 1); m++)
         {
-            l = i - 1;
-            h = 0.0;
-            scale = 0.0;
+          dd = Math.abs(d[m - 1]) + Math.abs(d[m]);
+
+          if ( (Math.abs(e[m - 1]) + dd) == dd)
+          {
+            break;
+          }
+        }
 
-            if (l > 1)
+        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))
             {
-                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]));
-                        }
-                    }
-                }
+              c = g / f;
+              r = Math.sqrt( (c * c) + 1.0);
+              e[i] = f * r;
+              s = 1.0 / r;
+              c *= s;
             }
             else
             {
-                e[i - 1] = value[i - 1][l - 1];
+              s = f / g;
+              r = Math.sqrt( (s * s) + 1.0);
+              e[i] = g * r;
+              c = 1.0 / r;
+              s *= c;
             }
 
-            d[i - 1] = h;
-        }
-
-        d[0] = 0.0;
-        e[0] = 0.0;
-
-        for (i = 1; i <= n; i++)
-        {
-            l = i - 1;
+            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;
 
-            if (d[i - 1] != 0.0)
+            for (k = 1; k <= n; k++)
             {
-                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]);
-                    }
-                }
+              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[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;
-            }
+          d[l - 1] = d[l - 1] - p;
+          e[l - 1] = g;
+          e[m - 1] = 0.0;
         }
+      }
+      while (m != l);
     }
-
-    /**
-     * DOCUMENT ME!
-     */
-    public void tqli()
+  }
+
+  /**
+   * 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--)
     {
-        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++)
+      l = i - 1;
+      h = 0.0;
+      scale = 0.0;
+
+      if (l > 0)
+      {
+        for (k = 0; k < l; k++)
         {
-            e[i - 2] = e[i - 1];
+          scale += Math.abs(value[i][k]);
         }
 
-        e[n - 1] = 0.0;
-
-        for (l = 1; l <= n; l++)
+        if (scale == 0.0)
         {
-            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);
+          e[i] = value[i][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--)
+        else
         {
-            l = i - 1;
-            h = 0.0;
-            scale = 0.0;
-
-            if (l > 0)
+          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++)
             {
-                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]));
-                        }
-                    }
-                }
+              g += (value[j][k] * value[i][k]);
             }
-            else
+
+            for (k = j; k < l; k++)
             {
-                e[i] = value[i][l];
+              g += (value[k][j] * value[i][k]);
             }
 
-            d[i] = h;
-        }
-
-        d[0] = 0.0;
-        e[0] = 0.0;
-
-        for (i = 0; i < n; i++)
-        {
-            l = i - 1;
+            e[j] = g / h;
+            f += (e[j] * value[i][j]);
+          }
 
-            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]);
-                    }
-                }
-            }
+          hh = f / (h + h);
 
-            d[i] = value[i][i];
-            value[i][i] = 1.0;
+          for (j = 0; j < l; j++)
+          {
+            f = value[i][j];
+            g = e[j] - (hh * f);
+            e[j] = g;
 
-            for (j = 0; j < l; j++)
+            for (k = 0; k < j; k++)
             {
-                value[j][i] = 0.0;
-                value[i][j] = 0.0;
+              value[j][k] -= ( (f * e[k]) + (g * value[i][k]));
             }
+          }
         }
+      }
+      else
+      {
+        e[i] = value[i][l];
+      }
+
+      d[i] = h;
     }
 
-    /**
-     * 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];
-        }
+    d[0] = 0.0;
+    e[0] = 0.0;
 
-        e[n - 1] = 0.0;
+    for (i = 0; i < n; i++)
+    {
+      l = i - 1;
 
-        for (l = 1; l <= n; l++)
+      if (d[i] != 0.0)
+      {
+        for (j = 0; j < l; j++)
         {
-            iter = 0;
+          g = 0.0;
 
-            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);
+          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]);
+          }
         }
-    }
+      }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param a DOCUMENT ME!
-     * @param b DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public double sign(double a, double b)
+      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++)
     {
-        if (b < 0)
-        {
-            return -Math.abs(a);
-        }
-        else
-        {
-            return Math.abs(a);
-        }
+      e[i - 2] = e[i - 1];
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param n DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public double[] getColumn(int n)
+    e[n - 1] = 0.0;
+
+    for (l = 1; l <= n; l++)
     {
-        double[] out = new double[rows];
+      iter = 0;
 
-        for (int i = 0; i < rows; i++)
+      do
+      {
+        for (m = l; m <= (n - 1); m++)
         {
-            out[i] = value[i][n];
-        }
-
-        return out;
-    }
+          dd = Math.abs(d[m - 1]) + Math.abs(d[m]);
 
-    /**
-     * 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]);
+          if ( (Math.abs(e[m - 1]) + dd) == dd)
+          {
+            break;
+          }
         }
-    }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param ps DOCUMENT ME!
-     */
-    public void printE(PrintStream ps)
-    {
-        for (int j = 0; j < rows; j++)
+        if (m != l)
         {
-            Format.print(ps, "%15.4e", e[j]);
-        }
-    }
+          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;
+            }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param args DOCUMENT ME!
-     */
-    public static void main(String[] args)
-    {
-        int n = Integer.parseInt(args[0]);
-        double[][] in = new double[n][n];
+            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 (int i = 0; i < n; i++)
-        {
-            for (int j = 0; j < n; j++)
+            for (k = 1; k <= n; k++)
             {
-                in[i][j] = (double) Math.random();
+              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];
+    }
 
-        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();
+    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 ba90370..eff8dea 100755
--- a/src/jalview/math/RotatableMatrix.java
+++ b/src/jalview/math/RotatableMatrix.java
@@ -1,24 +1,23 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 jalview.math;
 
-
 /**
  * DOCUMENT ME!
  *
@@ -27,306 +26,306 @@ package jalview.math;
  */
 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()
+  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')
     {
-        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]);
-    }
+      rot[0][0] = (float) costheta;
 
-    /**
-     * 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);
+      rot[0][1] = (float) - sintheta;
 
-        float sintheta = (float) Math.sin((degrees * Math.PI) / (float) 180.0);
+      rot[0][2] = (float) 0.0;
 
-        if (axis == 'z')
-        {
-            rot[0][0] = (float) costheta;
+      rot[1][0] = (float) sintheta;
 
-            rot[0][1] = (float) -sintheta;
+      rot[1][1] = (float) costheta;
 
-            rot[0][2] = (float) 0.0;
+      rot[1][2] = (float) 0.0;
 
-            rot[1][0] = (float) sintheta;
+      rot[2][0] = (float) 0.0;
 
-            rot[1][1] = (float) costheta;
+      rot[2][1] = (float) 0.0;
 
-            rot[1][2] = (float) 0.0;
+      rot[2][2] = (float) 1.0;
 
-            rot[2][0] = (float) 0.0;
+      preMultiply(rot);
+    }
 
-            rot[2][1] = (float) 0.0;
+    if (axis == 'x')
+    {
+      rot[0][0] = (float) 1.0;
 
-            rot[2][2] = (float) 1.0;
+      rot[0][1] = (float) 0.0;
 
-            preMultiply(rot);
-        }
+      rot[0][2] = (float) 0.0;
 
-        if (axis == 'x')
-        {
-            rot[0][0] = (float) 1.0;
+      rot[1][0] = (float) 0.0;
 
-            rot[0][1] = (float) 0.0;
+      rot[1][1] = (float) costheta;
 
-            rot[0][2] = (float) 0.0;
+      rot[1][2] = (float) sintheta;
 
-            rot[1][0] = (float) 0.0;
+      rot[2][0] = (float) 0.0;
 
-            rot[1][1] = (float) costheta;
+      rot[2][1] = (float) - sintheta;
 
-            rot[1][2] = (float) sintheta;
+      rot[2][2] = (float) costheta;
 
-            rot[2][0] = (float) 0.0;
+      preMultiply(rot);
+    }
 
-            rot[2][1] = (float) -sintheta;
+    if (axis == 'y')
+    {
+      rot[0][0] = (float) costheta;
 
-            rot[2][2] = (float) costheta;
+      rot[0][1] = (float) 0.0;
 
-            preMultiply(rot);
-        }
+      rot[0][2] = (float) - sintheta;
 
-        if (axis == 'y')
-        {
-            rot[0][0] = (float) costheta;
+      rot[1][0] = (float) 0.0;
 
-            rot[0][1] = (float) 0.0;
+      rot[1][1] = (float) 1.0;
 
-            rot[0][2] = (float) -sintheta;
+      rot[1][2] = (float) 0.0;
 
-            rot[1][0] = (float) 0.0;
+      rot[2][0] = (float) sintheta;
 
-            rot[1][1] = (float) 1.0;
+      rot[2][1] = (float) 0.0;
 
-            rot[1][2] = (float) 0.0;
+      rot[2][2] = (float) costheta;
 
-            rot[2][0] = (float) sintheta;
+      preMultiply(rot);
+    }
+  }
 
-            rot[2][1] = (float) 0.0;
+  /**
+   * DOCUMENT ME!
+   *
+   * @param vect DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public float[] vectorMultiply(float[] vect)
+  {
+    temp[0] = vect[0];
 
-            rot[2][2] = (float) costheta;
+    temp[1] = vect[1];
 
-            preMultiply(rot);
-        }
-    }
+    temp[2] = vect[2];
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param vect DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public float[] vectorMultiply(float[] vect)
+    for (int i = 0; i < 3; i++)
     {
-        temp[0] = vect[0];
-
-        temp[1] = vect[1];
+      temp[i] = (matrix[i][0] * vect[0]) + (matrix[i][1] * vect[1]) +
+          (matrix[i][2] * vect[2]);
+    }
 
-        temp[2] = vect[2];
+    vect[0] = temp[0];
 
-        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[1] = temp[1];
 
-        vect[0] = temp[0];
+    vect[2] = temp[2];
 
-        vect[1] = temp[1];
+    return vect;
+  }
 
-        vect[2] = temp[2];
+  /**
+   * DOCUMENT ME!
+   *
+   * @param mat DOCUMENT ME!
+   */
+  public void preMultiply(float[][] mat)
+  {
+    float[][] tmp = new float[3][3];
 
-        return vect;
+    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]);
+      }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param mat DOCUMENT ME!
-     */
-    public void preMultiply(float[][] mat)
+    for (int i = 0; i < 3; i++)
     {
-        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];
-            }
-        }
+      for (int j = 0; j < 3; j++)
+      {
+        matrix[i][j] = tmp[i][j];
+      }
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param mat DOCUMENT ME!
-     */
-    public void postMultiply(float[][] mat)
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param mat DOCUMENT ME!
+   */
+  public void postMultiply(float[][] mat)
+  {
+    float[][] tmp = new float[3][3];
+
+    for (int i = 0; i < 3; i++)
     {
-        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];
-            }
-        }
+      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]);
+      }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param args DOCUMENT ME!
-     */
-    public static void main(String[] args)
+    for (int i = 0; i < 3; i++)
     {
-        RotatableMatrix m = new RotatableMatrix(3, 3);
+      for (int j = 0; j < 3; j++)
+      {
+        matrix[i][j] = tmp[i][j];
+      }
+    }
+  }
 
-        m.addElement(0, 0, 1);
+  /**
+   * DOCUMENT ME!
+   *
+   * @param args DOCUMENT ME!
+   */
+  public static void main(String[] args)
+  {
+    RotatableMatrix m = new RotatableMatrix(3, 3);
 
-        m.addElement(0, 1, 0);
+    m.addElement(0, 0, 1);
 
-        m.addElement(0, 2, 0);
+    m.addElement(0, 1, 0);
 
-        m.addElement(1, 0, 0);
+    m.addElement(0, 2, 0);
 
-        m.addElement(1, 1, 2);
+    m.addElement(1, 0, 0);
 
-        m.addElement(1, 2, 0);
+    m.addElement(1, 1, 2);
 
-        m.addElement(2, 0, 0);
+    m.addElement(1, 2, 0);
 
-        m.addElement(2, 1, 0);
+    m.addElement(2, 0, 0);
 
-        m.addElement(2, 2, 1);
+    m.addElement(2, 1, 0);
 
-        m.print();
+    m.addElement(2, 2, 1);
 
-        RotatableMatrix n = new RotatableMatrix(3, 3);
+    m.print();
 
-        n.addElement(0, 0, 2);
+    RotatableMatrix n = new RotatableMatrix(3, 3);
 
-        n.addElement(0, 1, 1);
+    n.addElement(0, 0, 2);
 
-        n.addElement(0, 2, 1);
+    n.addElement(0, 1, 1);
 
-        n.addElement(1, 0, 2);
+    n.addElement(0, 2, 1);
 
-        n.addElement(1, 1, 1);
+    n.addElement(1, 0, 2);
 
-        n.addElement(1, 2, 1);
+    n.addElement(1, 1, 1);
 
-        n.addElement(2, 0, 2);
+    n.addElement(1, 2, 1);
 
-        n.addElement(2, 1, 1);
+    n.addElement(2, 0, 2);
 
-        n.addElement(2, 2, 1);
+    n.addElement(2, 1, 1);
 
-        n.print();
+    n.addElement(2, 2, 1);
 
-        //m.postMultiply(n.matrix);
-        //m.print();
-        //     m.rotate(45,'z',new RotatableMatrix(3,3));
-        float[] vect = new float[3];
+    n.print();
 
-        vect[0] = 2;
+    //m.postMultiply(n.matrix);
+    //m.print();
+    //     m.rotate(45,'z',new RotatableMatrix(3,3));
+    float[] vect = new float[3];
 
-        vect[1] = 4;
+    vect[0] = 2;
 
-        vect[2] = 6;
+    vect[1] = 4;
 
-        vect = m.vectorMultiply(vect);
+    vect[2] = 6;
 
-        System.out.println(vect[0] + " " + vect[1] + " " + vect[2]);
-    }
+    vect = m.vectorMultiply(vect);
 
-    /**
-     * DOCUMENT ME!
-     */
-    public void setIdentity()
-    {
-        matrix[0][0] = (float) 1.0;
+    System.out.println(vect[0] + " " + vect[1] + " " + vect[2]);
+  }
 
-        matrix[1][1] = (float) 1.0;
+  /**
+   * DOCUMENT ME!
+   */
+  public void setIdentity()
+  {
+    matrix[0][0] = (float) 1.0;
 
-        matrix[2][2] = (float) 1.0;
+    matrix[1][1] = (float) 1.0;
 
-        matrix[0][1] = (float) 0.0;
+    matrix[2][2] = (float) 1.0;
 
-        matrix[0][2] = (float) 0.0;
+    matrix[0][1] = (float) 0.0;
 
-        matrix[1][0] = (float) 0.0;
+    matrix[0][2] = (float) 0.0;
 
-        matrix[1][2] = (float) 0.0;
+    matrix[1][0] = (float) 0.0;
 
-        matrix[2][0] = (float) 0.0;
+    matrix[1][2] = (float) 0.0;
 
-        matrix[2][1] = (float) 0.0;
-    }
+    matrix[2][0] = (float) 0.0;
+
+    matrix[2][1] = (float) 0.0;
+  }
 }
diff --git a/src/jalview/schemabinding/version2/Annotation.java b/src/jalview/schemabinding/version2/Annotation.java
index 61f9413..c9f79cb 100755
--- a/src/jalview/schemabinding/version2/Annotation.java
+++ b/src/jalview/schemabinding/version2/Annotation.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,610 +7,626 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
 //---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import java.util.*;
 
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import java.util.Enumeration;
-import java.util.Vector;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
+import org.exolab.castor.xml.*;
 
 /**
  * Class Annotation.
- * 
+ *
  * @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 _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();
-        _annotationElementList = new Vector();
-    } //-- jalview.schemabinding.version2.Annotation()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method addAnnotationElement
-     * 
-     * 
-     * 
-     * @param vAnnotationElement
-     */
-    public void addAnnotationElement(jalview.schemabinding.version2.AnnotationElement vAnnotationElement)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _annotationElementList.addElement(vAnnotationElement);
-    } //-- void addAnnotationElement(jalview.schemabinding.version2.AnnotationElement) 
-
-    /**
-     * Method addAnnotationElement
-     * 
-     * 
-     * 
-     * @param index
-     * @param vAnnotationElement
-     */
-    public void addAnnotationElement(int index, jalview.schemabinding.version2.AnnotationElement vAnnotationElement)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _annotationElementList.insertElementAt(vAnnotationElement, index);
-    } //-- void addAnnotationElement(int, jalview.schemabinding.version2.AnnotationElement) 
-
-    /**
-     * Method deleteGraph
-     * 
-     */
-    public void deleteGraph()
-    {
-        this._has_graph= false;
-    } //-- void deleteGraph() 
-
-    /**
-     * Method deleteGraphColour
-     * 
-     */
-    public void deleteGraphColour()
-    {
-        this._has_graphColour= false;
-    } //-- void deleteGraphColour() 
-
-    /**
-     * Method deleteGraphGroup
-     * 
-     */
-    public void deleteGraphGroup()
-    {
-        this._has_graphGroup= false;
-    } //-- void deleteGraphGroup() 
-
-    /**
-     * Method deleteGraphType
-     * 
-     */
-    public void deleteGraphType()
-    {
-        this._has_graphType= false;
-    } //-- void deleteGraphType() 
-
-    /**
-     * Method enumerateAnnotationElement
-     * 
-     * 
-     * 
-     * @return Enumeration
-     */
-    public java.util.Enumeration enumerateAnnotationElement()
-    {
-        return _annotationElementList.elements();
-    } //-- java.util.Enumeration enumerateAnnotationElement() 
-
-    /**
-     * Method getAnnotationElement
-     * 
-     * 
-     * 
-     * @param index
-     * @return AnnotationElement
-     */
-    public jalview.schemabinding.version2.AnnotationElement getAnnotationElement(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _annotationElementList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        
-        return (jalview.schemabinding.version2.AnnotationElement) _annotationElementList.elementAt(index);
-    } //-- jalview.schemabinding.version2.AnnotationElement getAnnotationElement(int) 
-
-    /**
-     * Method getAnnotationElement
-     * 
-     * 
-     * 
-     * @return AnnotationElement
-     */
-    public jalview.schemabinding.version2.AnnotationElement[] getAnnotationElement()
-    {
-        int size = _annotationElementList.size();
-        jalview.schemabinding.version2.AnnotationElement[] mArray = new jalview.schemabinding.version2.AnnotationElement[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = (jalview.schemabinding.version2.AnnotationElement) _annotationElementList.elementAt(index);
-        }
-        return mArray;
-    } //-- jalview.schemabinding.version2.AnnotationElement[] getAnnotationElement() 
-
-    /**
-     * Method getAnnotationElementCount
-     * 
-     * 
-     * 
-     * @return int
-     */
-    public int getAnnotationElementCount()
-    {
-        return _annotationElementList.size();
-    } //-- int getAnnotationElementCount() 
-
-    /**
-     * Returns the value of field 'description'.
-     * 
-     * @return String
-     * @return the value of field 'description'.
-     */
-    public java.lang.String getDescription()
-    {
-        return this._description;
-    } //-- java.lang.String getDescription() 
-
-    /**
-     * Returns the value of field 'graph'.
-     * 
-     * @return boolean
-     * @return the value of field 'graph'.
-     */
-    public boolean getGraph()
-    {
-        return this._graph;
-    } //-- boolean getGraph() 
-
-    /**
-     * Returns the value of field 'graphColour'.
-     * 
-     * @return int
-     * @return the value of field 'graphColour'.
-     */
-    public int getGraphColour()
-    {
-        return this._graphColour;
-    } //-- int getGraphColour() 
-
-    /**
-     * Returns the value of field 'graphGroup'.
-     * 
-     * @return int
-     * @return the value of field 'graphGroup'.
-     */
-    public int getGraphGroup()
-    {
-        return this._graphGroup;
-    } //-- int getGraphGroup() 
-
-    /**
-     * Returns the value of field 'graphType'.
-     * 
-     * @return int
-     * @return the value of field 'graphType'.
-     */
-    public int getGraphType()
-    {
-        return this._graphType;
-    } //-- int getGraphType() 
-
-    /**
-     * Returns the value of field 'id'.
-     * 
-     * @return String
-     * @return the value of field 'id'.
-     */
-    public java.lang.String getId()
-    {
-        return this._id;
-    } //-- java.lang.String getId() 
-
-    /**
-     * Returns the value of field 'label'.
-     * 
-     * @return String
-     * @return the value of field 'label'.
-     */
-    public java.lang.String getLabel()
-    {
-        return this._label;
-    } //-- java.lang.String getLabel() 
-
-    /**
-     * Returns the value of field 'sequenceRef'.
-     * 
-     * @return String
-     * @return the value of field 'sequenceRef'.
-     */
-    public java.lang.String getSequenceRef()
-    {
-        return this._sequenceRef;
-    } //-- java.lang.String getSequenceRef() 
-
-    /**
-     * Returns the value of field 'thresholdLine'.
-     * 
-     * @return ThresholdLine
-     * @return the value of field 'thresholdLine'.
-     */
-    public jalview.schemabinding.version2.ThresholdLine getThresholdLine()
-    {
-        return this._thresholdLine;
-    } //-- jalview.schemabinding.version2.ThresholdLine getThresholdLine() 
-
-    /**
-     * Method hasGraph
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasGraph()
-    {
-        return this._has_graph;
-    } //-- boolean hasGraph() 
-
-    /**
-     * Method hasGraphColour
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasGraphColour()
-    {
-        return this._has_graphColour;
-    } //-- boolean hasGraphColour() 
-
-    /**
-     * Method hasGraphGroup
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasGraphGroup()
-    {
-        return this._has_graphGroup;
-    } //-- boolean hasGraphGroup() 
-
-    /**
-     * Method hasGraphType
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasGraphType()
-    {
-        return this._has_graphType;
-    } //-- boolean hasGraphType() 
-
-    /**
-     * Method isValid
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean isValid()
-    {
-        try {
-            validate();
-        }
-        catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    } //-- boolean isValid() 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param out
-     */
-    public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, out);
-    } //-- void marshal(java.io.Writer) 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param handler
-     */
-    public void marshal(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, handler);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
-
-    /**
-     * Method removeAllAnnotationElement
-     * 
-     */
-    public void removeAllAnnotationElement()
-    {
-        _annotationElementList.removeAllElements();
-    } //-- void removeAllAnnotationElement() 
-
-    /**
-     * Method removeAnnotationElement
-     * 
-     * 
-     * 
-     * @param index
-     * @return AnnotationElement
-     */
-    public jalview.schemabinding.version2.AnnotationElement removeAnnotationElement(int index)
-    {
-        java.lang.Object obj = _annotationElementList.elementAt(index);
-        _annotationElementList.removeElementAt(index);
-        return (jalview.schemabinding.version2.AnnotationElement) obj;
-    } //-- jalview.schemabinding.version2.AnnotationElement removeAnnotationElement(int) 
-
-    /**
-     * Method setAnnotationElement
-     * 
-     * 
-     * 
-     * @param index
-     * @param vAnnotationElement
-     */
-    public void setAnnotationElement(int index, jalview.schemabinding.version2.AnnotationElement vAnnotationElement)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _annotationElementList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        _annotationElementList.setElementAt(vAnnotationElement, index);
-    } //-- void setAnnotationElement(int, jalview.schemabinding.version2.AnnotationElement) 
-
-    /**
-     * Method setAnnotationElement
-     * 
-     * 
-     * 
-     * @param annotationElementArray
-     */
-    public void setAnnotationElement(jalview.schemabinding.version2.AnnotationElement[] annotationElementArray)
-    {
-        //-- copy array
-        _annotationElementList.removeAllElements();
-        for (int i = 0; i < annotationElementArray.length; i++) {
-            _annotationElementList.addElement(annotationElementArray[i]);
-        }
-    } //-- void setAnnotationElement(jalview.schemabinding.version2.AnnotationElement) 
-
-    /**
-     * Sets the value of field 'description'.
-     * 
-     * @param description the value of field 'description'.
-     */
-    public void setDescription(java.lang.String description)
-    {
-        this._description = description;
-    } //-- void setDescription(java.lang.String) 
-
-    /**
-     * Sets the value of field 'graph'.
-     * 
-     * @param graph the value of field 'graph'.
-     */
-    public void setGraph(boolean graph)
-    {
-        this._graph = graph;
-        this._has_graph = true;
-    } //-- void setGraph(boolean) 
-
-    /**
-     * Sets the value of field 'graphColour'.
-     * 
-     * @param graphColour the value of field 'graphColour'.
-     */
-    public void setGraphColour(int graphColour)
-    {
-        this._graphColour = graphColour;
-        this._has_graphColour = true;
-    } //-- void setGraphColour(int) 
-
-    /**
-     * Sets the value of field 'graphGroup'.
-     * 
-     * @param graphGroup the value of field 'graphGroup'.
-     */
-    public void setGraphGroup(int graphGroup)
-    {
-        this._graphGroup = graphGroup;
-        this._has_graphGroup = true;
-    } //-- void setGraphGroup(int) 
-
-    /**
-     * Sets the value of field 'graphType'.
-     * 
-     * @param graphType the value of field 'graphType'.
-     */
-    public void setGraphType(int graphType)
-    {
-        this._graphType = graphType;
-        this._has_graphType = true;
-    } //-- void setGraphType(int) 
-
-    /**
-     * Sets the value of field 'id'.
-     * 
-     * @param id the value of field 'id'.
-     */
-    public void setId(java.lang.String id)
-    {
-        this._id = id;
-    } //-- void setId(java.lang.String) 
-
-    /**
-     * Sets the value of field 'label'.
-     * 
-     * @param label the value of field 'label'.
-     */
-    public void setLabel(java.lang.String label)
-    {
-        this._label = label;
-    } //-- void setLabel(java.lang.String) 
-
-    /**
-     * Sets the value of field 'sequenceRef'.
-     * 
-     * @param sequenceRef the value of field 'sequenceRef'.
-     */
-    public void setSequenceRef(java.lang.String sequenceRef)
-    {
-        this._sequenceRef = sequenceRef;
-    } //-- void setSequenceRef(java.lang.String) 
-
-    /**
-     * Sets the value of field 'thresholdLine'.
-     * 
-     * @param thresholdLine the value of field 'thresholdLine'.
-     */
-    public void setThresholdLine(jalview.schemabinding.version2.ThresholdLine thresholdLine)
-    {
-        this._thresholdLine = thresholdLine;
-    } //-- void setThresholdLine(jalview.schemabinding.version2.ThresholdLine) 
-
-    /**
-     * Method unmarshal
-     * 
-     * 
-     * 
-     * @param reader
-     * @return Object
-     */
-    public static java.lang.Object unmarshal(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);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
-
-    /**
-     * Method validate
-     * 
-     */
-    public void validate()
-        throws org.exolab.castor.xml.ValidationException
-    {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    } //-- void validate() 
+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 _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();
+    _annotationElementList = new Vector();
+  } //-- jalview.schemabinding.version2.Annotation()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Method addAnnotationElement
+   *
+   *
+   *
+   * @param vAnnotationElement
+   */
+  public void addAnnotationElement(jalview.schemabinding.version2.
+                                   AnnotationElement vAnnotationElement)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _annotationElementList.addElement(vAnnotationElement);
+  } //-- void addAnnotationElement(jalview.schemabinding.version2.AnnotationElement)
+
+  /**
+   * Method addAnnotationElement
+   *
+   *
+   *
+   * @param index
+   * @param vAnnotationElement
+   */
+  public void addAnnotationElement(int index,
+                                   jalview.schemabinding.version2.AnnotationElement
+                                   vAnnotationElement)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _annotationElementList.insertElementAt(vAnnotationElement, index);
+  } //-- void addAnnotationElement(int, jalview.schemabinding.version2.AnnotationElement)
+
+  /**
+   * Method deleteGraph
+   *
+   */
+  public void deleteGraph()
+  {
+    this._has_graph = false;
+  } //-- void deleteGraph()
+
+  /**
+   * Method deleteGraphColour
+   *
+   */
+  public void deleteGraphColour()
+  {
+    this._has_graphColour = false;
+  } //-- void deleteGraphColour()
+
+  /**
+   * Method deleteGraphGroup
+   *
+   */
+  public void deleteGraphGroup()
+  {
+    this._has_graphGroup = false;
+  } //-- void deleteGraphGroup()
+
+  /**
+   * Method deleteGraphType
+   *
+   */
+  public void deleteGraphType()
+  {
+    this._has_graphType = false;
+  } //-- void deleteGraphType()
+
+  /**
+   * Method enumerateAnnotationElement
+   *
+   *
+   *
+   * @return Enumeration
+   */
+  public java.util.Enumeration enumerateAnnotationElement()
+  {
+    return _annotationElementList.elements();
+  } //-- java.util.Enumeration enumerateAnnotationElement()
+
+  /**
+   * Method getAnnotationElement
+   *
+   *
+   *
+   * @param index
+   * @return AnnotationElement
+   */
+  public jalview.schemabinding.version2.AnnotationElement getAnnotationElement(int
+      index)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _annotationElementList.size()))
+    {
+      throw new IndexOutOfBoundsException();
+    }
+
+    return (jalview.schemabinding.version2.AnnotationElement)
+        _annotationElementList.elementAt(index);
+  } //-- jalview.schemabinding.version2.AnnotationElement getAnnotationElement(int)
+
+  /**
+   * Method getAnnotationElement
+   *
+   *
+   *
+   * @return AnnotationElement
+   */
+  public jalview.schemabinding.version2.AnnotationElement[]
+      getAnnotationElement()
+  {
+    int size = _annotationElementList.size();
+    jalview.schemabinding.version2.AnnotationElement[] mArray = new jalview.
+        schemabinding.version2.AnnotationElement[size];
+    for (int index = 0; index < size; index++)
+    {
+      mArray[index] = (jalview.schemabinding.version2.AnnotationElement)
+          _annotationElementList.elementAt(index);
+    }
+    return mArray;
+  } //-- jalview.schemabinding.version2.AnnotationElement[] getAnnotationElement()
+
+  /**
+   * Method getAnnotationElementCount
+   *
+   *
+   *
+   * @return int
+   */
+  public int getAnnotationElementCount()
+  {
+    return _annotationElementList.size();
+  } //-- int getAnnotationElementCount()
+
+  /**
+   * Returns the value of field 'description'.
+   *
+   * @return String
+   * @return the value of field 'description'.
+   */
+  public java.lang.String getDescription()
+  {
+    return this._description;
+  } //-- java.lang.String getDescription()
+
+  /**
+   * Returns the value of field 'graph'.
+   *
+   * @return boolean
+   * @return the value of field 'graph'.
+   */
+  public boolean getGraph()
+  {
+    return this._graph;
+  } //-- boolean getGraph()
+
+  /**
+   * Returns the value of field 'graphColour'.
+   *
+   * @return int
+   * @return the value of field 'graphColour'.
+   */
+  public int getGraphColour()
+  {
+    return this._graphColour;
+  } //-- int getGraphColour()
+
+  /**
+   * Returns the value of field 'graphGroup'.
+   *
+   * @return int
+   * @return the value of field 'graphGroup'.
+   */
+  public int getGraphGroup()
+  {
+    return this._graphGroup;
+  } //-- int getGraphGroup()
+
+  /**
+   * Returns the value of field 'graphType'.
+   *
+   * @return int
+   * @return the value of field 'graphType'.
+   */
+  public int getGraphType()
+  {
+    return this._graphType;
+  } //-- int getGraphType()
+
+  /**
+   * Returns the value of field 'id'.
+   *
+   * @return String
+   * @return the value of field 'id'.
+   */
+  public java.lang.String getId()
+  {
+    return this._id;
+  } //-- java.lang.String getId()
+
+  /**
+   * Returns the value of field 'label'.
+   *
+   * @return String
+   * @return the value of field 'label'.
+   */
+  public java.lang.String getLabel()
+  {
+    return this._label;
+  } //-- java.lang.String getLabel()
+
+  /**
+   * Returns the value of field 'sequenceRef'.
+   *
+   * @return String
+   * @return the value of field 'sequenceRef'.
+   */
+  public java.lang.String getSequenceRef()
+  {
+    return this._sequenceRef;
+  } //-- java.lang.String getSequenceRef()
+
+  /**
+   * Returns the value of field 'thresholdLine'.
+   *
+   * @return ThresholdLine
+   * @return the value of field 'thresholdLine'.
+   */
+  public jalview.schemabinding.version2.ThresholdLine getThresholdLine()
+  {
+    return this._thresholdLine;
+  } //-- jalview.schemabinding.version2.ThresholdLine getThresholdLine()
+
+  /**
+   * Method hasGraph
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasGraph()
+  {
+    return this._has_graph;
+  } //-- boolean hasGraph()
+
+  /**
+   * Method hasGraphColour
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasGraphColour()
+  {
+    return this._has_graphColour;
+  } //-- boolean hasGraphColour()
+
+  /**
+   * Method hasGraphGroup
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasGraphGroup()
+  {
+    return this._has_graphGroup;
+  } //-- boolean hasGraphGroup()
+
+  /**
+   * Method hasGraphType
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasGraphType()
+  {
+    return this._has_graphType;
+  } //-- boolean hasGraphType()
+
+  /**
+   * Method isValid
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    }
+    catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  } //-- boolean isValid()
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param out
+   */
+  public void marshal(java.io.Writer out)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, out);
+  } //-- void marshal(java.io.Writer)
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param handler
+   */
+  public void marshal(org.xml.sax.ContentHandler handler)
+      throws java.io.IOException, org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, handler);
+  } //-- void marshal(org.xml.sax.ContentHandler)
+
+  /**
+   * Method removeAllAnnotationElement
+   *
+   */
+  public void removeAllAnnotationElement()
+  {
+    _annotationElementList.removeAllElements();
+  } //-- void removeAllAnnotationElement()
+
+  /**
+   * Method removeAnnotationElement
+   *
+   *
+   *
+   * @param index
+   * @return AnnotationElement
+   */
+  public jalview.schemabinding.version2.AnnotationElement
+      removeAnnotationElement(int index)
+  {
+    java.lang.Object obj = _annotationElementList.elementAt(index);
+    _annotationElementList.removeElementAt(index);
+    return (jalview.schemabinding.version2.AnnotationElement) obj;
+  } //-- jalview.schemabinding.version2.AnnotationElement removeAnnotationElement(int)
+
+  /**
+   * Method setAnnotationElement
+   *
+   *
+   *
+   * @param index
+   * @param vAnnotationElement
+   */
+  public void setAnnotationElement(int index,
+                                   jalview.schemabinding.version2.AnnotationElement
+                                   vAnnotationElement)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _annotationElementList.size()))
+    {
+      throw new IndexOutOfBoundsException();
+    }
+    _annotationElementList.setElementAt(vAnnotationElement, index);
+  } //-- void setAnnotationElement(int, jalview.schemabinding.version2.AnnotationElement)
+
+  /**
+   * Method setAnnotationElement
+   *
+   *
+   *
+   * @param annotationElementArray
+   */
+  public void setAnnotationElement(jalview.schemabinding.version2.
+                                   AnnotationElement[] annotationElementArray)
+  {
+    //-- copy array
+    _annotationElementList.removeAllElements();
+    for (int i = 0; i < annotationElementArray.length; i++)
+    {
+      _annotationElementList.addElement(annotationElementArray[i]);
+    }
+  } //-- void setAnnotationElement(jalview.schemabinding.version2.AnnotationElement)
+
+  /**
+   * Sets the value of field 'description'.
+   *
+   * @param description the value of field 'description'.
+   */
+  public void setDescription(java.lang.String description)
+  {
+    this._description = description;
+  } //-- void setDescription(java.lang.String)
+
+  /**
+   * Sets the value of field 'graph'.
+   *
+   * @param graph the value of field 'graph'.
+   */
+  public void setGraph(boolean graph)
+  {
+    this._graph = graph;
+    this._has_graph = true;
+  } //-- void setGraph(boolean)
+
+  /**
+   * Sets the value of field 'graphColour'.
+   *
+   * @param graphColour the value of field 'graphColour'.
+   */
+  public void setGraphColour(int graphColour)
+  {
+    this._graphColour = graphColour;
+    this._has_graphColour = true;
+  } //-- void setGraphColour(int)
+
+  /**
+   * Sets the value of field 'graphGroup'.
+   *
+   * @param graphGroup the value of field 'graphGroup'.
+   */
+  public void setGraphGroup(int graphGroup)
+  {
+    this._graphGroup = graphGroup;
+    this._has_graphGroup = true;
+  } //-- void setGraphGroup(int)
+
+  /**
+   * Sets the value of field 'graphType'.
+   *
+   * @param graphType the value of field 'graphType'.
+   */
+  public void setGraphType(int graphType)
+  {
+    this._graphType = graphType;
+    this._has_graphType = true;
+  } //-- void setGraphType(int)
+
+  /**
+   * Sets the value of field 'id'.
+   *
+   * @param id the value of field 'id'.
+   */
+  public void setId(java.lang.String id)
+  {
+    this._id = id;
+  } //-- void setId(java.lang.String)
+
+  /**
+   * Sets the value of field 'label'.
+   *
+   * @param label the value of field 'label'.
+   */
+  public void setLabel(java.lang.String label)
+  {
+    this._label = label;
+  } //-- void setLabel(java.lang.String)
+
+  /**
+   * Sets the value of field 'sequenceRef'.
+   *
+   * @param sequenceRef the value of field 'sequenceRef'.
+   */
+  public void setSequenceRef(java.lang.String sequenceRef)
+  {
+    this._sequenceRef = sequenceRef;
+  } //-- void setSequenceRef(java.lang.String)
+
+  /**
+   * Sets the value of field 'thresholdLine'.
+   *
+   * @param thresholdLine the value of field 'thresholdLine'.
+   */
+  public void setThresholdLine(jalview.schemabinding.version2.ThresholdLine
+                               thresholdLine)
+  {
+    this._thresholdLine = thresholdLine;
+  } //-- void setThresholdLine(jalview.schemabinding.version2.ThresholdLine)
+
+  /**
+   * Method unmarshal
+   *
+   *
+   *
+   * @param reader
+   * @return Object
+   */
+  public static java.lang.Object unmarshal(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);
+  } //-- java.lang.Object unmarshal(java.io.Reader)
+
+  /**
+   * Method validate
+   *
+   */
+  public void validate()
+      throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.
+        Validator();
+    validator.validate(this);
+  } //-- void validate()
 
 }
diff --git a/src/jalview/schemabinding/version2/AnnotationColours.java b/src/jalview/schemabinding/version2/AnnotationColours.java
index b2af2c4..67d6ad8 100755
--- a/src/jalview/schemabinding/version2/AnnotationColours.java
+++ b/src/jalview/schemabinding/version2/AnnotationColours.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,379 +7,379 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
+import org.exolab.castor.xml.*;
 
 /**
  * Class AnnotationColours.
- * 
+ *
  * @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();
-    } //-- jalview.schemabinding.version2.AnnotationColours()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method deleteAboveThreshold
-     * 
-     */
-    public void deleteAboveThreshold()
-    {
-        this._has_aboveThreshold= false;
-    } //-- void deleteAboveThreshold() 
-
-    /**
-     * Method deleteMaxColour
-     * 
-     */
-    public void deleteMaxColour()
-    {
-        this._has_maxColour= false;
-    } //-- void deleteMaxColour() 
-
-    /**
-     * Method deleteMinColour
-     * 
-     */
-    public void deleteMinColour()
-    {
-        this._has_minColour= false;
-    } //-- void deleteMinColour() 
-
-    /**
-     * Method deleteThreshold
-     * 
-     */
-    public void deleteThreshold()
-    {
-        this._has_threshold= false;
-    } //-- void deleteThreshold() 
-
-    /**
-     * Returns the value of field 'aboveThreshold'.
-     * 
-     * @return int
-     * @return the value of field 'aboveThreshold'.
-     */
-    public int getAboveThreshold()
-    {
-        return this._aboveThreshold;
-    } //-- int getAboveThreshold() 
-
-    /**
-     * Returns the value of field 'annotation'.
-     * 
-     * @return String
-     * @return the value of field 'annotation'.
-     */
-    public java.lang.String getAnnotation()
-    {
-        return this._annotation;
-    } //-- java.lang.String getAnnotation() 
-
-    /**
-     * Returns the value of field 'colourScheme'.
-     * 
-     * @return String
-     * @return the value of field 'colourScheme'.
-     */
-    public java.lang.String getColourScheme()
-    {
-        return this._colourScheme;
-    } //-- java.lang.String getColourScheme() 
-
-    /**
-     * Returns the value of field 'maxColour'.
-     * 
-     * @return int
-     * @return the value of field 'maxColour'.
-     */
-    public int getMaxColour()
-    {
-        return this._maxColour;
-    } //-- int getMaxColour() 
-
-    /**
-     * Returns the value of field 'minColour'.
-     * 
-     * @return int
-     * @return the value of field 'minColour'.
-     */
-    public int getMinColour()
-    {
-        return this._minColour;
-    } //-- int getMinColour() 
-
-    /**
-     * Returns the value of field 'threshold'.
-     * 
-     * @return float
-     * @return the value of field 'threshold'.
-     */
-    public float getThreshold()
-    {
-        return this._threshold;
-    } //-- float getThreshold() 
-
-    /**
-     * Method hasAboveThreshold
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasAboveThreshold()
-    {
-        return this._has_aboveThreshold;
-    } //-- boolean hasAboveThreshold() 
-
-    /**
-     * Method hasMaxColour
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasMaxColour()
-    {
-        return this._has_maxColour;
-    } //-- boolean hasMaxColour() 
-
-    /**
-     * Method hasMinColour
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasMinColour()
-    {
-        return this._has_minColour;
-    } //-- boolean hasMinColour() 
-
-    /**
-     * Method hasThreshold
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasThreshold()
-    {
-        return this._has_threshold;
-    } //-- boolean hasThreshold() 
-
-    /**
-     * Method isValid
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean isValid()
-    {
-        try {
-            validate();
-        }
-        catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    } //-- boolean isValid() 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param out
-     */
-    public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, out);
-    } //-- void marshal(java.io.Writer) 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param handler
-     */
-    public void marshal(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, handler);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
-
-    /**
-     * Sets the value of field 'aboveThreshold'.
-     * 
-     * @param aboveThreshold the value of field 'aboveThreshold'.
-     */
-    public void setAboveThreshold(int aboveThreshold)
-    {
-        this._aboveThreshold = aboveThreshold;
-        this._has_aboveThreshold = true;
-    } //-- void setAboveThreshold(int) 
-
-    /**
-     * Sets the value of field 'annotation'.
-     * 
-     * @param annotation the value of field 'annotation'.
-     */
-    public void setAnnotation(java.lang.String annotation)
-    {
-        this._annotation = annotation;
-    } //-- void setAnnotation(java.lang.String) 
-
-    /**
-     * Sets the value of field 'colourScheme'.
-     * 
-     * @param colourScheme the value of field 'colourScheme'.
-     */
-    public void setColourScheme(java.lang.String colourScheme)
-    {
-        this._colourScheme = colourScheme;
-    } //-- void setColourScheme(java.lang.String) 
-
-    /**
-     * Sets the value of field 'maxColour'.
-     * 
-     * @param maxColour the value of field 'maxColour'.
-     */
-    public void setMaxColour(int maxColour)
-    {
-        this._maxColour = maxColour;
-        this._has_maxColour = true;
-    } //-- void setMaxColour(int) 
-
-    /**
-     * Sets the value of field 'minColour'.
-     * 
-     * @param minColour the value of field 'minColour'.
-     */
-    public void setMinColour(int minColour)
-    {
-        this._minColour = minColour;
-        this._has_minColour = true;
-    } //-- void setMinColour(int) 
-
-    /**
-     * Sets the value of field 'threshold'.
-     * 
-     * @param threshold the value of field 'threshold'.
-     */
-    public void setThreshold(float threshold)
-    {
-        this._threshold = threshold;
-        this._has_threshold = true;
-    } //-- void setThreshold(float) 
-
-    /**
-     * Method unmarshal
-     * 
-     * 
-     * 
-     * @param reader
-     * @return Object
-     */
-    public static java.lang.Object unmarshal(java.io.Reader reader)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+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();
+  } //-- jalview.schemabinding.version2.AnnotationColours()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Method deleteAboveThreshold
+   *
+   */
+  public void deleteAboveThreshold()
+  {
+    this._has_aboveThreshold = false;
+  } //-- void deleteAboveThreshold()
+
+  /**
+   * Method deleteMaxColour
+   *
+   */
+  public void deleteMaxColour()
+  {
+    this._has_maxColour = false;
+  } //-- void deleteMaxColour()
+
+  /**
+   * Method deleteMinColour
+   *
+   */
+  public void deleteMinColour()
+  {
+    this._has_minColour = false;
+  } //-- void deleteMinColour()
+
+  /**
+   * Method deleteThreshold
+   *
+   */
+  public void deleteThreshold()
+  {
+    this._has_threshold = false;
+  } //-- void deleteThreshold()
+
+  /**
+   * Returns the value of field 'aboveThreshold'.
+   *
+   * @return int
+   * @return the value of field 'aboveThreshold'.
+   */
+  public int getAboveThreshold()
+  {
+    return this._aboveThreshold;
+  } //-- int getAboveThreshold()
+
+  /**
+   * Returns the value of field 'annotation'.
+   *
+   * @return String
+   * @return the value of field 'annotation'.
+   */
+  public java.lang.String getAnnotation()
+  {
+    return this._annotation;
+  } //-- java.lang.String getAnnotation()
+
+  /**
+   * Returns the value of field 'colourScheme'.
+   *
+   * @return String
+   * @return the value of field 'colourScheme'.
+   */
+  public java.lang.String getColourScheme()
+  {
+    return this._colourScheme;
+  } //-- java.lang.String getColourScheme()
+
+  /**
+   * Returns the value of field 'maxColour'.
+   *
+   * @return int
+   * @return the value of field 'maxColour'.
+   */
+  public int getMaxColour()
+  {
+    return this._maxColour;
+  } //-- int getMaxColour()
+
+  /**
+   * Returns the value of field 'minColour'.
+   *
+   * @return int
+   * @return the value of field 'minColour'.
+   */
+  public int getMinColour()
+  {
+    return this._minColour;
+  } //-- int getMinColour()
+
+  /**
+   * Returns the value of field 'threshold'.
+   *
+   * @return float
+   * @return the value of field 'threshold'.
+   */
+  public float getThreshold()
+  {
+    return this._threshold;
+  } //-- float getThreshold()
+
+  /**
+   * Method hasAboveThreshold
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasAboveThreshold()
+  {
+    return this._has_aboveThreshold;
+  } //-- boolean hasAboveThreshold()
+
+  /**
+   * Method hasMaxColour
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasMaxColour()
+  {
+    return this._has_maxColour;
+  } //-- boolean hasMaxColour()
+
+  /**
+   * Method hasMinColour
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasMinColour()
+  {
+    return this._has_minColour;
+  } //-- boolean hasMinColour()
+
+  /**
+   * Method hasThreshold
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasThreshold()
+  {
+    return this._has_threshold;
+  } //-- boolean hasThreshold()
+
+  /**
+   * Method isValid
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean isValid()
+  {
+    try
     {
-        return (jalview.schemabinding.version2.AnnotationColours) Unmarshaller.unmarshal(jalview.schemabinding.version2.AnnotationColours.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
-
-    /**
-     * Method validate
-     * 
-     */
-    public void validate()
-        throws org.exolab.castor.xml.ValidationException
+      validate();
+    }
+    catch (org.exolab.castor.xml.ValidationException vex)
     {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    } //-- void validate() 
+      return false;
+    }
+    return true;
+  } //-- boolean isValid()
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param out
+   */
+  public void marshal(java.io.Writer out)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, out);
+  } //-- void marshal(java.io.Writer)
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param handler
+   */
+  public void marshal(org.xml.sax.ContentHandler handler)
+      throws java.io.IOException, org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, handler);
+  } //-- void marshal(org.xml.sax.ContentHandler)
+
+  /**
+   * Sets the value of field 'aboveThreshold'.
+   *
+   * @param aboveThreshold the value of field 'aboveThreshold'.
+   */
+  public void setAboveThreshold(int aboveThreshold)
+  {
+    this._aboveThreshold = aboveThreshold;
+    this._has_aboveThreshold = true;
+  } //-- void setAboveThreshold(int)
+
+  /**
+   * Sets the value of field 'annotation'.
+   *
+   * @param annotation the value of field 'annotation'.
+   */
+  public void setAnnotation(java.lang.String annotation)
+  {
+    this._annotation = annotation;
+  } //-- void setAnnotation(java.lang.String)
+
+  /**
+   * Sets the value of field 'colourScheme'.
+   *
+   * @param colourScheme the value of field 'colourScheme'.
+   */
+  public void setColourScheme(java.lang.String colourScheme)
+  {
+    this._colourScheme = colourScheme;
+  } //-- void setColourScheme(java.lang.String)
+
+  /**
+   * Sets the value of field 'maxColour'.
+   *
+   * @param maxColour the value of field 'maxColour'.
+   */
+  public void setMaxColour(int maxColour)
+  {
+    this._maxColour = maxColour;
+    this._has_maxColour = true;
+  } //-- void setMaxColour(int)
+
+  /**
+   * Sets the value of field 'minColour'.
+   *
+   * @param minColour the value of field 'minColour'.
+   */
+  public void setMinColour(int minColour)
+  {
+    this._minColour = minColour;
+    this._has_minColour = true;
+  } //-- void setMinColour(int)
+
+  /**
+   * Sets the value of field 'threshold'.
+   *
+   * @param threshold the value of field 'threshold'.
+   */
+  public void setThreshold(float threshold)
+  {
+    this._threshold = threshold;
+    this._has_threshold = true;
+  } //-- void setThreshold(float)
+
+  /**
+   * Method unmarshal
+   *
+   *
+   *
+   * @param reader
+   * @return Object
+   */
+  public static java.lang.Object unmarshal(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);
+  } //-- java.lang.Object unmarshal(java.io.Reader)
+
+  /**
+   * Method validate
+   *
+   */
+  public void validate()
+      throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.
+        Validator();
+    validator.validate(this);
+  } //-- void validate()
 
 }
diff --git a/src/jalview/schemabinding/version2/AnnotationColoursDescriptor.java b/src/jalview/schemabinding/version2/AnnotationColoursDescriptor.java
index c3c06e6..f8cc3a1 100755
--- a/src/jalview/schemabinding/version2/AnnotationColoursDescriptor.java
+++ b/src/jalview/schemabinding/version2/AnnotationColoursDescriptor.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,400 +7,456 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
-import org.exolab.castor.mapping.AccessMode;
-import org.exolab.castor.xml.TypeValidator;
-import org.exolab.castor.xml.XMLFieldDescriptor;
 import org.exolab.castor.xml.validators.*;
 
 /**
  * Class AnnotationColoursDescriptor.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class AnnotationColoursDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field nsPrefix
-     */
-    private java.lang.String nsPrefix;
-
-    /**
-     * Field nsURI
-     */
-    private java.lang.String nsURI;
-
-    /**
-     * Field xmlName
-     */
-    private java.lang.String xmlName;
-
-    /**
-     * Field identity
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor identity;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public AnnotationColoursDescriptor() {
-        super();
-        nsURI = "www.jalview.org";
-        xmlName = "AnnotationColours";
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.xml.XMLFieldHandler              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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _aboveThreshold
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            IntegerValidator typeValidator= new IntegerValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _annotation
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            StringValidator typeValidator = new StringValidator();
-            typeValidator.setWhiteSpace("preserve");
-            fieldValidator.setValidator(typeValidator);
+public class AnnotationColoursDescriptor
+    extends org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  //--------------------------/
+  //- Class/Member Variables -/
+  //--------------------------/
+
+  /**
+   * Field nsPrefix
+   */
+  private java.lang.String nsPrefix;
+
+  /**
+   * Field nsURI
+   */
+  private java.lang.String nsURI;
+
+  /**
+   * Field xmlName
+   */
+  private java.lang.String xmlName;
+
+  /**
+   * Field identity
+   */
+  private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+  //----------------/
+  //- Constructors -/
+  //----------------/
+
+  public AnnotationColoursDescriptor()
+  {
+    super();
+    nsURI = "www.jalview.org";
+    xmlName = "AnnotationColours";
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.xml.XMLFieldHandler 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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _minColour
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            IntegerValidator typeValidator= new IntegerValidator();
-            fieldValidator.setValidator(typeValidator);
+        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());
         }
-        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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _maxColour
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            IntegerValidator typeValidator= new IntegerValidator();
-            fieldValidator.setValidator(typeValidator);
+        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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _colourScheme
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            StringValidator typeValidator = new StringValidator();
-            typeValidator.setWhiteSpace("preserve");
-            fieldValidator.setValidator(typeValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    });
+    desc.setHandler(handler);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _aboveThreshold
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      IntegerValidator typeValidator = new IntegerValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    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);
         }
-        desc.setValidator(fieldValidator);
-        //-- _threshold
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(float.class, "_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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _threshold
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            FloatValidator typeValidator = new FloatValidator();
-            fieldValidator.setValidator(typeValidator);
+        catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-    } //-- jalview.schemabinding.version2.AnnotationColoursDescriptor()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method getAccessMode
-     * 
-     * 
-     * 
-     * @return AccessMode
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode()
-    {
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
-
-    /**
-     * Method getExtends
-     * 
-     * 
-     * 
-     * @return ClassDescriptor
-     */
-    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+      }
+    });
+    desc.setHandler(handler);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _annotation
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      StringValidator typeValidator = new StringValidator();
+      typeValidator.setWhiteSpace("preserve");
+      fieldValidator.setValidator(typeValidator);
+    }
+    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;
-    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
-
-    /**
-     * Method getIdentity
-     * 
-     * 
-     * 
-     * @return FieldDescriptor
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
-    {
-        return identity;
-    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
-
-    /**
-     * Method getJavaClass
-     * 
-     * 
-     * 
-     * @return Class
-     */
-    public java.lang.Class getJavaClass()
-    {
-        return jalview.schemabinding.version2.AnnotationColours.class;
-    } //-- java.lang.Class getJavaClass() 
-
-    /**
-     * Method getNameSpacePrefix
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpacePrefix()
-    {
-        return nsPrefix;
-    } //-- java.lang.String getNameSpacePrefix() 
-
-    /**
-     * Method getNameSpaceURI
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpaceURI()
+      }
+    });
+    desc.setHandler(handler);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _minColour
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      IntegerValidator typeValidator = new IntegerValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    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()
     {
-        return nsURI;
-    } //-- java.lang.String getNameSpaceURI() 
-
-    /**
-     * Method getValidator
-     * 
-     * 
-     * 
-     * @return TypeValidator
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator()
+      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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _maxColour
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      IntegerValidator typeValidator = new IntegerValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    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()
     {
-        return this;
-    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
-
-    /**
-     * Method getXMLName
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getXMLName()
+      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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _colourScheme
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      StringValidator typeValidator = new StringValidator();
+      typeValidator.setWhiteSpace("preserve");
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    //-- _threshold
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(float.class,
+        "_threshold", "threshold", org.exolab.castor.xml.NodeType.Attribute);
+    handler = (new org.exolab.castor.xml.XMLFieldHandler()
     {
-        return xmlName;
-    } //-- java.lang.String getXMLName() 
+      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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _threshold
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      FloatValidator typeValidator = new FloatValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    //-- initialize element descriptors
+
+  } //-- jalview.schemabinding.version2.AnnotationColoursDescriptor()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Method getAccessMode
+   *
+   *
+   *
+   * @return AccessMode
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
+
+  /**
+   * Method getExtends
+   *
+   *
+   *
+   * @return ClassDescriptor
+   */
+  public org.exolab.castor.mapping.ClassDescriptor getExtends()
+  {
+    return null;
+  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
+
+  /**
+   * Method getIdentity
+   *
+   *
+   *
+   * @return FieldDescriptor
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return identity;
+  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
+
+  /**
+   * Method getJavaClass
+   *
+   *
+   *
+   * @return Class
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.AnnotationColours.class;
+  } //-- java.lang.Class getJavaClass()
+
+  /**
+   * Method getNameSpacePrefix
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return nsPrefix;
+  } //-- java.lang.String getNameSpacePrefix()
+
+  /**
+   * Method getNameSpaceURI
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return nsURI;
+  } //-- java.lang.String getNameSpaceURI()
+
+  /**
+   * Method getValidator
+   *
+   *
+   *
+   * @return TypeValidator
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  } //-- org.exolab.castor.xml.TypeValidator getValidator()
+
+  /**
+   * Method getXMLName
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getXMLName()
+  {
+    return xmlName;
+  } //-- java.lang.String getXMLName()
 
 }
diff --git a/src/jalview/schemabinding/version2/AnnotationDescriptor.java b/src/jalview/schemabinding/version2/AnnotationDescriptor.java
index 34047b3..7ba7e67 100755
--- a/src/jalview/schemabinding/version2/AnnotationDescriptor.java
+++ b/src/jalview/schemabinding/version2/AnnotationDescriptor.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,550 +7,643 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
-import org.exolab.castor.mapping.AccessMode;
-import org.exolab.castor.xml.TypeValidator;
-import org.exolab.castor.xml.XMLFieldDescriptor;
 import org.exolab.castor.xml.validators.*;
 
 /**
  * Class AnnotationDescriptor.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class AnnotationDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field nsPrefix
-     */
-    private java.lang.String nsPrefix;
-
-    /**
-     * Field nsURI
-     */
-    private java.lang.String nsURI;
-
-    /**
-     * Field xmlName
-     */
-    private java.lang.String xmlName;
-
-    /**
-     * Field identity
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor identity;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public AnnotationDescriptor() {
-        super();
-        nsURI = "www.vamsas.ac.uk/jalview/version2";
-        xmlName = "Annotation";
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.xml.XMLFieldHandler              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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _graph
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            BooleanValidator typeValidator = new BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+public class AnnotationDescriptor
+    extends org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  //--------------------------/
+  //- Class/Member Variables -/
+  //--------------------------/
+
+  /**
+   * Field nsPrefix
+   */
+  private java.lang.String nsPrefix;
+
+  /**
+   * Field nsURI
+   */
+  private java.lang.String nsURI;
+
+  /**
+   * Field xmlName
+   */
+  private java.lang.String xmlName;
+
+  /**
+   * Field identity
+   */
+  private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+  //----------------/
+  //- Constructors -/
+  //----------------/
+
+  public AnnotationDescriptor()
+  {
+    super();
+    nsURI = "www.vamsas.ac.uk/jalview/version2";
+    xmlName = "Annotation";
+
+    //-- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.xml.XMLFieldHandler 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);
-        //-- _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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _graphType
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            IntegerValidator typeValidator= new IntegerValidator();
-            fieldValidator.setValidator(typeValidator);
+        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());
         }
-        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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _sequenceRef
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            StringValidator typeValidator = new StringValidator();
-            typeValidator.setWhiteSpace("preserve");
-            fieldValidator.setValidator(typeValidator);
+        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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _graphColour
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            IntegerValidator typeValidator= new IntegerValidator();
-            fieldValidator.setValidator(typeValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    });
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _graph
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { //-- local scope
+      BooleanValidator typeValidator = new 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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _graphGroup
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            IntegerValidator typeValidator= new IntegerValidator();
-            fieldValidator.setValidator(typeValidator);
+        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());
         }
-        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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _id
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            StringValidator typeValidator = new StringValidator();
-            typeValidator.setWhiteSpace("preserve");
-            fieldValidator.setValidator(typeValidator);
+        catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        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 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
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    });
+    desc.setHandler(handler);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _graphType
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      IntegerValidator typeValidator = new IntegerValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    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);
         }
-        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
-            StringValidator typeValidator = new StringValidator();
-            typeValidator.setWhiteSpace("preserve");
-            fieldValidator.setValidator(typeValidator);
+        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: _sequenceRef
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      StringValidator typeValidator = new StringValidator();
+      typeValidator.setWhiteSpace("preserve");
+      fieldValidator.setValidator(typeValidator);
+    }
+    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);
-        //-- _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
-            StringValidator typeValidator = new StringValidator();
-            typeValidator.setWhiteSpace("preserve");
-            fieldValidator.setValidator(typeValidator);
+        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());
         }
-        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
+        catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-    } //-- jalview.schemabinding.version2.AnnotationDescriptor()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method getAccessMode
-     * 
-     * 
-     * 
-     * @return AccessMode
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode()
-    {
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
-
-    /**
-     * Method getExtends
-     * 
-     * 
-     * 
-     * @return ClassDescriptor
-     */
-    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+      }
+    });
+    desc.setHandler(handler);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _graphColour
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      IntegerValidator typeValidator = new IntegerValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    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;
-    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
-
-    /**
-     * Method getIdentity
-     * 
-     * 
-     * 
-     * @return FieldDescriptor
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
-    {
-        return identity;
-    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
-
-    /**
-     * Method getJavaClass
-     * 
-     * 
-     * 
-     * @return Class
-     */
-    public java.lang.Class getJavaClass()
+      }
+    });
+    desc.setHandler(handler);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _graphGroup
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      IntegerValidator typeValidator = new IntegerValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    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()
     {
-        return jalview.schemabinding.version2.Annotation.class;
-    } //-- java.lang.Class getJavaClass() 
-
-    /**
-     * Method getNameSpacePrefix
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpacePrefix()
+      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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _id
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      StringValidator typeValidator = new StringValidator();
+      typeValidator.setWhiteSpace("preserve");
+      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()
     {
-        return nsPrefix;
-    } //-- java.lang.String getNameSpacePrefix() 
-
-    /**
-     * Method getNameSpaceURI
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpaceURI()
+      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 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()
     {
-        return nsURI;
-    } //-- java.lang.String getNameSpaceURI() 
-
-    /**
-     * Method getValidator
-     * 
-     * 
-     * 
-     * @return TypeValidator
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator()
+      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
+      StringValidator typeValidator = new StringValidator();
+      typeValidator.setWhiteSpace("preserve");
+      fieldValidator.setValidator(typeValidator);
+    }
+    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()
     {
-        return this;
-    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
-
-    /**
-     * Method getXMLName
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getXMLName()
+      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
+      StringValidator typeValidator = new StringValidator();
+      typeValidator.setWhiteSpace("preserve");
+      fieldValidator.setValidator(typeValidator);
+    }
+    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()
     {
-        return xmlName;
-    } //-- java.lang.String getXMLName() 
+      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
+    }
+    desc.setValidator(fieldValidator);
+  } //-- jalview.schemabinding.version2.AnnotationDescriptor()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Method getAccessMode
+   *
+   *
+   *
+   * @return AccessMode
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
+
+  /**
+   * Method getExtends
+   *
+   *
+   *
+   * @return ClassDescriptor
+   */
+  public org.exolab.castor.mapping.ClassDescriptor getExtends()
+  {
+    return null;
+  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
+
+  /**
+   * Method getIdentity
+   *
+   *
+   *
+   * @return FieldDescriptor
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return identity;
+  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
+
+  /**
+   * Method getJavaClass
+   *
+   *
+   *
+   * @return Class
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.Annotation.class;
+  } //-- java.lang.Class getJavaClass()
+
+  /**
+   * Method getNameSpacePrefix
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return nsPrefix;
+  } //-- java.lang.String getNameSpacePrefix()
+
+  /**
+   * Method getNameSpaceURI
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return nsURI;
+  } //-- java.lang.String getNameSpaceURI()
+
+  /**
+   * Method getValidator
+   *
+   *
+   *
+   * @return TypeValidator
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  } //-- org.exolab.castor.xml.TypeValidator getValidator()
+
+  /**
+   * Method getXMLName
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getXMLName()
+  {
+    return xmlName;
+  } //-- java.lang.String getXMLName()
 
 }
diff --git a/src/jalview/schemabinding/version2/AnnotationElement.java b/src/jalview/schemabinding/version2/AnnotationElement.java
index 2507197..57c0b2c 100755
--- a/src/jalview/schemabinding/version2/AnnotationElement.java
+++ b/src/jalview/schemabinding/version2/AnnotationElement.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,353 +7,353 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
+import org.exolab.castor.xml.*;
 
 /**
  * Class AnnotationElement.
- * 
+ *
  * @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();
-    } //-- jalview.schemabinding.version2.AnnotationElement()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method deleteColour
-     * 
-     */
-    public void deleteColour()
-    {
-        this._has_colour= false;
-    } //-- void deleteColour() 
-
-    /**
-     * Method deletePosition
-     * 
-     */
-    public void deletePosition()
-    {
-        this._has_position= false;
-    } //-- void deletePosition() 
-
-    /**
-     * Method deleteValue
-     * 
-     */
-    public void deleteValue()
-    {
-        this._has_value= false;
-    } //-- void deleteValue() 
-
-    /**
-     * Returns the value of field 'colour'.
-     * 
-     * @return int
-     * @return the value of field 'colour'.
-     */
-    public int getColour()
-    {
-        return this._colour;
-    } //-- int getColour() 
-
-    /**
-     * Returns the value of field 'description'.
-     * 
-     * @return String
-     * @return the value of field 'description'.
-     */
-    public java.lang.String getDescription()
-    {
-        return this._description;
-    } //-- java.lang.String getDescription() 
-
-    /**
-     * Returns the value of field 'displayCharacter'.
-     * 
-     * @return String
-     * @return the value of field 'displayCharacter'.
-     */
-    public java.lang.String getDisplayCharacter()
-    {
-        return this._displayCharacter;
-    } //-- java.lang.String getDisplayCharacter() 
-
-    /**
-     * Returns the value of field 'position'.
-     * 
-     * @return int
-     * @return the value of field 'position'.
-     */
-    public int getPosition()
-    {
-        return this._position;
-    } //-- int getPosition() 
-
-    /**
-     * Returns the value of field 'secondaryStructure'.
-     * 
-     * @return String
-     * @return the value of field 'secondaryStructure'.
-     */
-    public java.lang.String getSecondaryStructure()
-    {
-        return this._secondaryStructure;
-    } //-- java.lang.String getSecondaryStructure() 
-
-    /**
-     * Returns the value of field 'value'.
-     * 
-     * @return float
-     * @return the value of field 'value'.
-     */
-    public float getValue()
-    {
-        return this._value;
-    } //-- float getValue() 
-
-    /**
-     * Method hasColour
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasColour()
-    {
-        return this._has_colour;
-    } //-- boolean hasColour() 
-
-    /**
-     * Method hasPosition
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasPosition()
-    {
-        return this._has_position;
-    } //-- boolean hasPosition() 
-
-    /**
-     * Method hasValue
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasValue()
-    {
-        return this._has_value;
-    } //-- boolean hasValue() 
-
-    /**
-     * Method isValid
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean isValid()
-    {
-        try {
-            validate();
-        }
-        catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    } //-- boolean isValid() 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param out
-     */
-    public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, out);
-    } //-- void marshal(java.io.Writer) 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param handler
-     */
-    public void marshal(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, handler);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
-
-    /**
-     * Sets the value of field 'colour'.
-     * 
-     * @param colour the value of field 'colour'.
-     */
-    public void setColour(int colour)
-    {
-        this._colour = colour;
-        this._has_colour = true;
-    } //-- void setColour(int) 
-
-    /**
-     * Sets the value of field 'description'.
-     * 
-     * @param description the value of field 'description'.
-     */
-    public void setDescription(java.lang.String description)
-    {
-        this._description = description;
-    } //-- void setDescription(java.lang.String) 
-
-    /**
-     * Sets the value of field 'displayCharacter'.
-     * 
-     * @param displayCharacter the value of field 'displayCharacter'
-     */
-    public void setDisplayCharacter(java.lang.String displayCharacter)
-    {
-        this._displayCharacter = displayCharacter;
-    } //-- void setDisplayCharacter(java.lang.String) 
-
-    /**
-     * Sets the value of field 'position'.
-     * 
-     * @param position the value of field 'position'.
-     */
-    public void setPosition(int position)
-    {
-        this._position = position;
-        this._has_position = true;
-    } //-- void setPosition(int) 
-
-    /**
-     * Sets the value of field 'secondaryStructure'.
-     * 
-     * @param secondaryStructure the value of field
-     * 'secondaryStructure'.
-     */
-    public void setSecondaryStructure(java.lang.String secondaryStructure)
-    {
-        this._secondaryStructure = secondaryStructure;
-    } //-- void setSecondaryStructure(java.lang.String) 
-
-    /**
-     * Sets the value of field 'value'.
-     * 
-     * @param value the value of field 'value'.
-     */
-    public void setValue(float value)
-    {
-        this._value = value;
-        this._has_value = true;
-    } //-- void setValue(float) 
-
-    /**
-     * Method unmarshal
-     * 
-     * 
-     * 
-     * @param reader
-     * @return Object
-     */
-    public static java.lang.Object unmarshal(java.io.Reader reader)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+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();
+  } //-- jalview.schemabinding.version2.AnnotationElement()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Method deleteColour
+   *
+   */
+  public void deleteColour()
+  {
+    this._has_colour = false;
+  } //-- void deleteColour()
+
+  /**
+   * Method deletePosition
+   *
+   */
+  public void deletePosition()
+  {
+    this._has_position = false;
+  } //-- void deletePosition()
+
+  /**
+   * Method deleteValue
+   *
+   */
+  public void deleteValue()
+  {
+    this._has_value = false;
+  } //-- void deleteValue()
+
+  /**
+   * Returns the value of field 'colour'.
+   *
+   * @return int
+   * @return the value of field 'colour'.
+   */
+  public int getColour()
+  {
+    return this._colour;
+  } //-- int getColour()
+
+  /**
+   * Returns the value of field 'description'.
+   *
+   * @return String
+   * @return the value of field 'description'.
+   */
+  public java.lang.String getDescription()
+  {
+    return this._description;
+  } //-- java.lang.String getDescription()
+
+  /**
+   * Returns the value of field 'displayCharacter'.
+   *
+   * @return String
+   * @return the value of field 'displayCharacter'.
+   */
+  public java.lang.String getDisplayCharacter()
+  {
+    return this._displayCharacter;
+  } //-- java.lang.String getDisplayCharacter()
+
+  /**
+   * Returns the value of field 'position'.
+   *
+   * @return int
+   * @return the value of field 'position'.
+   */
+  public int getPosition()
+  {
+    return this._position;
+  } //-- int getPosition()
+
+  /**
+   * Returns the value of field 'secondaryStructure'.
+   *
+   * @return String
+   * @return the value of field 'secondaryStructure'.
+   */
+  public java.lang.String getSecondaryStructure()
+  {
+    return this._secondaryStructure;
+  } //-- java.lang.String getSecondaryStructure()
+
+  /**
+   * Returns the value of field 'value'.
+   *
+   * @return float
+   * @return the value of field 'value'.
+   */
+  public float getValue()
+  {
+    return this._value;
+  } //-- float getValue()
+
+  /**
+   * Method hasColour
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasColour()
+  {
+    return this._has_colour;
+  } //-- boolean hasColour()
+
+  /**
+   * Method hasPosition
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasPosition()
+  {
+    return this._has_position;
+  } //-- boolean hasPosition()
+
+  /**
+   * Method hasValue
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasValue()
+  {
+    return this._has_value;
+  } //-- boolean hasValue()
+
+  /**
+   * Method isValid
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean isValid()
+  {
+    try
     {
-        return (jalview.schemabinding.version2.AnnotationElement) Unmarshaller.unmarshal(jalview.schemabinding.version2.AnnotationElement.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
-
-    /**
-     * Method validate
-     * 
-     */
-    public void validate()
-        throws org.exolab.castor.xml.ValidationException
+      validate();
+    }
+    catch (org.exolab.castor.xml.ValidationException vex)
     {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    } //-- void validate() 
+      return false;
+    }
+    return true;
+  } //-- boolean isValid()
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param out
+   */
+  public void marshal(java.io.Writer out)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, out);
+  } //-- void marshal(java.io.Writer)
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param handler
+   */
+  public void marshal(org.xml.sax.ContentHandler handler)
+      throws java.io.IOException, org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, handler);
+  } //-- void marshal(org.xml.sax.ContentHandler)
+
+  /**
+   * Sets the value of field 'colour'.
+   *
+   * @param colour the value of field 'colour'.
+   */
+  public void setColour(int colour)
+  {
+    this._colour = colour;
+    this._has_colour = true;
+  } //-- void setColour(int)
+
+  /**
+   * Sets the value of field 'description'.
+   *
+   * @param description the value of field 'description'.
+   */
+  public void setDescription(java.lang.String description)
+  {
+    this._description = description;
+  } //-- void setDescription(java.lang.String)
+
+  /**
+   * Sets the value of field 'displayCharacter'.
+   *
+   * @param displayCharacter the value of field 'displayCharacter'
+   */
+  public void setDisplayCharacter(java.lang.String displayCharacter)
+  {
+    this._displayCharacter = displayCharacter;
+  } //-- void setDisplayCharacter(java.lang.String)
+
+  /**
+   * Sets the value of field 'position'.
+   *
+   * @param position the value of field 'position'.
+   */
+  public void setPosition(int position)
+  {
+    this._position = position;
+    this._has_position = true;
+  } //-- void setPosition(int)
+
+  /**
+   * Sets the value of field 'secondaryStructure'.
+   *
+   * @param secondaryStructure the value of field
+   * 'secondaryStructure'.
+   */
+  public void setSecondaryStructure(java.lang.String secondaryStructure)
+  {
+    this._secondaryStructure = secondaryStructure;
+  } //-- void setSecondaryStructure(java.lang.String)
+
+  /**
+   * Sets the value of field 'value'.
+   *
+   * @param value the value of field 'value'.
+   */
+  public void setValue(float value)
+  {
+    this._value = value;
+    this._has_value = true;
+  } //-- void setValue(float)
+
+  /**
+   * Method unmarshal
+   *
+   *
+   *
+   * @param reader
+   * @return Object
+   */
+  public static java.lang.Object unmarshal(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);
+  } //-- java.lang.Object unmarshal(java.io.Reader)
+
+  /**
+   * Method validate
+   *
+   */
+  public void validate()
+      throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.
+        Validator();
+    validator.validate(this);
+  } //-- void validate()
 
 }
diff --git a/src/jalview/schemabinding/version2/AnnotationElementDescriptor.java b/src/jalview/schemabinding/version2/AnnotationElementDescriptor.java
index 0eab95b..058788d 100755
--- a/src/jalview/schemabinding/version2/AnnotationElementDescriptor.java
+++ b/src/jalview/schemabinding/version2/AnnotationElementDescriptor.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,407 +7,462 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
-import org.exolab.castor.mapping.AccessMode;
-import org.exolab.castor.xml.TypeValidator;
-import org.exolab.castor.xml.XMLFieldDescriptor;
 import org.exolab.castor.xml.validators.*;
 
 /**
  * Class AnnotationElementDescriptor.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class AnnotationElementDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field nsPrefix
-     */
-    private java.lang.String nsPrefix;
-
-    /**
-     * Field nsURI
-     */
-    private java.lang.String nsURI;
-
-    /**
-     * Field xmlName
-     */
-    private java.lang.String xmlName;
-
-    /**
-     * Field identity
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor identity;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public AnnotationElementDescriptor() {
-        super();
-        nsURI = "www.vamsas.ac.uk/jalview/version2";
-        xmlName = "annotationElement";
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.xml.XMLFieldHandler              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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _position
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            IntegerValidator typeValidator= new IntegerValidator();
-            fieldValidator.setValidator(typeValidator);
+public class AnnotationElementDescriptor
+    extends org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  //--------------------------/
+  //- Class/Member Variables -/
+  //--------------------------/
+
+  /**
+   * Field nsPrefix
+   */
+  private java.lang.String nsPrefix;
+
+  /**
+   * Field nsURI
+   */
+  private java.lang.String nsURI;
+
+  /**
+   * Field xmlName
+   */
+  private java.lang.String xmlName;
+
+  /**
+   * Field identity
+   */
+  private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+  //----------------/
+  //- Constructors -/
+  //----------------/
+
+  public AnnotationElementDescriptor()
+  {
+    super();
+    nsURI = "www.vamsas.ac.uk/jalview/version2";
+    xmlName = "annotationElement";
+
+    //-- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.xml.XMLFieldHandler 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);
-        //-- _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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _colour
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            IntegerValidator typeValidator= new IntegerValidator();
-            fieldValidator.setValidator(typeValidator);
+        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());
         }
-        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
-            StringValidator typeValidator = new StringValidator();
-            typeValidator.setWhiteSpace("preserve");
-            fieldValidator.setValidator(typeValidator);
+        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
-            {
-                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
-            StringValidator typeValidator = new StringValidator();
-            typeValidator.setWhiteSpace("preserve");
-            fieldValidator.setValidator(typeValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    });
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _position
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { //-- local scope
+      IntegerValidator typeValidator = new IntegerValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    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);
-        //-- _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
-            StringValidator typeValidator = new StringValidator();
-            typeValidator.setLength(1);
-            typeValidator.setWhiteSpace("preserve");
-            fieldValidator.setValidator(typeValidator);
+        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());
         }
-        desc.setValidator(fieldValidator);
-        //-- _value
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(float.class, "_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
-            FloatValidator typeValidator = new FloatValidator();
-            fieldValidator.setValidator(typeValidator);
+        catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-    } //-- jalview.schemabinding.version2.AnnotationElementDescriptor()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method getAccessMode
-     * 
-     * 
-     * 
-     * @return AccessMode
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode()
-    {
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
-
-    /**
-     * Method getExtends
-     * 
-     * 
-     * 
-     * @return ClassDescriptor
-     */
-    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+      }
+    });
+    desc.setHandler(handler);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _colour
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      IntegerValidator typeValidator = new IntegerValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    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;
-    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
-
-    /**
-     * Method getIdentity
-     * 
-     * 
-     * 
-     * @return FieldDescriptor
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
-    {
-        return identity;
-    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
-
-    /**
-     * Method getJavaClass
-     * 
-     * 
-     * 
-     * @return Class
-     */
-    public java.lang.Class getJavaClass()
-    {
-        return jalview.schemabinding.version2.AnnotationElement.class;
-    } //-- java.lang.Class getJavaClass() 
-
-    /**
-     * Method getNameSpacePrefix
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpacePrefix()
-    {
-        return nsPrefix;
-    } //-- java.lang.String getNameSpacePrefix() 
-
-    /**
-     * Method getNameSpaceURI
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpaceURI()
+      }
+    });
+    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
+      StringValidator typeValidator = new StringValidator();
+      typeValidator.setWhiteSpace("preserve");
+      fieldValidator.setValidator(typeValidator);
+    }
+    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()
     {
-        return nsURI;
-    } //-- java.lang.String getNameSpaceURI() 
-
-    /**
-     * Method getValidator
-     * 
-     * 
-     * 
-     * @return TypeValidator
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator()
+      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
+      StringValidator typeValidator = new StringValidator();
+      typeValidator.setWhiteSpace("preserve");
+      fieldValidator.setValidator(typeValidator);
+    }
+    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()
     {
-        return this;
-    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
-
-    /**
-     * Method getXMLName
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getXMLName()
+      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
+      StringValidator typeValidator = new StringValidator();
+      typeValidator.setLength(1);
+      typeValidator.setWhiteSpace("preserve");
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    //-- _value
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(float.class,
+        "_value", "value", org.exolab.castor.xml.NodeType.Element);
+    handler = (new org.exolab.castor.xml.XMLFieldHandler()
     {
-        return xmlName;
-    } //-- java.lang.String getXMLName() 
+      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
+      FloatValidator typeValidator = new FloatValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+  } //-- jalview.schemabinding.version2.AnnotationElementDescriptor()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Method getAccessMode
+   *
+   *
+   *
+   * @return AccessMode
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
+
+  /**
+   * Method getExtends
+   *
+   *
+   *
+   * @return ClassDescriptor
+   */
+  public org.exolab.castor.mapping.ClassDescriptor getExtends()
+  {
+    return null;
+  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
+
+  /**
+   * Method getIdentity
+   *
+   *
+   *
+   * @return FieldDescriptor
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return identity;
+  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
+
+  /**
+   * Method getJavaClass
+   *
+   *
+   *
+   * @return Class
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.AnnotationElement.class;
+  } //-- java.lang.Class getJavaClass()
+
+  /**
+   * Method getNameSpacePrefix
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return nsPrefix;
+  } //-- java.lang.String getNameSpacePrefix()
+
+  /**
+   * Method getNameSpaceURI
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return nsURI;
+  } //-- java.lang.String getNameSpaceURI()
+
+  /**
+   * Method getValidator
+   *
+   *
+   *
+   * @return TypeValidator
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  } //-- org.exolab.castor.xml.TypeValidator getValidator()
+
+  /**
+   * Method getXMLName
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getXMLName()
+  {
+    return xmlName;
+  } //-- java.lang.String getXMLName()
 
 }
diff --git a/src/jalview/schemabinding/version2/Colour.java b/src/jalview/schemabinding/version2/Colour.java
index bcc4642..2b2dba7 100755
--- a/src/jalview/schemabinding/version2/Colour.java
+++ b/src/jalview/schemabinding/version2/Colour.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,167 +7,166 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
+import org.exolab.castor.xml.*;
 
 /**
  * Class Colour.
- * 
+ *
  * @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();
-    } //-- jalview.schemabinding.version2.Colour()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Returns the value of field 'name'.
-     * 
-     * @return String
-     * @return the value of field 'name'.
-     */
-    public java.lang.String getName()
-    {
-        return this._name;
-    } //-- java.lang.String getName() 
-
-    /**
-     * Returns the value of field 'RGB'.
-     * 
-     * @return String
-     * @return the value of field 'RGB'.
-     */
-    public java.lang.String getRGB()
-    {
-        return this._RGB;
-    } //-- java.lang.String getRGB() 
-
-    /**
-     * Method isValid
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean isValid()
-    {
-        try {
-            validate();
-        }
-        catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    } //-- boolean isValid() 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param out
-     */
-    public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, out);
-    } //-- void marshal(java.io.Writer) 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param handler
-     */
-    public void marshal(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, handler);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
-
-    /**
-     * Sets the value of field 'name'.
-     * 
-     * @param name the value of field 'name'.
-     */
-    public void setName(java.lang.String name)
-    {
-        this._name = name;
-    } //-- void setName(java.lang.String) 
-
-    /**
-     * Sets the value of field 'RGB'.
-     * 
-     * @param RGB the value of field 'RGB'.
-     */
-    public void setRGB(java.lang.String RGB)
-    {
-        this._RGB = RGB;
-    } //-- void setRGB(java.lang.String) 
-
-    /**
-     * Method unmarshal
-     * 
-     * 
-     * 
-     * @param reader
-     * @return Object
-     */
-    public static java.lang.Object unmarshal(java.io.Reader reader)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+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();
+  } //-- jalview.schemabinding.version2.Colour()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Returns the value of field 'name'.
+   *
+   * @return String
+   * @return the value of field 'name'.
+   */
+  public java.lang.String getName()
+  {
+    return this._name;
+  } //-- java.lang.String getName()
+
+  /**
+   * Returns the value of field 'RGB'.
+   *
+   * @return String
+   * @return the value of field 'RGB'.
+   */
+  public java.lang.String getRGB()
+  {
+    return this._RGB;
+  } //-- java.lang.String getRGB()
+
+  /**
+   * Method isValid
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean isValid()
+  {
+    try
     {
-        return (jalview.schemabinding.version2.Colour) Unmarshaller.unmarshal(jalview.schemabinding.version2.Colour.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
-
-    /**
-     * Method validate
-     * 
-     */
-    public void validate()
-        throws org.exolab.castor.xml.ValidationException
+      validate();
+    }
+    catch (org.exolab.castor.xml.ValidationException vex)
     {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    } //-- void validate() 
+      return false;
+    }
+    return true;
+  } //-- boolean isValid()
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param out
+   */
+  public void marshal(java.io.Writer out)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, out);
+  } //-- void marshal(java.io.Writer)
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param handler
+   */
+  public void marshal(org.xml.sax.ContentHandler handler)
+      throws java.io.IOException, org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, handler);
+  } //-- void marshal(org.xml.sax.ContentHandler)
+
+  /**
+   * Sets the value of field 'name'.
+   *
+   * @param name the value of field 'name'.
+   */
+  public void setName(java.lang.String name)
+  {
+    this._name = name;
+  } //-- void setName(java.lang.String)
+
+  /**
+   * Sets the value of field 'RGB'.
+   *
+   * @param RGB the value of field 'RGB'.
+   */
+  public void setRGB(java.lang.String RGB)
+  {
+    this._RGB = RGB;
+  } //-- void setRGB(java.lang.String)
+
+  /**
+   * Method unmarshal
+   *
+   *
+   *
+   * @param reader
+   * @return Object
+   */
+  public static java.lang.Object unmarshal(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);
+  } //-- java.lang.Object unmarshal(java.io.Reader)
+
+  /**
+   * Method validate
+   *
+   */
+  public void validate()
+      throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.
+        Validator();
+    validator.validate(this);
+  } //-- void validate()
 
 }
diff --git a/src/jalview/schemabinding/version2/ColourDescriptor.java b/src/jalview/schemabinding/version2/ColourDescriptor.java
index 7aa3a82..7865ccf 100755
--- a/src/jalview/schemabinding/version2/ColourDescriptor.java
+++ b/src/jalview/schemabinding/version2/ColourDescriptor.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,237 +7,248 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
-import org.exolab.castor.mapping.AccessMode;
-import org.exolab.castor.xml.TypeValidator;
-import org.exolab.castor.xml.XMLFieldDescriptor;
 import org.exolab.castor.xml.validators.*;
 
 /**
  * Class ColourDescriptor.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class ColourDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field nsPrefix
-     */
-    private java.lang.String nsPrefix;
-
-    /**
-     * Field nsURI
-     */
-    private java.lang.String nsURI;
-
-    /**
-     * Field xmlName
-     */
-    private java.lang.String xmlName;
-
-    /**
-     * Field identity
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor identity;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public ColourDescriptor() {
-        super();
-        xmlName = "colour";
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.xml.XMLFieldHandler              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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _name
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            StringValidator typeValidator = new StringValidator();
-            typeValidator.setWhiteSpace("preserve");
-            fieldValidator.setValidator(typeValidator);
+public class ColourDescriptor
+    extends org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  //--------------------------/
+  //- Class/Member Variables -/
+  //--------------------------/
+
+  /**
+   * Field nsPrefix
+   */
+  private java.lang.String nsPrefix;
+
+  /**
+   * Field nsURI
+   */
+  private java.lang.String nsURI;
+
+  /**
+   * Field xmlName
+   */
+  private java.lang.String xmlName;
+
+  /**
+   * Field identity
+   */
+  private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+  //----------------/
+  //- Constructors -/
+  //----------------/
+
+  public ColourDescriptor()
+  {
+    super();
+    xmlName = "colour";
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.xml.XMLFieldHandler 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);
         }
-        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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _RGB
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            StringValidator typeValidator = new StringValidator();
-            typeValidator.setWhiteSpace("preserve");
-            fieldValidator.setValidator(typeValidator);
+        catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-    } //-- jalview.schemabinding.version2.ColourDescriptor()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method getAccessMode
-     * 
-     * 
-     * 
-     * @return AccessMode
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode()
-    {
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
-
-    /**
-     * Method getExtends
-     * 
-     * 
-     * 
-     * @return ClassDescriptor
-     */
-    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+      }
+    });
+    desc.setHandler(handler);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _name
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      StringValidator typeValidator = new StringValidator();
+      typeValidator.setWhiteSpace("preserve");
+      fieldValidator.setValidator(typeValidator);
+    }
+    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;
-    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
-
-    /**
-     * Method getIdentity
-     * 
-     * 
-     * 
-     * @return FieldDescriptor
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
-    {
-        return identity;
-    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
-
-    /**
-     * Method getJavaClass
-     * 
-     * 
-     * 
-     * @return Class
-     */
-    public java.lang.Class getJavaClass()
-    {
-        return jalview.schemabinding.version2.Colour.class;
-    } //-- java.lang.Class getJavaClass() 
-
-    /**
-     * Method getNameSpacePrefix
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpacePrefix()
-    {
-        return nsPrefix;
-    } //-- java.lang.String getNameSpacePrefix() 
-
-    /**
-     * Method getNameSpaceURI
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpaceURI()
-    {
-        return nsURI;
-    } //-- java.lang.String getNameSpaceURI() 
-
-    /**
-     * Method getValidator
-     * 
-     * 
-     * 
-     * @return TypeValidator
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator()
-    {
-        return this;
-    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
-
-    /**
-     * Method getXMLName
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getXMLName()
-    {
-        return xmlName;
-    } //-- java.lang.String getXMLName() 
+      }
+    });
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _RGB
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { //-- local scope
+      StringValidator typeValidator = new StringValidator();
+      typeValidator.setWhiteSpace("preserve");
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    //-- initialize element descriptors
+
+  } //-- jalview.schemabinding.version2.ColourDescriptor()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Method getAccessMode
+   *
+   *
+   *
+   * @return AccessMode
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
+
+  /**
+   * Method getExtends
+   *
+   *
+   *
+   * @return ClassDescriptor
+   */
+  public org.exolab.castor.mapping.ClassDescriptor getExtends()
+  {
+    return null;
+  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
+
+  /**
+   * Method getIdentity
+   *
+   *
+   *
+   * @return FieldDescriptor
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return identity;
+  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
+
+  /**
+   * Method getJavaClass
+   *
+   *
+   *
+   * @return Class
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.Colour.class;
+  } //-- java.lang.Class getJavaClass()
+
+  /**
+   * Method getNameSpacePrefix
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return nsPrefix;
+  } //-- java.lang.String getNameSpacePrefix()
+
+  /**
+   * Method getNameSpaceURI
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return nsURI;
+  } //-- java.lang.String getNameSpaceURI()
+
+  /**
+   * Method getValidator
+   *
+   *
+   *
+   * @return TypeValidator
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  } //-- org.exolab.castor.xml.TypeValidator getValidator()
+
+  /**
+   * Method getXMLName
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getXMLName()
+  {
+    return xmlName;
+  } //-- java.lang.String getXMLName()
 
 }
diff --git a/src/jalview/schemabinding/version2/DBRef.java b/src/jalview/schemabinding/version2/DBRef.java
index 576a4ad..7c98b4e 100644
--- a/src/jalview/schemabinding/version2/DBRef.java
+++ b/src/jalview/schemabinding/version2/DBRef.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,193 +7,192 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
+import org.exolab.castor.xml.*;
 
 /**
  * Class DBRef.
- * 
+ *
  * @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;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public DBRef() {
-        super();
-    } //-- jalview.schemabinding.version2.DBRef()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Returns the value of field 'accessionId'.
-     * 
-     * @return String
-     * @return the value of field 'accessionId'.
-     */
-    public java.lang.String getAccessionId()
-    {
-        return this._accessionId;
-    } //-- java.lang.String getAccessionId() 
-
-    /**
-     * Returns the value of field 'source'.
-     * 
-     * @return String
-     * @return the value of field 'source'.
-     */
-    public java.lang.String getSource()
-    {
-        return this._source;
-    } //-- java.lang.String getSource() 
-
-    /**
-     * Returns the value of field 'version'.
-     * 
-     * @return String
-     * @return the value of field 'version'.
-     */
-    public java.lang.String getVersion()
-    {
-        return this._version;
-    } //-- java.lang.String getVersion() 
-
-    /**
-     * Method isValid
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean isValid()
-    {
-        try {
-            validate();
-        }
-        catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    } //-- boolean isValid() 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param out
-     */
-    public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, out);
-    } //-- void marshal(java.io.Writer) 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param handler
-     */
-    public void marshal(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, handler);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
-
-    /**
-     * Sets the value of field 'accessionId'.
-     * 
-     * @param accessionId the value of field 'accessionId'.
-     */
-    public void setAccessionId(java.lang.String accessionId)
-    {
-        this._accessionId = accessionId;
-    } //-- void setAccessionId(java.lang.String) 
-
-    /**
-     * Sets the value of field 'source'.
-     * 
-     * @param source the value of field 'source'.
-     */
-    public void setSource(java.lang.String source)
-    {
-        this._source = source;
-    } //-- void setSource(java.lang.String) 
-
-    /**
-     * Sets the value of field 'version'.
-     * 
-     * @param version the value of field 'version'.
-     */
-    public void setVersion(java.lang.String version)
-    {
-        this._version = version;
-    } //-- void setVersion(java.lang.String) 
-
-    /**
-     * Method unmarshal
-     * 
-     * 
-     * 
-     * @param reader
-     * @return Object
-     */
-    public static java.lang.Object unmarshal(java.io.Reader reader)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+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;
+
+  //----------------/
+  //- Constructors -/
+  //----------------/
+
+  public DBRef()
+  {
+    super();
+  } //-- jalview.schemabinding.version2.DBRef()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Returns the value of field 'accessionId'.
+   *
+   * @return String
+   * @return the value of field 'accessionId'.
+   */
+  public java.lang.String getAccessionId()
+  {
+    return this._accessionId;
+  } //-- java.lang.String getAccessionId()
+
+  /**
+   * Returns the value of field 'source'.
+   *
+   * @return String
+   * @return the value of field 'source'.
+   */
+  public java.lang.String getSource()
+  {
+    return this._source;
+  } //-- java.lang.String getSource()
+
+  /**
+   * Returns the value of field 'version'.
+   *
+   * @return String
+   * @return the value of field 'version'.
+   */
+  public java.lang.String getVersion()
+  {
+    return this._version;
+  } //-- java.lang.String getVersion()
+
+  /**
+   * Method isValid
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean isValid()
+  {
+    try
     {
-        return (jalview.schemabinding.version2.DBRef) Unmarshaller.unmarshal(jalview.schemabinding.version2.DBRef.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
-
-    /**
-     * Method validate
-     * 
-     */
-    public void validate()
-        throws org.exolab.castor.xml.ValidationException
+      validate();
+    }
+    catch (org.exolab.castor.xml.ValidationException vex)
     {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    } //-- void validate() 
+      return false;
+    }
+    return true;
+  } //-- boolean isValid()
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param out
+   */
+  public void marshal(java.io.Writer out)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, out);
+  } //-- void marshal(java.io.Writer)
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param handler
+   */
+  public void marshal(org.xml.sax.ContentHandler handler)
+      throws java.io.IOException, org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, handler);
+  } //-- void marshal(org.xml.sax.ContentHandler)
+
+  /**
+   * Sets the value of field 'accessionId'.
+   *
+   * @param accessionId the value of field 'accessionId'.
+   */
+  public void setAccessionId(java.lang.String accessionId)
+  {
+    this._accessionId = accessionId;
+  } //-- void setAccessionId(java.lang.String)
+
+  /**
+   * Sets the value of field 'source'.
+   *
+   * @param source the value of field 'source'.
+   */
+  public void setSource(java.lang.String source)
+  {
+    this._source = source;
+  } //-- void setSource(java.lang.String)
+
+  /**
+   * Sets the value of field 'version'.
+   *
+   * @param version the value of field 'version'.
+   */
+  public void setVersion(java.lang.String version)
+  {
+    this._version = version;
+  } //-- void setVersion(java.lang.String)
+
+  /**
+   * Method unmarshal
+   *
+   *
+   *
+   * @param reader
+   * @return Object
+   */
+  public static java.lang.Object unmarshal(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);
+  } //-- java.lang.Object unmarshal(java.io.Reader)
+
+  /**
+   * Method validate
+   *
+   */
+  public void validate()
+      throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.
+        Validator();
+    validator.validate(this);
+  } //-- void validate()
 
 }
diff --git a/src/jalview/schemabinding/version2/DBRefDescriptor.java b/src/jalview/schemabinding/version2/DBRefDescriptor.java
index 939d5b1..9ab9112 100644
--- a/src/jalview/schemabinding/version2/DBRefDescriptor.java
+++ b/src/jalview/schemabinding/version2/DBRefDescriptor.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,272 +7,293 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
-import org.exolab.castor.mapping.AccessMode;
-import org.exolab.castor.xml.TypeValidator;
-import org.exolab.castor.xml.XMLFieldDescriptor;
 import org.exolab.castor.xml.validators.*;
 
 /**
  * Class DBRefDescriptor.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class DBRefDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field nsPrefix
-     */
-    private java.lang.String nsPrefix;
-
-    /**
-     * Field nsURI
-     */
-    private java.lang.String nsURI;
-
-    /**
-     * Field xmlName
-     */
-    private java.lang.String xmlName;
-
-    /**
-     * Field identity
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor identity;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public DBRefDescriptor() {
-        super();
-        nsURI = "www.vamsas.ac.uk/jalview/version2";
-        xmlName = "DBRef";
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.xml.XMLFieldHandler              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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _source
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            StringValidator typeValidator = new StringValidator();
-            typeValidator.setWhiteSpace("preserve");
-            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.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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _version
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            StringValidator typeValidator = new StringValidator();
-            typeValidator.setWhiteSpace("preserve");
-            fieldValidator.setValidator(typeValidator);
+public class DBRefDescriptor
+    extends org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  //--------------------------/
+  //- Class/Member Variables -/
+  //--------------------------/
+
+  /**
+   * Field nsPrefix
+   */
+  private java.lang.String nsPrefix;
+
+  /**
+   * Field nsURI
+   */
+  private java.lang.String nsURI;
+
+  /**
+   * Field xmlName
+   */
+  private java.lang.String xmlName;
+
+  /**
+   * Field identity
+   */
+  private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+  //----------------/
+  //- Constructors -/
+  //----------------/
+
+  public DBRefDescriptor()
+  {
+    super();
+    nsURI = "www.vamsas.ac.uk/jalview/version2";
+    xmlName = "DBRef";
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.xml.XMLFieldHandler 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);
         }
-        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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _accessionId
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            StringValidator typeValidator = new StringValidator();
-            typeValidator.setWhiteSpace("preserve");
-            fieldValidator.setValidator(typeValidator);
+        catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-    } //-- jalview.schemabinding.version2.DBRefDescriptor()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method getAccessMode
-     * 
-     * 
-     * 
-     * @return AccessMode
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode()
-    {
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
-
-    /**
-     * Method getExtends
-     * 
-     * 
-     * 
-     * @return ClassDescriptor
-     */
-    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+      }
+    });
+    desc.setHandler(handler);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _source
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      StringValidator typeValidator = new StringValidator();
+      typeValidator.setWhiteSpace("preserve");
+      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.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;
-    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
-
-    /**
-     * Method getIdentity
-     * 
-     * 
-     * 
-     * @return FieldDescriptor
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
-    {
-        return identity;
-    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
-
-    /**
-     * Method getJavaClass
-     * 
-     * 
-     * 
-     * @return Class
-     */
-    public java.lang.Class getJavaClass()
-    {
-        return jalview.schemabinding.version2.DBRef.class;
-    } //-- java.lang.Class getJavaClass() 
-
-    /**
-     * Method getNameSpacePrefix
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpacePrefix()
-    {
-        return nsPrefix;
-    } //-- java.lang.String getNameSpacePrefix() 
-
-    /**
-     * Method getNameSpaceURI
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpaceURI()
-    {
-        return nsURI;
-    } //-- java.lang.String getNameSpaceURI() 
-
-    /**
-     * Method getValidator
-     * 
-     * 
-     * 
-     * @return TypeValidator
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator()
-    {
-        return this;
-    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
-
-    /**
-     * Method getXMLName
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getXMLName()
+      }
+    });
+    desc.setHandler(handler);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _version
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      StringValidator typeValidator = new StringValidator();
+      typeValidator.setWhiteSpace("preserve");
+      fieldValidator.setValidator(typeValidator);
+    }
+    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()
     {
-        return xmlName;
-    } //-- java.lang.String getXMLName() 
+      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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _accessionId
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      StringValidator typeValidator = new StringValidator();
+      typeValidator.setWhiteSpace("preserve");
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    //-- initialize element descriptors
+
+  } //-- jalview.schemabinding.version2.DBRefDescriptor()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Method getAccessMode
+   *
+   *
+   *
+   * @return AccessMode
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
+
+  /**
+   * Method getExtends
+   *
+   *
+   *
+   * @return ClassDescriptor
+   */
+  public org.exolab.castor.mapping.ClassDescriptor getExtends()
+  {
+    return null;
+  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
+
+  /**
+   * Method getIdentity
+   *
+   *
+   *
+   * @return FieldDescriptor
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return identity;
+  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
+
+  /**
+   * Method getJavaClass
+   *
+   *
+   *
+   * @return Class
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.DBRef.class;
+  } //-- java.lang.Class getJavaClass()
+
+  /**
+   * Method getNameSpacePrefix
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return nsPrefix;
+  } //-- java.lang.String getNameSpacePrefix()
+
+  /**
+   * Method getNameSpaceURI
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return nsURI;
+  } //-- java.lang.String getNameSpaceURI()
+
+  /**
+   * Method getValidator
+   *
+   *
+   *
+   * @return TypeValidator
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  } //-- org.exolab.castor.xml.TypeValidator getValidator()
+
+  /**
+   * Method getXMLName
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getXMLName()
+  {
+    return xmlName;
+  } //-- java.lang.String getXMLName()
 
 }
diff --git a/src/jalview/schemabinding/version2/Feature.java b/src/jalview/schemabinding/version2/Feature.java
index 305e287..2f7f2fa 100755
--- a/src/jalview/schemabinding/version2/Feature.java
+++ b/src/jalview/schemabinding/version2/Feature.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,531 +7,540 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
 //---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import java.util.*;
 
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import java.util.Enumeration;
-import java.util.Vector;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
+import org.exolab.castor.xml.*;
 
 /**
  * Class Feature.
- * 
+ *
  * @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();
-        _otherDataList = new Vector();
-    } //-- jalview.schemabinding.version2.Feature()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method addOtherData
-     * 
-     * 
-     * 
-     * @param vOtherData
-     */
-    public void addOtherData(jalview.schemabinding.version2.OtherData vOtherData)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _otherDataList.addElement(vOtherData);
-    } //-- void addOtherData(jalview.schemabinding.version2.OtherData) 
-
-    /**
-     * Method addOtherData
-     * 
-     * 
-     * 
-     * @param index
-     * @param vOtherData
-     */
-    public void addOtherData(int index, jalview.schemabinding.version2.OtherData vOtherData)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _otherDataList.insertElementAt(vOtherData, index);
-    } //-- void addOtherData(int, jalview.schemabinding.version2.OtherData) 
-
-    /**
-     * Method deleteBegin
-     * 
-     */
-    public void deleteBegin()
-    {
-        this._has_begin= false;
-    } //-- void deleteBegin() 
-
-    /**
-     * Method deleteEnd
-     * 
-     */
-    public void deleteEnd()
-    {
-        this._has_end= false;
-    } //-- void deleteEnd() 
-
-    /**
-     * Method deleteScore
-     * 
-     */
-    public void deleteScore()
-    {
-        this._has_score= false;
-    } //-- void deleteScore() 
-
-    /**
-     * Method enumerateOtherData
-     * 
-     * 
-     * 
-     * @return Enumeration
-     */
-    public java.util.Enumeration enumerateOtherData()
-    {
-        return _otherDataList.elements();
-    } //-- java.util.Enumeration enumerateOtherData() 
-
-    /**
-     * Returns the value of field 'begin'.
-     * 
-     * @return int
-     * @return the value of field 'begin'.
-     */
-    public int getBegin()
-    {
-        return this._begin;
-    } //-- int getBegin() 
-
-    /**
-     * Returns the value of field 'description'.
-     * 
-     * @return String
-     * @return the value of field 'description'.
-     */
-    public java.lang.String getDescription()
-    {
-        return this._description;
-    } //-- java.lang.String getDescription() 
-
-    /**
-     * Returns the value of field 'end'.
-     * 
-     * @return int
-     * @return the value of field 'end'.
-     */
-    public int getEnd()
-    {
-        return this._end;
-    } //-- int getEnd() 
-
-    /**
-     * Returns the value of field 'featureGroup'.
-     * 
-     * @return String
-     * @return the value of field 'featureGroup'.
-     */
-    public java.lang.String getFeatureGroup()
-    {
-        return this._featureGroup;
-    } //-- java.lang.String getFeatureGroup() 
-
-    /**
-     * Method getOtherData
-     * 
-     * 
-     * 
-     * @param index
-     * @return OtherData
-     */
-    public jalview.schemabinding.version2.OtherData getOtherData(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _otherDataList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        
-        return (jalview.schemabinding.version2.OtherData) _otherDataList.elementAt(index);
-    } //-- jalview.schemabinding.version2.OtherData getOtherData(int) 
-
-    /**
-     * Method getOtherData
-     * 
-     * 
-     * 
-     * @return OtherData
-     */
-    public jalview.schemabinding.version2.OtherData[] getOtherData()
-    {
-        int size = _otherDataList.size();
-        jalview.schemabinding.version2.OtherData[] mArray = new jalview.schemabinding.version2.OtherData[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = (jalview.schemabinding.version2.OtherData) _otherDataList.elementAt(index);
-        }
-        return mArray;
-    } //-- jalview.schemabinding.version2.OtherData[] getOtherData() 
-
-    /**
-     * Method getOtherDataCount
-     * 
-     * 
-     * 
-     * @return int
-     */
-    public int getOtherDataCount()
-    {
-        return _otherDataList.size();
-    } //-- int getOtherDataCount() 
-
-    /**
-     * Returns the value of field 'score'.
-     * 
-     * @return float
-     * @return the value of field 'score'.
-     */
-    public float getScore()
-    {
-        return this._score;
-    } //-- float getScore() 
-
-    /**
-     * Returns the value of field 'status'.
-     * 
-     * @return String
-     * @return the value of field 'status'.
-     */
-    public java.lang.String getStatus()
-    {
-        return this._status;
-    } //-- java.lang.String getStatus() 
-
-    /**
-     * Returns the value of field 'type'.
-     * 
-     * @return String
-     * @return the value of field 'type'.
-     */
-    public java.lang.String getType()
-    {
-        return this._type;
-    } //-- java.lang.String getType() 
-
-    /**
-     * Method hasBegin
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasBegin()
-    {
-        return this._has_begin;
-    } //-- boolean hasBegin() 
-
-    /**
-     * Method hasEnd
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasEnd()
-    {
-        return this._has_end;
-    } //-- boolean hasEnd() 
-
-    /**
-     * Method hasScore
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasScore()
-    {
-        return this._has_score;
-    } //-- boolean hasScore() 
-
-    /**
-     * Method isValid
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean isValid()
-    {
-        try {
-            validate();
-        }
-        catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    } //-- boolean isValid() 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param out
-     */
-    public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, out);
-    } //-- void marshal(java.io.Writer) 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param handler
-     */
-    public void marshal(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, handler);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
-
-    /**
-     * Method removeAllOtherData
-     * 
-     */
-    public void removeAllOtherData()
-    {
-        _otherDataList.removeAllElements();
-    } //-- void removeAllOtherData() 
-
-    /**
-     * Method removeOtherData
-     * 
-     * 
-     * 
-     * @param index
-     * @return OtherData
-     */
-    public jalview.schemabinding.version2.OtherData removeOtherData(int index)
-    {
-        java.lang.Object obj = _otherDataList.elementAt(index);
-        _otherDataList.removeElementAt(index);
-        return (jalview.schemabinding.version2.OtherData) obj;
-    } //-- jalview.schemabinding.version2.OtherData removeOtherData(int) 
-
-    /**
-     * Sets the value of field 'begin'.
-     * 
-     * @param begin the value of field 'begin'.
-     */
-    public void setBegin(int begin)
-    {
-        this._begin = begin;
-        this._has_begin = true;
-    } //-- void setBegin(int) 
-
-    /**
-     * Sets the value of field 'description'.
-     * 
-     * @param description the value of field 'description'.
-     */
-    public void setDescription(java.lang.String description)
-    {
-        this._description = description;
-    } //-- void setDescription(java.lang.String) 
-
-    /**
-     * Sets the value of field 'end'.
-     * 
-     * @param end the value of field 'end'.
-     */
-    public void setEnd(int end)
-    {
-        this._end = end;
-        this._has_end = true;
-    } //-- void setEnd(int) 
-
-    /**
-     * Sets the value of field 'featureGroup'.
-     * 
-     * @param featureGroup the value of field 'featureGroup'.
-     */
-    public void setFeatureGroup(java.lang.String featureGroup)
-    {
-        this._featureGroup = featureGroup;
-    } //-- void setFeatureGroup(java.lang.String) 
-
-    /**
-     * Method setOtherData
-     * 
-     * 
-     * 
-     * @param index
-     * @param vOtherData
-     */
-    public void setOtherData(int index, jalview.schemabinding.version2.OtherData vOtherData)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _otherDataList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        _otherDataList.setElementAt(vOtherData, index);
-    } //-- void setOtherData(int, jalview.schemabinding.version2.OtherData) 
-
-    /**
-     * Method setOtherData
-     * 
-     * 
-     * 
-     * @param otherDataArray
-     */
-    public void setOtherData(jalview.schemabinding.version2.OtherData[] otherDataArray)
-    {
-        //-- copy array
-        _otherDataList.removeAllElements();
-        for (int i = 0; i < otherDataArray.length; i++) {
-            _otherDataList.addElement(otherDataArray[i]);
-        }
-    } //-- void setOtherData(jalview.schemabinding.version2.OtherData) 
-
-    /**
-     * Sets the value of field 'score'.
-     * 
-     * @param score the value of field 'score'.
-     */
-    public void setScore(float score)
-    {
-        this._score = score;
-        this._has_score = true;
-    } //-- void setScore(float) 
-
-    /**
-     * Sets the value of field 'status'.
-     * 
-     * @param status the value of field 'status'.
-     */
-    public void setStatus(java.lang.String status)
-    {
-        this._status = status;
-    } //-- void setStatus(java.lang.String) 
-
-    /**
-     * Sets the value of field 'type'.
-     * 
-     * @param type the value of field 'type'.
-     */
-    public void setType(java.lang.String type)
-    {
-        this._type = type;
-    } //-- void setType(java.lang.String) 
-
-    /**
-     * Method unmarshal
-     * 
-     * 
-     * 
-     * @param reader
-     * @return Object
-     */
-    public static java.lang.Object unmarshal(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);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
-
-    /**
-     * Method validate
-     * 
-     */
-    public void validate()
-        throws org.exolab.castor.xml.ValidationException
-    {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    } //-- void validate() 
+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();
+    _otherDataList = new Vector();
+  } //-- jalview.schemabinding.version2.Feature()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Method addOtherData
+   *
+   *
+   *
+   * @param vOtherData
+   */
+  public void addOtherData(jalview.schemabinding.version2.OtherData vOtherData)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _otherDataList.addElement(vOtherData);
+  } //-- void addOtherData(jalview.schemabinding.version2.OtherData)
+
+  /**
+   * Method addOtherData
+   *
+   *
+   *
+   * @param index
+   * @param vOtherData
+   */
+  public void addOtherData(int index,
+                           jalview.schemabinding.version2.OtherData vOtherData)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _otherDataList.insertElementAt(vOtherData, index);
+  } //-- void addOtherData(int, jalview.schemabinding.version2.OtherData)
+
+  /**
+   * Method deleteBegin
+   *
+   */
+  public void deleteBegin()
+  {
+    this._has_begin = false;
+  } //-- void deleteBegin()
+
+  /**
+   * Method deleteEnd
+   *
+   */
+  public void deleteEnd()
+  {
+    this._has_end = false;
+  } //-- void deleteEnd()
+
+  /**
+   * Method deleteScore
+   *
+   */
+  public void deleteScore()
+  {
+    this._has_score = false;
+  } //-- void deleteScore()
+
+  /**
+   * Method enumerateOtherData
+   *
+   *
+   *
+   * @return Enumeration
+   */
+  public java.util.Enumeration enumerateOtherData()
+  {
+    return _otherDataList.elements();
+  } //-- java.util.Enumeration enumerateOtherData()
+
+  /**
+   * Returns the value of field 'begin'.
+   *
+   * @return int
+   * @return the value of field 'begin'.
+   */
+  public int getBegin()
+  {
+    return this._begin;
+  } //-- int getBegin()
+
+  /**
+   * Returns the value of field 'description'.
+   *
+   * @return String
+   * @return the value of field 'description'.
+   */
+  public java.lang.String getDescription()
+  {
+    return this._description;
+  } //-- java.lang.String getDescription()
+
+  /**
+   * Returns the value of field 'end'.
+   *
+   * @return int
+   * @return the value of field 'end'.
+   */
+  public int getEnd()
+  {
+    return this._end;
+  } //-- int getEnd()
+
+  /**
+   * Returns the value of field 'featureGroup'.
+   *
+   * @return String
+   * @return the value of field 'featureGroup'.
+   */
+  public java.lang.String getFeatureGroup()
+  {
+    return this._featureGroup;
+  } //-- java.lang.String getFeatureGroup()
+
+  /**
+   * Method getOtherData
+   *
+   *
+   *
+   * @param index
+   * @return OtherData
+   */
+  public jalview.schemabinding.version2.OtherData getOtherData(int index)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _otherDataList.size()))
+    {
+      throw new IndexOutOfBoundsException();
+    }
+
+    return (jalview.schemabinding.version2.OtherData) _otherDataList.elementAt(
+        index);
+  } //-- jalview.schemabinding.version2.OtherData getOtherData(int)
+
+  /**
+   * Method getOtherData
+   *
+   *
+   *
+   * @return OtherData
+   */
+  public jalview.schemabinding.version2.OtherData[] getOtherData()
+  {
+    int size = _otherDataList.size();
+    jalview.schemabinding.version2.OtherData[] mArray = new jalview.
+        schemabinding.version2.OtherData[size];
+    for (int index = 0; index < size; index++)
+    {
+      mArray[index] = (jalview.schemabinding.version2.OtherData) _otherDataList.
+          elementAt(index);
+    }
+    return mArray;
+  } //-- jalview.schemabinding.version2.OtherData[] getOtherData()
+
+  /**
+   * Method getOtherDataCount
+   *
+   *
+   *
+   * @return int
+   */
+  public int getOtherDataCount()
+  {
+    return _otherDataList.size();
+  } //-- int getOtherDataCount()
+
+  /**
+   * Returns the value of field 'score'.
+   *
+   * @return float
+   * @return the value of field 'score'.
+   */
+  public float getScore()
+  {
+    return this._score;
+  } //-- float getScore()
+
+  /**
+   * Returns the value of field 'status'.
+   *
+   * @return String
+   * @return the value of field 'status'.
+   */
+  public java.lang.String getStatus()
+  {
+    return this._status;
+  } //-- java.lang.String getStatus()
+
+  /**
+   * Returns the value of field 'type'.
+   *
+   * @return String
+   * @return the value of field 'type'.
+   */
+  public java.lang.String getType()
+  {
+    return this._type;
+  } //-- java.lang.String getType()
+
+  /**
+   * Method hasBegin
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasBegin()
+  {
+    return this._has_begin;
+  } //-- boolean hasBegin()
+
+  /**
+   * Method hasEnd
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasEnd()
+  {
+    return this._has_end;
+  } //-- boolean hasEnd()
+
+  /**
+   * Method hasScore
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasScore()
+  {
+    return this._has_score;
+  } //-- boolean hasScore()
+
+  /**
+   * Method isValid
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    }
+    catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  } //-- boolean isValid()
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param out
+   */
+  public void marshal(java.io.Writer out)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, out);
+  } //-- void marshal(java.io.Writer)
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param handler
+   */
+  public void marshal(org.xml.sax.ContentHandler handler)
+      throws java.io.IOException, org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, handler);
+  } //-- void marshal(org.xml.sax.ContentHandler)
+
+  /**
+   * Method removeAllOtherData
+   *
+   */
+  public void removeAllOtherData()
+  {
+    _otherDataList.removeAllElements();
+  } //-- void removeAllOtherData()
+
+  /**
+   * Method removeOtherData
+   *
+   *
+   *
+   * @param index
+   * @return OtherData
+   */
+  public jalview.schemabinding.version2.OtherData removeOtherData(int index)
+  {
+    java.lang.Object obj = _otherDataList.elementAt(index);
+    _otherDataList.removeElementAt(index);
+    return (jalview.schemabinding.version2.OtherData) obj;
+  } //-- jalview.schemabinding.version2.OtherData removeOtherData(int)
+
+  /**
+   * Sets the value of field 'begin'.
+   *
+   * @param begin the value of field 'begin'.
+   */
+  public void setBegin(int begin)
+  {
+    this._begin = begin;
+    this._has_begin = true;
+  } //-- void setBegin(int)
+
+  /**
+   * Sets the value of field 'description'.
+   *
+   * @param description the value of field 'description'.
+   */
+  public void setDescription(java.lang.String description)
+  {
+    this._description = description;
+  } //-- void setDescription(java.lang.String)
+
+  /**
+   * Sets the value of field 'end'.
+   *
+   * @param end the value of field 'end'.
+   */
+  public void setEnd(int end)
+  {
+    this._end = end;
+    this._has_end = true;
+  } //-- void setEnd(int)
+
+  /**
+   * Sets the value of field 'featureGroup'.
+   *
+   * @param featureGroup the value of field 'featureGroup'.
+   */
+  public void setFeatureGroup(java.lang.String featureGroup)
+  {
+    this._featureGroup = featureGroup;
+  } //-- void setFeatureGroup(java.lang.String)
+
+  /**
+   * Method setOtherData
+   *
+   *
+   *
+   * @param index
+   * @param vOtherData
+   */
+  public void setOtherData(int index,
+                           jalview.schemabinding.version2.OtherData vOtherData)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _otherDataList.size()))
+    {
+      throw new IndexOutOfBoundsException();
+    }
+    _otherDataList.setElementAt(vOtherData, index);
+  } //-- void setOtherData(int, jalview.schemabinding.version2.OtherData)
+
+  /**
+   * Method setOtherData
+   *
+   *
+   *
+   * @param otherDataArray
+   */
+  public void setOtherData(jalview.schemabinding.version2.OtherData[]
+                           otherDataArray)
+  {
+    //-- copy array
+    _otherDataList.removeAllElements();
+    for (int i = 0; i < otherDataArray.length; i++)
+    {
+      _otherDataList.addElement(otherDataArray[i]);
+    }
+  } //-- void setOtherData(jalview.schemabinding.version2.OtherData)
+
+  /**
+   * Sets the value of field 'score'.
+   *
+   * @param score the value of field 'score'.
+   */
+  public void setScore(float score)
+  {
+    this._score = score;
+    this._has_score = true;
+  } //-- void setScore(float)
+
+  /**
+   * Sets the value of field 'status'.
+   *
+   * @param status the value of field 'status'.
+   */
+  public void setStatus(java.lang.String status)
+  {
+    this._status = status;
+  } //-- void setStatus(java.lang.String)
+
+  /**
+   * Sets the value of field 'type'.
+   *
+   * @param type the value of field 'type'.
+   */
+  public void setType(java.lang.String type)
+  {
+    this._type = type;
+  } //-- void setType(java.lang.String)
+
+  /**
+   * Method unmarshal
+   *
+   *
+   *
+   * @param reader
+   * @return Object
+   */
+  public static java.lang.Object unmarshal(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);
+  } //-- java.lang.Object unmarshal(java.io.Reader)
+
+  /**
+   * Method validate
+   *
+   */
+  public void validate()
+      throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.
+        Validator();
+    validator.validate(this);
+  } //-- void validate()
 
 }
diff --git a/src/jalview/schemabinding/version2/FeatureDescriptor.java b/src/jalview/schemabinding/version2/FeatureDescriptor.java
index d0b9372..0641afa 100755
--- a/src/jalview/schemabinding/version2/FeatureDescriptor.java
+++ b/src/jalview/schemabinding/version2/FeatureDescriptor.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,471 +7,542 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
-import org.exolab.castor.mapping.AccessMode;
-import org.exolab.castor.xml.TypeValidator;
-import org.exolab.castor.xml.XMLFieldDescriptor;
 import org.exolab.castor.xml.validators.*;
 
 /**
  * Class FeatureDescriptor.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class FeatureDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field nsPrefix
-     */
-    private java.lang.String nsPrefix;
-
-    /**
-     * Field nsURI
-     */
-    private java.lang.String nsURI;
-
-    /**
-     * Field xmlName
-     */
-    private java.lang.String xmlName;
-
-    /**
-     * Field identity
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor identity;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public FeatureDescriptor() {
-        super();
-        nsURI = "www.jalview.org";
-        xmlName = "feature";
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.xml.XMLFieldHandler              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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _begin
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            IntegerValidator typeValidator= new IntegerValidator();
-            fieldValidator.setValidator(typeValidator);
+public class FeatureDescriptor
+    extends org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  //--------------------------/
+  //- Class/Member Variables -/
+  //--------------------------/
+
+  /**
+   * Field nsPrefix
+   */
+  private java.lang.String nsPrefix;
+
+  /**
+   * Field nsURI
+   */
+  private java.lang.String nsURI;
+
+  /**
+   * Field xmlName
+   */
+  private java.lang.String xmlName;
+
+  /**
+   * Field identity
+   */
+  private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+  //----------------/
+  //- Constructors -/
+  //----------------/
+
+  public FeatureDescriptor()
+  {
+    super();
+    nsURI = "www.jalview.org";
+    xmlName = "feature";
+
+    //-- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.xml.XMLFieldHandler 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);
-        //-- _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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _end
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            IntegerValidator typeValidator= new IntegerValidator();
-            fieldValidator.setValidator(typeValidator);
+        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());
         }
-        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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _type
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            StringValidator typeValidator = new StringValidator();
-            typeValidator.setWhiteSpace("preserve");
-            fieldValidator.setValidator(typeValidator);
+        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.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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _description
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            StringValidator typeValidator = new StringValidator();
-            typeValidator.setWhiteSpace("preserve");
-            fieldValidator.setValidator(typeValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    });
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _begin
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { //-- local scope
+      IntegerValidator typeValidator = new IntegerValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    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;
         }
-        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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _status
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            StringValidator typeValidator = new StringValidator();
-            typeValidator.setWhiteSpace("preserve");
-            fieldValidator.setValidator(typeValidator);
+        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());
         }
-        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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _featureGroup
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            StringValidator typeValidator = new StringValidator();
-            typeValidator.setWhiteSpace("preserve");
-            fieldValidator.setValidator(typeValidator);
+        catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _score
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(float.class, "_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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _score
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            FloatValidator typeValidator = new FloatValidator();
-            fieldValidator.setValidator(typeValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    });
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _end
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { //-- local scope
+      IntegerValidator typeValidator = new IntegerValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    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);
         }
-        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 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
+        catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-    } //-- jalview.schemabinding.version2.FeatureDescriptor()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method getAccessMode
-     * 
-     * 
-     * 
-     * @return AccessMode
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode()
-    {
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
-
-    /**
-     * Method getExtends
-     * 
-     * 
-     * 
-     * @return ClassDescriptor
-     */
-    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+      }
+    });
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _type
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { //-- local scope
+      StringValidator typeValidator = new StringValidator();
+      typeValidator.setWhiteSpace("preserve");
+      fieldValidator.setValidator(typeValidator);
+    }
+    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;
-    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
-
-    /**
-     * Method getIdentity
-     * 
-     * 
-     * 
-     * @return FieldDescriptor
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
-    {
-        return identity;
-    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
-
-    /**
-     * Method getJavaClass
-     * 
-     * 
-     * 
-     * @return Class
-     */
-    public java.lang.Class getJavaClass()
-    {
-        return jalview.schemabinding.version2.Feature.class;
-    } //-- java.lang.Class getJavaClass() 
-
-    /**
-     * Method getNameSpacePrefix
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpacePrefix()
+      }
+    });
+    desc.setHandler(handler);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _description
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      StringValidator typeValidator = new StringValidator();
+      typeValidator.setWhiteSpace("preserve");
+      fieldValidator.setValidator(typeValidator);
+    }
+    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()
     {
-        return nsPrefix;
-    } //-- java.lang.String getNameSpacePrefix() 
-
-    /**
-     * Method getNameSpaceURI
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpaceURI()
+      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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _status
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      StringValidator typeValidator = new StringValidator();
+      typeValidator.setWhiteSpace("preserve");
+      fieldValidator.setValidator(typeValidator);
+    }
+    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()
     {
-        return nsURI;
-    } //-- java.lang.String getNameSpaceURI() 
-
-    /**
-     * Method getValidator
-     * 
-     * 
-     * 
-     * @return TypeValidator
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator()
+      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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _featureGroup
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      StringValidator typeValidator = new StringValidator();
+      typeValidator.setWhiteSpace("preserve");
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    //-- _score
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(float.class,
+        "_score", "score", org.exolab.castor.xml.NodeType.Attribute);
+    handler = (new org.exolab.castor.xml.XMLFieldHandler()
     {
-        return this;
-    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
-
-    /**
-     * Method getXMLName
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getXMLName()
+      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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _score
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      FloatValidator typeValidator = new FloatValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    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()
     {
-        return xmlName;
-    } //-- java.lang.String getXMLName() 
+      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 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);
+  } //-- jalview.schemabinding.version2.FeatureDescriptor()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Method getAccessMode
+   *
+   *
+   *
+   * @return AccessMode
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
+
+  /**
+   * Method getExtends
+   *
+   *
+   *
+   * @return ClassDescriptor
+   */
+  public org.exolab.castor.mapping.ClassDescriptor getExtends()
+  {
+    return null;
+  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
+
+  /**
+   * Method getIdentity
+   *
+   *
+   *
+   * @return FieldDescriptor
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return identity;
+  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
+
+  /**
+   * Method getJavaClass
+   *
+   *
+   *
+   * @return Class
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.Feature.class;
+  } //-- java.lang.Class getJavaClass()
+
+  /**
+   * Method getNameSpacePrefix
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return nsPrefix;
+  } //-- java.lang.String getNameSpacePrefix()
+
+  /**
+   * Method getNameSpaceURI
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return nsURI;
+  } //-- java.lang.String getNameSpaceURI()
+
+  /**
+   * Method getValidator
+   *
+   *
+   *
+   * @return TypeValidator
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  } //-- org.exolab.castor.xml.TypeValidator getValidator()
+
+  /**
+   * Method getXMLName
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getXMLName()
+  {
+    return xmlName;
+  } //-- java.lang.String getXMLName()
 
 }
diff --git a/src/jalview/schemabinding/version2/FeatureSettings.java b/src/jalview/schemabinding/version2/FeatureSettings.java
index c20a83c..2dad54a 100755
--- a/src/jalview/schemabinding/version2/FeatureSettings.java
+++ b/src/jalview/schemabinding/version2/FeatureSettings.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,268 +7,276 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
 //---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import java.util.*;
 
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import java.util.Enumeration;
-import java.util.Vector;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
+import org.exolab.castor.xml.*;
 
 /**
  * Class FeatureSettings.
- * 
+ *
  * @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();
+    _settingList = new Vector();
+  } //-- jalview.schemabinding.version2.FeatureSettings()
 
-      //----------------/
-     //- Constructors -/
-    //----------------/
+  //-----------/
+  //- Methods -/
+  //-----------/
 
-    public FeatureSettings() {
-        super();
-        _settingList = new Vector();
-    } //-- jalview.schemabinding.version2.FeatureSettings()
+  /**
+   * Method addSetting
+   *
+   *
+   *
+   * @param vSetting
+   */
+  public void addSetting(jalview.schemabinding.version2.Setting vSetting)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _settingList.addElement(vSetting);
+  } //-- void addSetting(jalview.schemabinding.version2.Setting)
 
+  /**
+   * Method addSetting
+   *
+   *
+   *
+   * @param index
+   * @param vSetting
+   */
+  public void addSetting(int index,
+                         jalview.schemabinding.version2.Setting vSetting)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _settingList.insertElementAt(vSetting, index);
+  } //-- void addSetting(int, jalview.schemabinding.version2.Setting)
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+  /**
+   * Method enumerateSetting
+   *
+   *
+   *
+   * @return Enumeration
+   */
+  public java.util.Enumeration enumerateSetting()
+  {
+    return _settingList.elements();
+  } //-- java.util.Enumeration enumerateSetting()
 
-    /**
-     * Method addSetting
-     * 
-     * 
-     * 
-     * @param vSetting
-     */
-    public void addSetting(jalview.schemabinding.version2.Setting vSetting)
-        throws java.lang.IndexOutOfBoundsException
+  /**
+   * Method getSetting
+   *
+   *
+   *
+   * @param index
+   * @return Setting
+   */
+  public jalview.schemabinding.version2.Setting getSetting(int index)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _settingList.size()))
     {
-        _settingList.addElement(vSetting);
-    } //-- void addSetting(jalview.schemabinding.version2.Setting) 
+      throw new IndexOutOfBoundsException();
+    }
 
-    /**
-     * Method addSetting
-     * 
-     * 
-     * 
-     * @param index
-     * @param vSetting
-     */
-    public void addSetting(int index, jalview.schemabinding.version2.Setting vSetting)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _settingList.insertElementAt(vSetting, index);
-    } //-- void addSetting(int, jalview.schemabinding.version2.Setting) 
+    return (jalview.schemabinding.version2.Setting) _settingList.elementAt(
+        index);
+  } //-- jalview.schemabinding.version2.Setting getSetting(int)
 
-    /**
-     * Method enumerateSetting
-     * 
-     * 
-     * 
-     * @return Enumeration
-     */
-    public java.util.Enumeration enumerateSetting()
+  /**
+   * Method getSetting
+   *
+   *
+   *
+   * @return Setting
+   */
+  public jalview.schemabinding.version2.Setting[] getSetting()
+  {
+    int size = _settingList.size();
+    jalview.schemabinding.version2.Setting[] mArray = new jalview.schemabinding.
+        version2.Setting[size];
+    for (int index = 0; index < size; index++)
     {
-        return _settingList.elements();
-    } //-- java.util.Enumeration enumerateSetting() 
+      mArray[index] = (jalview.schemabinding.version2.Setting) _settingList.
+          elementAt(index);
+    }
+    return mArray;
+  } //-- jalview.schemabinding.version2.Setting[] getSetting()
 
-    /**
-     * Method getSetting
-     * 
-     * 
-     * 
-     * @param index
-     * @return Setting
-     */
-    public jalview.schemabinding.version2.Setting getSetting(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _settingList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        
-        return (jalview.schemabinding.version2.Setting) _settingList.elementAt(index);
-    } //-- jalview.schemabinding.version2.Setting getSetting(int) 
+  /**
+   * Method getSettingCount
+   *
+   *
+   *
+   * @return int
+   */
+  public int getSettingCount()
+  {
+    return _settingList.size();
+  } //-- int getSettingCount()
 
-    /**
-     * Method getSetting
-     * 
-     * 
-     * 
-     * @return Setting
-     */
-    public jalview.schemabinding.version2.Setting[] getSetting()
+  /**
+   * Method isValid
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean isValid()
+  {
+    try
     {
-        int size = _settingList.size();
-        jalview.schemabinding.version2.Setting[] mArray = new jalview.schemabinding.version2.Setting[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = (jalview.schemabinding.version2.Setting) _settingList.elementAt(index);
-        }
-        return mArray;
-    } //-- jalview.schemabinding.version2.Setting[] getSetting() 
-
-    /**
-     * Method getSettingCount
-     * 
-     * 
-     * 
-     * @return int
-     */
-    public int getSettingCount()
+      validate();
+    }
+    catch (org.exolab.castor.xml.ValidationException vex)
     {
-        return _settingList.size();
-    } //-- int getSettingCount() 
+      return false;
+    }
+    return true;
+  } //-- boolean isValid()
 
-    /**
-     * Method isValid
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean isValid()
-    {
-        try {
-            validate();
-        }
-        catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    } //-- boolean isValid() 
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param out
+   */
+  public void marshal(java.io.Writer out)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
 
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param out
-     */
-    public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, out);
-    } //-- void marshal(java.io.Writer) 
+    Marshaller.marshal(this, out);
+  } //-- void marshal(java.io.Writer)
 
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param handler
-     */
-    public void marshal(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, handler);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param handler
+   */
+  public void marshal(org.xml.sax.ContentHandler handler)
+      throws java.io.IOException, org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
 
-    /**
-     * Method removeAllSetting
-     * 
-     */
-    public void removeAllSetting()
-    {
-        _settingList.removeAllElements();
-    } //-- void removeAllSetting() 
+    Marshaller.marshal(this, handler);
+  } //-- void marshal(org.xml.sax.ContentHandler)
 
-    /**
-     * Method removeSetting
-     * 
-     * 
-     * 
-     * @param index
-     * @return Setting
-     */
-    public jalview.schemabinding.version2.Setting removeSetting(int index)
-    {
-        java.lang.Object obj = _settingList.elementAt(index);
-        _settingList.removeElementAt(index);
-        return (jalview.schemabinding.version2.Setting) obj;
-    } //-- jalview.schemabinding.version2.Setting removeSetting(int) 
+  /**
+   * Method removeAllSetting
+   *
+   */
+  public void removeAllSetting()
+  {
+    _settingList.removeAllElements();
+  } //-- void removeAllSetting()
 
-    /**
-     * Method setSetting
-     * 
-     * 
-     * 
-     * @param index
-     * @param vSetting
-     */
-    public void setSetting(int index, jalview.schemabinding.version2.Setting vSetting)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _settingList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        _settingList.setElementAt(vSetting, index);
-    } //-- void setSetting(int, jalview.schemabinding.version2.Setting) 
+  /**
+   * Method removeSetting
+   *
+   *
+   *
+   * @param index
+   * @return Setting
+   */
+  public jalview.schemabinding.version2.Setting removeSetting(int index)
+  {
+    java.lang.Object obj = _settingList.elementAt(index);
+    _settingList.removeElementAt(index);
+    return (jalview.schemabinding.version2.Setting) obj;
+  } //-- jalview.schemabinding.version2.Setting removeSetting(int)
 
-    /**
-     * Method setSetting
-     * 
-     * 
-     * 
-     * @param settingArray
-     */
-    public void setSetting(jalview.schemabinding.version2.Setting[] settingArray)
+  /**
+   * Method setSetting
+   *
+   *
+   *
+   * @param index
+   * @param vSetting
+   */
+  public void setSetting(int index,
+                         jalview.schemabinding.version2.Setting vSetting)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _settingList.size()))
     {
-        //-- copy array
-        _settingList.removeAllElements();
-        for (int i = 0; i < settingArray.length; i++) {
-            _settingList.addElement(settingArray[i]);
-        }
-    } //-- void setSetting(jalview.schemabinding.version2.Setting) 
+      throw new IndexOutOfBoundsException();
+    }
+    _settingList.setElementAt(vSetting, index);
+  } //-- void setSetting(int, jalview.schemabinding.version2.Setting)
 
-    /**
-     * Method unmarshal
-     * 
-     * 
-     * 
-     * @param reader
-     * @return Object
-     */
-    public static java.lang.Object unmarshal(java.io.Reader reader)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+  /**
+   * Method setSetting
+   *
+   *
+   *
+   * @param settingArray
+   */
+  public void setSetting(jalview.schemabinding.version2.Setting[] settingArray)
+  {
+    //-- copy array
+    _settingList.removeAllElements();
+    for (int i = 0; i < settingArray.length; i++)
     {
-        return (jalview.schemabinding.version2.FeatureSettings) Unmarshaller.unmarshal(jalview.schemabinding.version2.FeatureSettings.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
+      _settingList.addElement(settingArray[i]);
+    }
+  } //-- void setSetting(jalview.schemabinding.version2.Setting)
 
-    /**
-     * Method validate
-     * 
-     */
-    public void validate()
-        throws org.exolab.castor.xml.ValidationException
-    {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    } //-- void validate() 
+  /**
+   * Method unmarshal
+   *
+   *
+   *
+   * @param reader
+   * @return Object
+   */
+  public static java.lang.Object unmarshal(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);
+  } //-- java.lang.Object unmarshal(java.io.Reader)
+
+  /**
+   * Method validate
+   *
+   */
+  public void validate()
+      throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.
+        Validator();
+    validator.validate(this);
+  } //-- void validate()
 
 }
diff --git a/src/jalview/schemabinding/version2/FeatureSettingsDescriptor.java b/src/jalview/schemabinding/version2/FeatureSettingsDescriptor.java
index 219037e..d355c81 100755
--- a/src/jalview/schemabinding/version2/FeatureSettingsDescriptor.java
+++ b/src/jalview/schemabinding/version2/FeatureSettingsDescriptor.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,202 +7,207 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
 //---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
 
-import org.exolab.castor.mapping.AccessMode;
-import org.exolab.castor.xml.TypeValidator;
-import org.exolab.castor.xml.XMLFieldDescriptor;
-import org.exolab.castor.xml.validators.*;
 
 /**
  * Class FeatureSettingsDescriptor.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class FeatureSettingsDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field nsPrefix
-     */
-    private java.lang.String nsPrefix;
-
-    /**
-     * Field nsURI
-     */
-    private java.lang.String nsURI;
-
-    /**
-     * Field xmlName
-     */
-    private java.lang.String xmlName;
-
-    /**
-     * Field identity
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor identity;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public FeatureSettingsDescriptor() {
-        super();
-        nsURI = "www.jalview.org";
-        xmlName = "FeatureSettings";
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.xml.XMLFieldHandler              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 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);
-    } //-- jalview.schemabinding.version2.FeatureSettingsDescriptor()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method getAccessMode
-     * 
-     * 
-     * 
-     * @return AccessMode
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode()
-    {
-        return null;
-    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
-
-    /**
-     * Method getExtends
-     * 
-     * 
-     * 
-     * @return ClassDescriptor
-     */
-    public org.exolab.castor.mapping.ClassDescriptor getExtends()
-    {
-        return null;
-    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
-
-    /**
-     * Method getIdentity
-     * 
-     * 
-     * 
-     * @return FieldDescriptor
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
-    {
-        return identity;
-    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
-
-    /**
-     * Method getJavaClass
-     * 
-     * 
-     * 
-     * @return Class
-     */
-    public java.lang.Class getJavaClass()
+public class FeatureSettingsDescriptor
+    extends org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  //--------------------------/
+  //- Class/Member Variables -/
+  //--------------------------/
+
+  /**
+   * Field nsPrefix
+   */
+  private java.lang.String nsPrefix;
+
+  /**
+   * Field nsURI
+   */
+  private java.lang.String nsURI;
+
+  /**
+   * Field xmlName
+   */
+  private java.lang.String xmlName;
+
+  /**
+   * Field identity
+   */
+  private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+  //----------------/
+  //- Constructors -/
+  //----------------/
+
+  public FeatureSettingsDescriptor()
+  {
+    super();
+    nsURI = "www.jalview.org";
+    xmlName = "FeatureSettings";
+
+    //-- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.xml.XMLFieldHandler 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()
     {
-        return jalview.schemabinding.version2.FeatureSettings.class;
-    } //-- java.lang.Class getJavaClass() 
-
-    /**
-     * Method getNameSpacePrefix
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpacePrefix()
-    {
-        return nsPrefix;
-    } //-- java.lang.String getNameSpacePrefix() 
-
-    /**
-     * Method getNameSpaceURI
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpaceURI()
-    {
-        return nsURI;
-    } //-- java.lang.String getNameSpaceURI() 
-
-    /**
-     * Method getValidator
-     * 
-     * 
-     * 
-     * @return TypeValidator
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator()
-    {
-        return this;
-    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
-
-    /**
-     * Method getXMLName
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getXMLName()
-    {
-        return xmlName;
-    } //-- java.lang.String getXMLName() 
+      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 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);
+  } //-- jalview.schemabinding.version2.FeatureSettingsDescriptor()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Method getAccessMode
+   *
+   *
+   *
+   * @return AccessMode
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
+
+  /**
+   * Method getExtends
+   *
+   *
+   *
+   * @return ClassDescriptor
+   */
+  public org.exolab.castor.mapping.ClassDescriptor getExtends()
+  {
+    return null;
+  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
+
+  /**
+   * Method getIdentity
+   *
+   *
+   *
+   * @return FieldDescriptor
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return identity;
+  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
+
+  /**
+   * Method getJavaClass
+   *
+   *
+   *
+   * @return Class
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.FeatureSettings.class;
+  } //-- java.lang.Class getJavaClass()
+
+  /**
+   * Method getNameSpacePrefix
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return nsPrefix;
+  } //-- java.lang.String getNameSpacePrefix()
+
+  /**
+   * Method getNameSpaceURI
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return nsURI;
+  } //-- java.lang.String getNameSpaceURI()
+
+  /**
+   * Method getValidator
+   *
+   *
+   *
+   * @return TypeValidator
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  } //-- org.exolab.castor.xml.TypeValidator getValidator()
+
+  /**
+   * Method getXMLName
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getXMLName()
+  {
+    return xmlName;
+  } //-- java.lang.String getXMLName()
 
 }
diff --git a/src/jalview/schemabinding/version2/Features.java b/src/jalview/schemabinding/version2/Features.java
index 72321c6..f0ca998 100755
--- a/src/jalview/schemabinding/version2/Features.java
+++ b/src/jalview/schemabinding/version2/Features.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,112 +7,110 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
+import org.exolab.castor.xml.*;
 
 /**
  * Class Features.
- * 
+ *
  * @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();
+  } //-- jalview.schemabinding.version2.Features()
 
-    public Features() {
-        super();
-    } //-- jalview.schemabinding.version2.Features()
+  //-----------/
+  //- Methods -/
+  //-----------/
 
+  /**
+   * Method isValid
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    }
+    catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  } //-- boolean isValid()
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param out
+   */
+  public void marshal(java.io.Writer out)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
 
-    /**
-     * Method isValid
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean isValid()
-    {
-        try {
-            validate();
-        }
-        catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    } //-- boolean isValid() 
+    Marshaller.marshal(this, out);
+  } //-- void marshal(java.io.Writer)
 
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param out
-     */
-    public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, out);
-    } //-- void marshal(java.io.Writer) 
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param handler
+   */
+  public void marshal(org.xml.sax.ContentHandler handler)
+      throws java.io.IOException, org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
 
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param handler
-     */
-    public void marshal(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, handler);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
+    Marshaller.marshal(this, handler);
+  } //-- void marshal(org.xml.sax.ContentHandler)
 
-    /**
-     * Method unmarshal
-     * 
-     * 
-     * 
-     * @param reader
-     * @return Object
-     */
-    public static java.lang.Object unmarshal(java.io.Reader reader)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        return (jalview.schemabinding.version2.Features) Unmarshaller.unmarshal(jalview.schemabinding.version2.Features.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
+  /**
+   * Method unmarshal
+   *
+   *
+   *
+   * @param reader
+   * @return Object
+   */
+  public static java.lang.Object unmarshal(java.io.Reader reader)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.Features) Unmarshaller.unmarshal(
+        jalview.schemabinding.version2.Features.class, reader);
+  } //-- java.lang.Object unmarshal(java.io.Reader)
 
-    /**
-     * Method validate
-     * 
-     */
-    public void validate()
-        throws org.exolab.castor.xml.ValidationException
-    {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    } //-- void validate() 
+  /**
+   * Method validate
+   *
+   */
+  public void validate()
+      throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.
+        Validator();
+    validator.validate(this);
+  } //-- void validate()
 
 }
diff --git a/src/jalview/schemabinding/version2/FeaturesDescriptor.java b/src/jalview/schemabinding/version2/FeaturesDescriptor.java
index 5eea818..a0a98b9 100755
--- a/src/jalview/schemabinding/version2/FeaturesDescriptor.java
+++ b/src/jalview/schemabinding/version2/FeaturesDescriptor.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,160 +7,159 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
 //---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
 
-import org.exolab.castor.mapping.AccessMode;
-import org.exolab.castor.xml.TypeValidator;
-import org.exolab.castor.xml.XMLFieldDescriptor;
-import org.exolab.castor.xml.validators.*;
 
 /**
  * Class FeaturesDescriptor.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class FeaturesDescriptor extends FeatureDescriptor {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field nsPrefix
-     */
-    private java.lang.String nsPrefix;
-
-    /**
-     * Field nsURI
-     */
-    private java.lang.String nsURI;
-
-    /**
-     * Field xmlName
-     */
-    private java.lang.String xmlName;
-
-    /**
-     * Field identity
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor identity;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public FeaturesDescriptor() {
-        super();
-        setExtendsWithoutFlatten(new FeatureDescriptor());
-        nsURI = "www.jalview.org";
-        xmlName = "features";
-    } //-- jalview.schemabinding.version2.FeaturesDescriptor()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method getAccessMode
-     * 
-     * 
-     * 
-     * @return AccessMode
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode()
-    {
-        return null;
-    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
-
-    /**
-     * Method getExtends
-     * 
-     * 
-     * 
-     * @return ClassDescriptor
-     */
-    public org.exolab.castor.mapping.ClassDescriptor getExtends()
-    {
-        return super.getExtends();
-    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
-
-    /**
-     * Method getIdentity
-     * 
-     * 
-     * 
-     * @return FieldDescriptor
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
-    {
-        if (identity == null)
-            return super.getIdentity();
-        return identity;
-    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
-
-    /**
-     * Method getJavaClass
-     * 
-     * 
-     * 
-     * @return Class
-     */
-    public java.lang.Class getJavaClass()
-    {
-        return jalview.schemabinding.version2.Features.class;
-    } //-- java.lang.Class getJavaClass() 
-
-    /**
-     * Method getNameSpacePrefix
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpacePrefix()
-    {
-        return nsPrefix;
-    } //-- java.lang.String getNameSpacePrefix() 
-
-    /**
-     * Method getNameSpaceURI
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpaceURI()
-    {
-        return nsURI;
-    } //-- java.lang.String getNameSpaceURI() 
-
-    /**
-     * Method getValidator
-     * 
-     * 
-     * 
-     * @return TypeValidator
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator()
-    {
-        return this;
-    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
-
-    /**
-     * Method getXMLName
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getXMLName()
+public class FeaturesDescriptor
+    extends FeatureDescriptor
+{
+
+  //--------------------------/
+  //- Class/Member Variables -/
+  //--------------------------/
+
+  /**
+   * Field nsPrefix
+   */
+  private java.lang.String nsPrefix;
+
+  /**
+   * Field nsURI
+   */
+  private java.lang.String nsURI;
+
+  /**
+   * Field xmlName
+   */
+  private java.lang.String xmlName;
+
+  /**
+   * Field identity
+   */
+  private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+  //----------------/
+  //- Constructors -/
+  //----------------/
+
+  public FeaturesDescriptor()
+  {
+    super();
+    setExtendsWithoutFlatten(new FeatureDescriptor());
+    nsURI = "www.jalview.org";
+    xmlName = "features";
+  } //-- jalview.schemabinding.version2.FeaturesDescriptor()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Method getAccessMode
+   *
+   *
+   *
+   * @return AccessMode
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
+
+  /**
+   * Method getExtends
+   *
+   *
+   *
+   * @return ClassDescriptor
+   */
+  public org.exolab.castor.mapping.ClassDescriptor getExtends()
+  {
+    return super.getExtends();
+  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
+
+  /**
+   * Method getIdentity
+   *
+   *
+   *
+   * @return FieldDescriptor
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    if (identity == null)
     {
-        return xmlName;
-    } //-- java.lang.String getXMLName() 
+      return super.getIdentity();
+    }
+    return identity;
+  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
+
+  /**
+   * Method getJavaClass
+   *
+   *
+   *
+   * @return Class
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.Features.class;
+  } //-- java.lang.Class getJavaClass()
+
+  /**
+   * Method getNameSpacePrefix
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return nsPrefix;
+  } //-- java.lang.String getNameSpacePrefix()
+
+  /**
+   * Method getNameSpaceURI
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return nsURI;
+  } //-- java.lang.String getNameSpaceURI()
+
+  /**
+   * Method getValidator
+   *
+   *
+   *
+   * @return TypeValidator
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  } //-- org.exolab.castor.xml.TypeValidator getValidator()
+
+  /**
+   * Method getXMLName
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getXMLName()
+  {
+    return xmlName;
+  } //-- java.lang.String getXMLName()
 
 }
diff --git a/src/jalview/schemabinding/version2/HiddenColumns.java b/src/jalview/schemabinding/version2/HiddenColumns.java
index 5b83e64..305fa16 100644
--- a/src/jalview/schemabinding/version2/HiddenColumns.java
+++ b/src/jalview/schemabinding/version2/HiddenColumns.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,221 +7,220 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
+import org.exolab.castor.xml.*;
 
 /**
  * Class HiddenColumns.
- * 
+ *
  * @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();
-    } //-- jalview.schemabinding.version2.HiddenColumns()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method deleteEnd
-     * 
-     */
-    public void deleteEnd()
-    {
-        this._has_end= false;
-    } //-- void deleteEnd() 
-
-    /**
-     * Method deleteStart
-     * 
-     */
-    public void deleteStart()
-    {
-        this._has_start= false;
-    } //-- void deleteStart() 
-
-    /**
-     * Returns the value of field 'end'.
-     * 
-     * @return int
-     * @return the value of field 'end'.
-     */
-    public int getEnd()
-    {
-        return this._end;
-    } //-- int getEnd() 
-
-    /**
-     * Returns the value of field 'start'.
-     * 
-     * @return int
-     * @return the value of field 'start'.
-     */
-    public int getStart()
-    {
-        return this._start;
-    } //-- int getStart() 
-
-    /**
-     * Method hasEnd
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasEnd()
-    {
-        return this._has_end;
-    } //-- boolean hasEnd() 
-
-    /**
-     * Method hasStart
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasStart()
-    {
-        return this._has_start;
-    } //-- boolean hasStart() 
-
-    /**
-     * Method isValid
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean isValid()
-    {
-        try {
-            validate();
-        }
-        catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    } //-- boolean isValid() 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param out
-     */
-    public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, out);
-    } //-- void marshal(java.io.Writer) 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param handler
-     */
-    public void marshal(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, handler);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
-
-    /**
-     * Sets the value of field 'end'.
-     * 
-     * @param end the value of field 'end'.
-     */
-    public void setEnd(int end)
-    {
-        this._end = end;
-        this._has_end = true;
-    } //-- void setEnd(int) 
-
-    /**
-     * Sets the value of field 'start'.
-     * 
-     * @param start the value of field 'start'.
-     */
-    public void setStart(int start)
-    {
-        this._start = start;
-        this._has_start = true;
-    } //-- void setStart(int) 
-
-    /**
-     * Method unmarshal
-     * 
-     * 
-     * 
-     * @param reader
-     * @return Object
-     */
-    public static java.lang.Object unmarshal(java.io.Reader reader)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+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();
+  } //-- jalview.schemabinding.version2.HiddenColumns()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Method deleteEnd
+   *
+   */
+  public void deleteEnd()
+  {
+    this._has_end = false;
+  } //-- void deleteEnd()
+
+  /**
+   * Method deleteStart
+   *
+   */
+  public void deleteStart()
+  {
+    this._has_start = false;
+  } //-- void deleteStart()
+
+  /**
+   * Returns the value of field 'end'.
+   *
+   * @return int
+   * @return the value of field 'end'.
+   */
+  public int getEnd()
+  {
+    return this._end;
+  } //-- int getEnd()
+
+  /**
+   * Returns the value of field 'start'.
+   *
+   * @return int
+   * @return the value of field 'start'.
+   */
+  public int getStart()
+  {
+    return this._start;
+  } //-- int getStart()
+
+  /**
+   * Method hasEnd
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasEnd()
+  {
+    return this._has_end;
+  } //-- boolean hasEnd()
+
+  /**
+   * Method hasStart
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasStart()
+  {
+    return this._has_start;
+  } //-- boolean hasStart()
+
+  /**
+   * Method isValid
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean isValid()
+  {
+    try
     {
-        return (jalview.schemabinding.version2.HiddenColumns) Unmarshaller.unmarshal(jalview.schemabinding.version2.HiddenColumns.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
-
-    /**
-     * Method validate
-     * 
-     */
-    public void validate()
-        throws org.exolab.castor.xml.ValidationException
+      validate();
+    }
+    catch (org.exolab.castor.xml.ValidationException vex)
     {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    } //-- void validate() 
+      return false;
+    }
+    return true;
+  } //-- boolean isValid()
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param out
+   */
+  public void marshal(java.io.Writer out)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, out);
+  } //-- void marshal(java.io.Writer)
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param handler
+   */
+  public void marshal(org.xml.sax.ContentHandler handler)
+      throws java.io.IOException, org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, handler);
+  } //-- void marshal(org.xml.sax.ContentHandler)
+
+  /**
+   * Sets the value of field 'end'.
+   *
+   * @param end the value of field 'end'.
+   */
+  public void setEnd(int end)
+  {
+    this._end = end;
+    this._has_end = true;
+  } //-- void setEnd(int)
+
+  /**
+   * Sets the value of field 'start'.
+   *
+   * @param start the value of field 'start'.
+   */
+  public void setStart(int start)
+  {
+    this._start = start;
+    this._has_start = true;
+  } //-- void setStart(int)
+
+  /**
+   * Method unmarshal
+   *
+   *
+   *
+   * @param reader
+   * @return Object
+   */
+  public static java.lang.Object unmarshal(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);
+  } //-- java.lang.Object unmarshal(java.io.Reader)
+
+  /**
+   * Method validate
+   *
+   */
+  public void validate()
+      throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.
+        Validator();
+    validator.validate(this);
+  } //-- void validate()
 
 }
diff --git a/src/jalview/schemabinding/version2/HiddenColumnsDescriptor.java b/src/jalview/schemabinding/version2/HiddenColumnsDescriptor.java
index df99628..2d92682 100644
--- a/src/jalview/schemabinding/version2/HiddenColumnsDescriptor.java
+++ b/src/jalview/schemabinding/version2/HiddenColumnsDescriptor.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,246 +7,264 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
-import org.exolab.castor.mapping.AccessMode;
-import org.exolab.castor.xml.TypeValidator;
-import org.exolab.castor.xml.XMLFieldDescriptor;
 import org.exolab.castor.xml.validators.*;
 
 /**
  * Class HiddenColumnsDescriptor.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class HiddenColumnsDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field nsPrefix
-     */
-    private java.lang.String nsPrefix;
-
-    /**
-     * Field nsURI
-     */
-    private java.lang.String nsURI;
-
-    /**
-     * Field xmlName
-     */
-    private java.lang.String xmlName;
-
-    /**
-     * Field identity
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor identity;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public HiddenColumnsDescriptor() {
-        super();
-        nsURI = "www.jalview.org";
-        xmlName = "hiddenColumns";
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.xml.XMLFieldHandler              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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _start
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            IntegerValidator typeValidator= new IntegerValidator();
-            fieldValidator.setValidator(typeValidator);
+public class HiddenColumnsDescriptor
+    extends org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  //--------------------------/
+  //- Class/Member Variables -/
+  //--------------------------/
+
+  /**
+   * Field nsPrefix
+   */
+  private java.lang.String nsPrefix;
+
+  /**
+   * Field nsURI
+   */
+  private java.lang.String nsURI;
+
+  /**
+   * Field xmlName
+   */
+  private java.lang.String xmlName;
+
+  /**
+   * Field identity
+   */
+  private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+  //----------------/
+  //- Constructors -/
+  //----------------/
+
+  public HiddenColumnsDescriptor()
+  {
+    super();
+    nsURI = "www.jalview.org";
+    xmlName = "hiddenColumns";
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.xml.XMLFieldHandler 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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _end
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            IntegerValidator typeValidator= new IntegerValidator();
-            fieldValidator.setValidator(typeValidator);
+        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());
         }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-    } //-- jalview.schemabinding.version2.HiddenColumnsDescriptor()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method getAccessMode
-     * 
-     * 
-     * 
-     * @return AccessMode
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode()
-    {
+        catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
-
-    /**
-     * Method getExtends
-     * 
-     * 
-     * 
-     * @return ClassDescriptor
-     */
-    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+      }
+    });
+    desc.setHandler(handler);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _start
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      IntegerValidator typeValidator = new IntegerValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    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;
-    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
-
-    /**
-     * Method getIdentity
-     * 
-     * 
-     * 
-     * @return FieldDescriptor
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
-    {
-        return identity;
-    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
-
-    /**
-     * Method getJavaClass
-     * 
-     * 
-     * 
-     * @return Class
-     */
-    public java.lang.Class getJavaClass()
-    {
-        return jalview.schemabinding.version2.HiddenColumns.class;
-    } //-- java.lang.Class getJavaClass() 
-
-    /**
-     * Method getNameSpacePrefix
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpacePrefix()
-    {
-        return nsPrefix;
-    } //-- java.lang.String getNameSpacePrefix() 
-
-    /**
-     * Method getNameSpaceURI
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpaceURI()
-    {
-        return nsURI;
-    } //-- java.lang.String getNameSpaceURI() 
-
-    /**
-     * Method getValidator
-     * 
-     * 
-     * 
-     * @return TypeValidator
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator()
-    {
-        return this;
-    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
-
-    /**
-     * Method getXMLName
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getXMLName()
-    {
-        return xmlName;
-    } //-- java.lang.String getXMLName() 
+      }
+    });
+    desc.setHandler(handler);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _end
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      IntegerValidator typeValidator = new IntegerValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    //-- initialize element descriptors
+
+  } //-- jalview.schemabinding.version2.HiddenColumnsDescriptor()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Method getAccessMode
+   *
+   *
+   *
+   * @return AccessMode
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
+
+  /**
+   * Method getExtends
+   *
+   *
+   *
+   * @return ClassDescriptor
+   */
+  public org.exolab.castor.mapping.ClassDescriptor getExtends()
+  {
+    return null;
+  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
+
+  /**
+   * Method getIdentity
+   *
+   *
+   *
+   * @return FieldDescriptor
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return identity;
+  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
+
+  /**
+   * Method getJavaClass
+   *
+   *
+   *
+   * @return Class
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.HiddenColumns.class;
+  } //-- java.lang.Class getJavaClass()
+
+  /**
+   * Method getNameSpacePrefix
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return nsPrefix;
+  } //-- java.lang.String getNameSpacePrefix()
+
+  /**
+   * Method getNameSpaceURI
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return nsURI;
+  } //-- java.lang.String getNameSpaceURI()
+
+  /**
+   * Method getValidator
+   *
+   *
+   *
+   * @return TypeValidator
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  } //-- org.exolab.castor.xml.TypeValidator getValidator()
+
+  /**
+   * Method getXMLName
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getXMLName()
+  {
+    return xmlName;
+  } //-- java.lang.String getXMLName()
 
 }
diff --git a/src/jalview/schemabinding/version2/JGroup.java b/src/jalview/schemabinding/version2/JGroup.java
index 06eb940..49edb8d 100755
--- a/src/jalview/schemabinding/version2/JGroup.java
+++ b/src/jalview/schemabinding/version2/JGroup.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,903 +7,906 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
 //---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import java.util.*;
 
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import java.util.Enumeration;
-import java.util.Vector;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
+import org.exolab.castor.xml.*;
 
 /**
  * Class JGroup.
- * 
+ *
  * @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();
-        _seqList = new Vector();
-    } //-- jalview.schemabinding.version2.JGroup()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method addSeq
-     * 
-     * 
-     * 
-     * @param vSeq
-     */
-    public void addSeq(int vSeq)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _seqList.addElement(new java.lang.Integer(vSeq));
-    } //-- void addSeq(int) 
-
-    /**
-     * Method addSeq
-     * 
-     * 
-     * 
-     * @param index
-     * @param vSeq
-     */
-    public void addSeq(int index, int vSeq)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _seqList.insertElementAt(new java.lang.Integer(vSeq), index);
-    } //-- void addSeq(int, int) 
-
-    /**
-     * Method deleteColourText
-     * 
-     */
-    public void deleteColourText()
-    {
-        this._has_colourText= false;
-    } //-- void deleteColourText() 
-
-    /**
-     * Method deleteConsThreshold
-     * 
-     */
-    public void deleteConsThreshold()
-    {
-        this._has_consThreshold= false;
-    } //-- void deleteConsThreshold() 
-
-    /**
-     * Method deleteDisplayBoxes
-     * 
-     */
-    public void deleteDisplayBoxes()
-    {
-        this._has_displayBoxes= false;
-    } //-- void deleteDisplayBoxes() 
-
-    /**
-     * Method deleteDisplayText
-     * 
-     */
-    public void deleteDisplayText()
-    {
-        this._has_displayText= false;
-    } //-- void deleteDisplayText() 
-
-    /**
-     * Method deleteEnd
-     * 
-     */
-    public void deleteEnd()
-    {
-        this._has_end= false;
-    } //-- void deleteEnd() 
-
-    /**
-     * Method deleteOutlineColour
-     * 
-     */
-    public void deleteOutlineColour()
-    {
-        this._has_outlineColour= false;
-    } //-- void deleteOutlineColour() 
-
-    /**
-     * Method deletePidThreshold
-     * 
-     */
-    public void deletePidThreshold()
-    {
-        this._has_pidThreshold= false;
-    } //-- void deletePidThreshold() 
-
-    /**
-     * Method deleteStart
-     * 
-     */
-    public void deleteStart()
-    {
-        this._has_start= false;
-    } //-- void deleteStart() 
-
-    /**
-     * Method deleteTextCol1
-     * 
-     */
-    public void deleteTextCol1()
-    {
-        this._has_textCol1= false;
-    } //-- void deleteTextCol1() 
-
-    /**
-     * Method deleteTextCol2
-     * 
-     */
-    public void deleteTextCol2()
-    {
-        this._has_textCol2= false;
-    } //-- void deleteTextCol2() 
-
-    /**
-     * Method deleteTextColThreshold
-     * 
-     */
-    public void deleteTextColThreshold()
-    {
-        this._has_textColThreshold= false;
-    } //-- void deleteTextColThreshold() 
-
-    /**
-     * Method enumerateSeq
-     * 
-     * 
-     * 
-     * @return Enumeration
-     */
-    public java.util.Enumeration enumerateSeq()
-    {
-        return _seqList.elements();
-    } //-- java.util.Enumeration enumerateSeq() 
-
-    /**
-     * Returns the value of field 'colour'.
-     * 
-     * @return String
-     * @return the value of field 'colour'.
-     */
-    public java.lang.String getColour()
-    {
-        return this._colour;
-    } //-- java.lang.String getColour() 
-
-    /**
-     * Returns the value of field 'colourText'.
-     * 
-     * @return boolean
-     * @return the value of field 'colourText'.
-     */
-    public boolean getColourText()
-    {
-        return this._colourText;
-    } //-- boolean getColourText() 
-
-    /**
-     * Returns the value of field 'consThreshold'.
-     * 
-     * @return int
-     * @return the value of field 'consThreshold'.
-     */
-    public int getConsThreshold()
-    {
-        return this._consThreshold;
-    } //-- int getConsThreshold() 
-
-    /**
-     * Returns the value of field 'displayBoxes'.
-     * 
-     * @return boolean
-     * @return the value of field 'displayBoxes'.
-     */
-    public boolean getDisplayBoxes()
-    {
-        return this._displayBoxes;
-    } //-- boolean getDisplayBoxes() 
-
-    /**
-     * Returns the value of field 'displayText'.
-     * 
-     * @return boolean
-     * @return the value of field 'displayText'.
-     */
-    public boolean getDisplayText()
-    {
-        return this._displayText;
-    } //-- boolean getDisplayText() 
-
-    /**
-     * Returns the value of field 'end'.
-     * 
-     * @return int
-     * @return the value of field 'end'.
-     */
-    public int getEnd()
-    {
-        return this._end;
-    } //-- int getEnd() 
-
-    /**
-     * Returns the value of field 'name'.
-     * 
-     * @return String
-     * @return the value of field 'name'.
-     */
-    public java.lang.String getName()
-    {
-        return this._name;
-    } //-- java.lang.String getName() 
-
-    /**
-     * Returns the value of field 'outlineColour'.
-     * 
-     * @return int
-     * @return the value of field 'outlineColour'.
-     */
-    public int getOutlineColour()
-    {
-        return this._outlineColour;
-    } //-- int getOutlineColour() 
-
-    /**
-     * Returns the value of field 'pidThreshold'.
-     * 
-     * @return int
-     * @return the value of field 'pidThreshold'.
-     */
-    public int getPidThreshold()
-    {
-        return this._pidThreshold;
-    } //-- int getPidThreshold() 
-
-    /**
-     * Method getSeq
-     * 
-     * 
-     * 
-     * @param index
-     * @return int
-     */
-    public int getSeq(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _seqList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        
-        return ((java.lang.Integer)_seqList.elementAt(index)).intValue();
-    } //-- int getSeq(int) 
-
-    /**
-     * Method getSeq
-     * 
-     * 
-     * 
-     * @return int
-     */
-    public int[] getSeq()
-    {
-        int size = _seqList.size();
-        int[] mArray = new int[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = ((java.lang.Integer)_seqList.elementAt(index)).intValue();
-        }
-        return mArray;
-    } //-- int[] getSeq() 
-
-    /**
-     * Method getSeqCount
-     * 
-     * 
-     * 
-     * @return int
-     */
-    public int getSeqCount()
-    {
-        return _seqList.size();
-    } //-- int getSeqCount() 
-
-    /**
-     * Returns the value of field 'start'.
-     * 
-     * @return int
-     * @return the value of field 'start'.
-     */
-    public int getStart()
-    {
-        return this._start;
-    } //-- int getStart() 
-
-    /**
-     * Returns the value of field 'textCol1'.
-     * 
-     * @return int
-     * @return the value of field 'textCol1'.
-     */
-    public int getTextCol1()
-    {
-        return this._textCol1;
-    } //-- int getTextCol1() 
-
-    /**
-     * Returns the value of field 'textCol2'.
-     * 
-     * @return int
-     * @return the value of field 'textCol2'.
-     */
-    public int getTextCol2()
-    {
-        return this._textCol2;
-    } //-- int getTextCol2() 
-
-    /**
-     * Returns the value of field 'textColThreshold'.
-     * 
-     * @return int
-     * @return the value of field 'textColThreshold'.
-     */
-    public int getTextColThreshold()
-    {
-        return this._textColThreshold;
-    } //-- int getTextColThreshold() 
-
-    /**
-     * Method hasColourText
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasColourText()
-    {
-        return this._has_colourText;
-    } //-- boolean hasColourText() 
-
-    /**
-     * Method hasConsThreshold
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasConsThreshold()
-    {
-        return this._has_consThreshold;
-    } //-- boolean hasConsThreshold() 
-
-    /**
-     * Method hasDisplayBoxes
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasDisplayBoxes()
-    {
-        return this._has_displayBoxes;
-    } //-- boolean hasDisplayBoxes() 
-
-    /**
-     * Method hasDisplayText
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasDisplayText()
-    {
-        return this._has_displayText;
-    } //-- boolean hasDisplayText() 
-
-    /**
-     * Method hasEnd
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasEnd()
-    {
-        return this._has_end;
-    } //-- boolean hasEnd() 
-
-    /**
-     * Method hasOutlineColour
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasOutlineColour()
-    {
-        return this._has_outlineColour;
-    } //-- boolean hasOutlineColour() 
-
-    /**
-     * Method hasPidThreshold
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasPidThreshold()
-    {
-        return this._has_pidThreshold;
-    } //-- boolean hasPidThreshold() 
-
-    /**
-     * Method hasStart
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasStart()
-    {
-        return this._has_start;
-    } //-- boolean hasStart() 
-
-    /**
-     * Method hasTextCol1
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasTextCol1()
-    {
-        return this._has_textCol1;
-    } //-- boolean hasTextCol1() 
-
-    /**
-     * Method hasTextCol2
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasTextCol2()
-    {
-        return this._has_textCol2;
-    } //-- boolean hasTextCol2() 
-
-    /**
-     * Method hasTextColThreshold
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasTextColThreshold()
-    {
-        return this._has_textColThreshold;
-    } //-- boolean hasTextColThreshold() 
-
-    /**
-     * Method isValid
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean isValid()
-    {
-        try {
-            validate();
-        }
-        catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    } //-- boolean isValid() 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param out
-     */
-    public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, out);
-    } //-- void marshal(java.io.Writer) 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param handler
-     */
-    public void marshal(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, handler);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
-
-    /**
-     * Method removeAllSeq
-     * 
-     */
-    public void removeAllSeq()
-    {
-        _seqList.removeAllElements();
-    } //-- void removeAllSeq() 
-
-    /**
-     * Method removeSeq
-     * 
-     * 
-     * 
-     * @param index
-     * @return int
-     */
-    public int removeSeq(int index)
-    {
-        java.lang.Object obj = _seqList.elementAt(index);
-        _seqList.removeElementAt(index);
-        return ((java.lang.Integer)obj).intValue();
-    } //-- int removeSeq(int) 
-
-    /**
-     * Sets the value of field 'colour'.
-     * 
-     * @param colour the value of field 'colour'.
-     */
-    public void setColour(java.lang.String colour)
-    {
-        this._colour = colour;
-    } //-- void setColour(java.lang.String) 
-
-    /**
-     * Sets the value of field 'colourText'.
-     * 
-     * @param colourText the value of field 'colourText'.
-     */
-    public void setColourText(boolean colourText)
-    {
-        this._colourText = colourText;
-        this._has_colourText = true;
-    } //-- void setColourText(boolean) 
-
-    /**
-     * Sets the value of field 'consThreshold'.
-     * 
-     * @param consThreshold the value of field 'consThreshold'.
-     */
-    public void setConsThreshold(int consThreshold)
-    {
-        this._consThreshold = consThreshold;
-        this._has_consThreshold = true;
-    } //-- void setConsThreshold(int) 
-
-    /**
-     * Sets the value of field 'displayBoxes'.
-     * 
-     * @param displayBoxes the value of field 'displayBoxes'.
-     */
-    public void setDisplayBoxes(boolean displayBoxes)
-    {
-        this._displayBoxes = displayBoxes;
-        this._has_displayBoxes = true;
-    } //-- void setDisplayBoxes(boolean) 
-
-    /**
-     * Sets the value of field 'displayText'.
-     * 
-     * @param displayText the value of field 'displayText'.
-     */
-    public void setDisplayText(boolean displayText)
-    {
-        this._displayText = displayText;
-        this._has_displayText = true;
-    } //-- void setDisplayText(boolean) 
-
-    /**
-     * Sets the value of field 'end'.
-     * 
-     * @param end the value of field 'end'.
-     */
-    public void setEnd(int end)
-    {
-        this._end = end;
-        this._has_end = true;
-    } //-- void setEnd(int) 
-
-    /**
-     * Sets the value of field 'name'.
-     * 
-     * @param name the value of field 'name'.
-     */
-    public void setName(java.lang.String name)
-    {
-        this._name = name;
-    } //-- void setName(java.lang.String) 
-
-    /**
-     * Sets the value of field 'outlineColour'.
-     * 
-     * @param outlineColour the value of field 'outlineColour'.
-     */
-    public void setOutlineColour(int outlineColour)
-    {
-        this._outlineColour = outlineColour;
-        this._has_outlineColour = true;
-    } //-- void setOutlineColour(int) 
-
-    /**
-     * Sets the value of field 'pidThreshold'.
-     * 
-     * @param pidThreshold the value of field 'pidThreshold'.
-     */
-    public void setPidThreshold(int pidThreshold)
-    {
-        this._pidThreshold = pidThreshold;
-        this._has_pidThreshold = true;
-    } //-- void setPidThreshold(int) 
-
-    /**
-     * Method setSeq
-     * 
-     * 
-     * 
-     * @param index
-     * @param vSeq
-     */
-    public void setSeq(int index, int vSeq)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _seqList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        _seqList.setElementAt(new java.lang.Integer(vSeq), index);
-    } //-- void setSeq(int, int) 
-
-    /**
-     * Method setSeq
-     * 
-     * 
-     * 
-     * @param seqArray
-     */
-    public void setSeq(int[] seqArray)
-    {
-        //-- copy array
-        _seqList.removeAllElements();
-        for (int i = 0; i < seqArray.length; i++) {
-            _seqList.addElement(new java.lang.Integer(seqArray[i]));
-        }
-    } //-- void setSeq(int) 
-
-    /**
-     * Sets the value of field 'start'.
-     * 
-     * @param start the value of field 'start'.
-     */
-    public void setStart(int start)
-    {
-        this._start = start;
-        this._has_start = true;
-    } //-- void setStart(int) 
-
-    /**
-     * Sets the value of field 'textCol1'.
-     * 
-     * @param textCol1 the value of field 'textCol1'.
-     */
-    public void setTextCol1(int textCol1)
-    {
-        this._textCol1 = textCol1;
-        this._has_textCol1 = true;
-    } //-- void setTextCol1(int) 
-
-    /**
-     * Sets the value of field 'textCol2'.
-     * 
-     * @param textCol2 the value of field 'textCol2'.
-     */
-    public void setTextCol2(int textCol2)
-    {
-        this._textCol2 = textCol2;
-        this._has_textCol2 = true;
-    } //-- void setTextCol2(int) 
-
-    /**
-     * Sets the value of field 'textColThreshold'.
-     * 
-     * @param textColThreshold the value of field 'textColThreshold'
-     */
-    public void setTextColThreshold(int textColThreshold)
-    {
-        this._textColThreshold = textColThreshold;
-        this._has_textColThreshold = true;
-    } //-- void setTextColThreshold(int) 
-
-    /**
-     * Method unmarshal
-     * 
-     * 
-     * 
-     * @param reader
-     * @return Object
-     */
-    public static java.lang.Object unmarshal(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);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
-
-    /**
-     * Method validate
-     * 
-     */
-    public void validate()
-        throws org.exolab.castor.xml.ValidationException
-    {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    } //-- void validate() 
+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();
+    _seqList = new Vector();
+  } //-- jalview.schemabinding.version2.JGroup()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Method addSeq
+   *
+   *
+   *
+   * @param vSeq
+   */
+  public void addSeq(int vSeq)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _seqList.addElement(new java.lang.Integer(vSeq));
+  } //-- void addSeq(int)
+
+  /**
+   * Method addSeq
+   *
+   *
+   *
+   * @param index
+   * @param vSeq
+   */
+  public void addSeq(int index, int vSeq)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _seqList.insertElementAt(new java.lang.Integer(vSeq), index);
+  } //-- void addSeq(int, int)
+
+  /**
+   * Method deleteColourText
+   *
+   */
+  public void deleteColourText()
+  {
+    this._has_colourText = false;
+  } //-- void deleteColourText()
+
+  /**
+   * Method deleteConsThreshold
+   *
+   */
+  public void deleteConsThreshold()
+  {
+    this._has_consThreshold = false;
+  } //-- void deleteConsThreshold()
+
+  /**
+   * Method deleteDisplayBoxes
+   *
+   */
+  public void deleteDisplayBoxes()
+  {
+    this._has_displayBoxes = false;
+  } //-- void deleteDisplayBoxes()
+
+  /**
+   * Method deleteDisplayText
+   *
+   */
+  public void deleteDisplayText()
+  {
+    this._has_displayText = false;
+  } //-- void deleteDisplayText()
+
+  /**
+   * Method deleteEnd
+   *
+   */
+  public void deleteEnd()
+  {
+    this._has_end = false;
+  } //-- void deleteEnd()
+
+  /**
+   * Method deleteOutlineColour
+   *
+   */
+  public void deleteOutlineColour()
+  {
+    this._has_outlineColour = false;
+  } //-- void deleteOutlineColour()
+
+  /**
+   * Method deletePidThreshold
+   *
+   */
+  public void deletePidThreshold()
+  {
+    this._has_pidThreshold = false;
+  } //-- void deletePidThreshold()
+
+  /**
+   * Method deleteStart
+   *
+   */
+  public void deleteStart()
+  {
+    this._has_start = false;
+  } //-- void deleteStart()
+
+  /**
+   * Method deleteTextCol1
+   *
+   */
+  public void deleteTextCol1()
+  {
+    this._has_textCol1 = false;
+  } //-- void deleteTextCol1()
+
+  /**
+   * Method deleteTextCol2
+   *
+   */
+  public void deleteTextCol2()
+  {
+    this._has_textCol2 = false;
+  } //-- void deleteTextCol2()
+
+  /**
+   * Method deleteTextColThreshold
+   *
+   */
+  public void deleteTextColThreshold()
+  {
+    this._has_textColThreshold = false;
+  } //-- void deleteTextColThreshold()
+
+  /**
+   * Method enumerateSeq
+   *
+   *
+   *
+   * @return Enumeration
+   */
+  public java.util.Enumeration enumerateSeq()
+  {
+    return _seqList.elements();
+  } //-- java.util.Enumeration enumerateSeq()
+
+  /**
+   * Returns the value of field 'colour'.
+   *
+   * @return String
+   * @return the value of field 'colour'.
+   */
+  public java.lang.String getColour()
+  {
+    return this._colour;
+  } //-- java.lang.String getColour()
+
+  /**
+   * Returns the value of field 'colourText'.
+   *
+   * @return boolean
+   * @return the value of field 'colourText'.
+   */
+  public boolean getColourText()
+  {
+    return this._colourText;
+  } //-- boolean getColourText()
+
+  /**
+   * Returns the value of field 'consThreshold'.
+   *
+   * @return int
+   * @return the value of field 'consThreshold'.
+   */
+  public int getConsThreshold()
+  {
+    return this._consThreshold;
+  } //-- int getConsThreshold()
+
+  /**
+   * Returns the value of field 'displayBoxes'.
+   *
+   * @return boolean
+   * @return the value of field 'displayBoxes'.
+   */
+  public boolean getDisplayBoxes()
+  {
+    return this._displayBoxes;
+  } //-- boolean getDisplayBoxes()
+
+  /**
+   * Returns the value of field 'displayText'.
+   *
+   * @return boolean
+   * @return the value of field 'displayText'.
+   */
+  public boolean getDisplayText()
+  {
+    return this._displayText;
+  } //-- boolean getDisplayText()
+
+  /**
+   * Returns the value of field 'end'.
+   *
+   * @return int
+   * @return the value of field 'end'.
+   */
+  public int getEnd()
+  {
+    return this._end;
+  } //-- int getEnd()
+
+  /**
+   * Returns the value of field 'name'.
+   *
+   * @return String
+   * @return the value of field 'name'.
+   */
+  public java.lang.String getName()
+  {
+    return this._name;
+  } //-- java.lang.String getName()
+
+  /**
+   * Returns the value of field 'outlineColour'.
+   *
+   * @return int
+   * @return the value of field 'outlineColour'.
+   */
+  public int getOutlineColour()
+  {
+    return this._outlineColour;
+  } //-- int getOutlineColour()
+
+  /**
+   * Returns the value of field 'pidThreshold'.
+   *
+   * @return int
+   * @return the value of field 'pidThreshold'.
+   */
+  public int getPidThreshold()
+  {
+    return this._pidThreshold;
+  } //-- int getPidThreshold()
+
+  /**
+   * Method getSeq
+   *
+   *
+   *
+   * @param index
+   * @return int
+   */
+  public int getSeq(int index)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _seqList.size()))
+    {
+      throw new IndexOutOfBoundsException();
+    }
+
+    return ( (java.lang.Integer) _seqList.elementAt(index)).intValue();
+  } //-- int getSeq(int)
+
+  /**
+   * Method getSeq
+   *
+   *
+   *
+   * @return int
+   */
+  public int[] getSeq()
+  {
+    int size = _seqList.size();
+    int[] mArray = new int[size];
+    for (int index = 0; index < size; index++)
+    {
+      mArray[index] = ( (java.lang.Integer) _seqList.elementAt(index)).intValue();
+    }
+    return mArray;
+  } //-- int[] getSeq()
+
+  /**
+   * Method getSeqCount
+   *
+   *
+   *
+   * @return int
+   */
+  public int getSeqCount()
+  {
+    return _seqList.size();
+  } //-- int getSeqCount()
+
+  /**
+   * Returns the value of field 'start'.
+   *
+   * @return int
+   * @return the value of field 'start'.
+   */
+  public int getStart()
+  {
+    return this._start;
+  } //-- int getStart()
+
+  /**
+   * Returns the value of field 'textCol1'.
+   *
+   * @return int
+   * @return the value of field 'textCol1'.
+   */
+  public int getTextCol1()
+  {
+    return this._textCol1;
+  } //-- int getTextCol1()
+
+  /**
+   * Returns the value of field 'textCol2'.
+   *
+   * @return int
+   * @return the value of field 'textCol2'.
+   */
+  public int getTextCol2()
+  {
+    return this._textCol2;
+  } //-- int getTextCol2()
+
+  /**
+   * Returns the value of field 'textColThreshold'.
+   *
+   * @return int
+   * @return the value of field 'textColThreshold'.
+   */
+  public int getTextColThreshold()
+  {
+    return this._textColThreshold;
+  } //-- int getTextColThreshold()
+
+  /**
+   * Method hasColourText
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasColourText()
+  {
+    return this._has_colourText;
+  } //-- boolean hasColourText()
+
+  /**
+   * Method hasConsThreshold
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasConsThreshold()
+  {
+    return this._has_consThreshold;
+  } //-- boolean hasConsThreshold()
+
+  /**
+   * Method hasDisplayBoxes
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasDisplayBoxes()
+  {
+    return this._has_displayBoxes;
+  } //-- boolean hasDisplayBoxes()
+
+  /**
+   * Method hasDisplayText
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasDisplayText()
+  {
+    return this._has_displayText;
+  } //-- boolean hasDisplayText()
+
+  /**
+   * Method hasEnd
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasEnd()
+  {
+    return this._has_end;
+  } //-- boolean hasEnd()
+
+  /**
+   * Method hasOutlineColour
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasOutlineColour()
+  {
+    return this._has_outlineColour;
+  } //-- boolean hasOutlineColour()
+
+  /**
+   * Method hasPidThreshold
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasPidThreshold()
+  {
+    return this._has_pidThreshold;
+  } //-- boolean hasPidThreshold()
+
+  /**
+   * Method hasStart
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasStart()
+  {
+    return this._has_start;
+  } //-- boolean hasStart()
+
+  /**
+   * Method hasTextCol1
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasTextCol1()
+  {
+    return this._has_textCol1;
+  } //-- boolean hasTextCol1()
+
+  /**
+   * Method hasTextCol2
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasTextCol2()
+  {
+    return this._has_textCol2;
+  } //-- boolean hasTextCol2()
+
+  /**
+   * Method hasTextColThreshold
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasTextColThreshold()
+  {
+    return this._has_textColThreshold;
+  } //-- boolean hasTextColThreshold()
+
+  /**
+   * Method isValid
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    }
+    catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  } //-- boolean isValid()
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param out
+   */
+  public void marshal(java.io.Writer out)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, out);
+  } //-- void marshal(java.io.Writer)
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param handler
+   */
+  public void marshal(org.xml.sax.ContentHandler handler)
+      throws java.io.IOException, org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, handler);
+  } //-- void marshal(org.xml.sax.ContentHandler)
+
+  /**
+   * Method removeAllSeq
+   *
+   */
+  public void removeAllSeq()
+  {
+    _seqList.removeAllElements();
+  } //-- void removeAllSeq()
+
+  /**
+   * Method removeSeq
+   *
+   *
+   *
+   * @param index
+   * @return int
+   */
+  public int removeSeq(int index)
+  {
+    java.lang.Object obj = _seqList.elementAt(index);
+    _seqList.removeElementAt(index);
+    return ( (java.lang.Integer) obj).intValue();
+  } //-- int removeSeq(int)
+
+  /**
+   * Sets the value of field 'colour'.
+   *
+   * @param colour the value of field 'colour'.
+   */
+  public void setColour(java.lang.String colour)
+  {
+    this._colour = colour;
+  } //-- void setColour(java.lang.String)
+
+  /**
+   * Sets the value of field 'colourText'.
+   *
+   * @param colourText the value of field 'colourText'.
+   */
+  public void setColourText(boolean colourText)
+  {
+    this._colourText = colourText;
+    this._has_colourText = true;
+  } //-- void setColourText(boolean)
+
+  /**
+   * Sets the value of field 'consThreshold'.
+   *
+   * @param consThreshold the value of field 'consThreshold'.
+   */
+  public void setConsThreshold(int consThreshold)
+  {
+    this._consThreshold = consThreshold;
+    this._has_consThreshold = true;
+  } //-- void setConsThreshold(int)
+
+  /**
+   * Sets the value of field 'displayBoxes'.
+   *
+   * @param displayBoxes the value of field 'displayBoxes'.
+   */
+  public void setDisplayBoxes(boolean displayBoxes)
+  {
+    this._displayBoxes = displayBoxes;
+    this._has_displayBoxes = true;
+  } //-- void setDisplayBoxes(boolean)
+
+  /**
+   * Sets the value of field 'displayText'.
+   *
+   * @param displayText the value of field 'displayText'.
+   */
+  public void setDisplayText(boolean displayText)
+  {
+    this._displayText = displayText;
+    this._has_displayText = true;
+  } //-- void setDisplayText(boolean)
+
+  /**
+   * Sets the value of field 'end'.
+   *
+   * @param end the value of field 'end'.
+   */
+  public void setEnd(int end)
+  {
+    this._end = end;
+    this._has_end = true;
+  } //-- void setEnd(int)
+
+  /**
+   * Sets the value of field 'name'.
+   *
+   * @param name the value of field 'name'.
+   */
+  public void setName(java.lang.String name)
+  {
+    this._name = name;
+  } //-- void setName(java.lang.String)
+
+  /**
+   * Sets the value of field 'outlineColour'.
+   *
+   * @param outlineColour the value of field 'outlineColour'.
+   */
+  public void setOutlineColour(int outlineColour)
+  {
+    this._outlineColour = outlineColour;
+    this._has_outlineColour = true;
+  } //-- void setOutlineColour(int)
+
+  /**
+   * Sets the value of field 'pidThreshold'.
+   *
+   * @param pidThreshold the value of field 'pidThreshold'.
+   */
+  public void setPidThreshold(int pidThreshold)
+  {
+    this._pidThreshold = pidThreshold;
+    this._has_pidThreshold = true;
+  } //-- void setPidThreshold(int)
+
+  /**
+   * Method setSeq
+   *
+   *
+   *
+   * @param index
+   * @param vSeq
+   */
+  public void setSeq(int index, int vSeq)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _seqList.size()))
+    {
+      throw new IndexOutOfBoundsException();
+    }
+    _seqList.setElementAt(new java.lang.Integer(vSeq), index);
+  } //-- void setSeq(int, int)
+
+  /**
+   * Method setSeq
+   *
+   *
+   *
+   * @param seqArray
+   */
+  public void setSeq(int[] seqArray)
+  {
+    //-- copy array
+    _seqList.removeAllElements();
+    for (int i = 0; i < seqArray.length; i++)
+    {
+      _seqList.addElement(new java.lang.Integer(seqArray[i]));
+    }
+  } //-- void setSeq(int)
+
+  /**
+   * Sets the value of field 'start'.
+   *
+   * @param start the value of field 'start'.
+   */
+  public void setStart(int start)
+  {
+    this._start = start;
+    this._has_start = true;
+  } //-- void setStart(int)
+
+  /**
+   * Sets the value of field 'textCol1'.
+   *
+   * @param textCol1 the value of field 'textCol1'.
+   */
+  public void setTextCol1(int textCol1)
+  {
+    this._textCol1 = textCol1;
+    this._has_textCol1 = true;
+  } //-- void setTextCol1(int)
+
+  /**
+   * Sets the value of field 'textCol2'.
+   *
+   * @param textCol2 the value of field 'textCol2'.
+   */
+  public void setTextCol2(int textCol2)
+  {
+    this._textCol2 = textCol2;
+    this._has_textCol2 = true;
+  } //-- void setTextCol2(int)
+
+  /**
+   * Sets the value of field 'textColThreshold'.
+   *
+   * @param textColThreshold the value of field 'textColThreshold'
+   */
+  public void setTextColThreshold(int textColThreshold)
+  {
+    this._textColThreshold = textColThreshold;
+    this._has_textColThreshold = true;
+  } //-- void setTextColThreshold(int)
+
+  /**
+   * Method unmarshal
+   *
+   *
+   *
+   * @param reader
+   * @return Object
+   */
+  public static java.lang.Object unmarshal(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);
+  } //-- java.lang.Object unmarshal(java.io.Reader)
+
+  /**
+   * Method validate
+   *
+   */
+  public void validate()
+      throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.
+        Validator();
+    validator.validate(this);
+  } //-- void validate()
 
 }
diff --git a/src/jalview/schemabinding/version2/JGroupDescriptor.java b/src/jalview/schemabinding/version2/JGroupDescriptor.java
index 1985c61..15aeb79 100755
--- a/src/jalview/schemabinding/version2/JGroupDescriptor.java
+++ b/src/jalview/schemabinding/version2/JGroupDescriptor.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,731 +7,876 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
-import org.exolab.castor.mapping.AccessMode;
-import org.exolab.castor.xml.TypeValidator;
-import org.exolab.castor.xml.XMLFieldDescriptor;
 import org.exolab.castor.xml.validators.*;
 
 /**
  * Class JGroupDescriptor.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class JGroupDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field nsPrefix
-     */
-    private java.lang.String nsPrefix;
-
-    /**
-     * Field nsURI
-     */
-    private java.lang.String nsURI;
-
-    /**
-     * Field xmlName
-     */
-    private java.lang.String xmlName;
-
-    /**
-     * Field identity
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor identity;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public JGroupDescriptor() {
-        super();
-        nsURI = "www.jalview.org";
-        xmlName = "JGroup";
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.xml.XMLFieldHandler              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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _start
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            IntegerValidator typeValidator= new IntegerValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _end
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            IntegerValidator typeValidator= new IntegerValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _name
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            StringValidator typeValidator = new StringValidator();
-            typeValidator.setWhiteSpace("preserve");
-            fieldValidator.setValidator(typeValidator);
-        }
-        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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _colour
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            StringValidator typeValidator = new StringValidator();
-            typeValidator.setWhiteSpace("preserve");
-            fieldValidator.setValidator(typeValidator);
-        }
-        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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _consThreshold
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            IntegerValidator typeValidator= new IntegerValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _pidThreshold
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            IntegerValidator typeValidator= new IntegerValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _outlineColour
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            IntegerValidator typeValidator= new IntegerValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _displayBoxes
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            BooleanValidator typeValidator = new 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);
-            }
-            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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _displayText
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            BooleanValidator typeValidator = new 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);
-            }
-            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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _colourText
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            BooleanValidator typeValidator = new 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());
-                }
-            }
-            public java.lang.Object newInstance( java.lang.Object parent ) {
-                return null;
-            }
-        } );
-        desc.setHandler(handler);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _textCol1
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            IntegerValidator typeValidator= new IntegerValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _textCol2
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            IntegerValidator typeValidator= new IntegerValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _textColThreshold
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            IntegerValidator typeValidator= new IntegerValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-        //-- _seqList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_seqList", "seq", org.exolab.castor.xml.NodeType.Element);
-        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;
-                    // ignore null values for non optional primitives
-                    if (value == null) return;
-                    
-                    target.addSeq( ((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.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
-            IntegerValidator typeValidator= new IntegerValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        desc.setValidator(fieldValidator);
-    } //-- jalview.schemabinding.version2.JGroupDescriptor()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method getAccessMode
-     * 
-     * 
-     * 
-     * @return AccessMode
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode()
+public class JGroupDescriptor
+    extends org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  //--------------------------/
+  //- Class/Member Variables -/
+  //--------------------------/
+
+  /**
+   * Field nsPrefix
+   */
+  private java.lang.String nsPrefix;
+
+  /**
+   * Field nsURI
+   */
+  private java.lang.String nsURI;
+
+  /**
+   * Field xmlName
+   */
+  private java.lang.String xmlName;
+
+  /**
+   * Field identity
+   */
+  private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+  //----------------/
+  //- Constructors -/
+  //----------------/
+
+  public JGroupDescriptor()
+  {
+    super();
+    nsURI = "www.jalview.org";
+    xmlName = "JGroup";
+
+    //-- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.xml.XMLFieldHandler 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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _start
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      IntegerValidator typeValidator = new IntegerValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _end
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      IntegerValidator typeValidator = new IntegerValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _name
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      StringValidator typeValidator = new StringValidator();
+      typeValidator.setWhiteSpace("preserve");
+      fieldValidator.setValidator(typeValidator);
+    }
+    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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _colour
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      StringValidator typeValidator = new StringValidator();
+      typeValidator.setWhiteSpace("preserve");
+      fieldValidator.setValidator(typeValidator);
+    }
+    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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _consThreshold
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      IntegerValidator typeValidator = new IntegerValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _pidThreshold
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      IntegerValidator typeValidator = new IntegerValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    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;
-    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
-
-    /**
-     * Method getExtends
-     * 
-     * 
-     * 
-     * @return ClassDescriptor
-     */
-    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+      }
+    });
+    desc.setHandler(handler);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _outlineColour
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      IntegerValidator typeValidator = new IntegerValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    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;
-    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
-
-    /**
-     * Method getIdentity
-     * 
-     * 
-     * 
-     * @return FieldDescriptor
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+      }
+    });
+    desc.setHandler(handler);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _displayBoxes
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      BooleanValidator typeValidator = new 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()
     {
-        return identity;
-    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
-
-    /**
-     * Method getJavaClass
-     * 
-     * 
-     * 
-     * @return Class
-     */
-    public java.lang.Class getJavaClass()
+      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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _displayText
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      BooleanValidator typeValidator = new 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()
     {
-        return jalview.schemabinding.version2.JGroup.class;
-    } //-- java.lang.Class getJavaClass() 
-
-    /**
-     * Method getNameSpacePrefix
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpacePrefix()
+      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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _colourText
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      BooleanValidator typeValidator = new 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()
     {
-        return nsPrefix;
-    } //-- java.lang.String getNameSpacePrefix() 
-
-    /**
-     * Method getNameSpaceURI
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpaceURI()
+      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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _textCol1
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      IntegerValidator typeValidator = new IntegerValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    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()
     {
-        return nsURI;
-    } //-- java.lang.String getNameSpaceURI() 
-
-    /**
-     * Method getValidator
-     * 
-     * 
-     * 
-     * @return TypeValidator
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator()
+      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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _textCol2
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      IntegerValidator typeValidator = new IntegerValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    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()
     {
-        return this;
-    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
-
-    /**
-     * Method getXMLName
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getXMLName()
+      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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _textColThreshold
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      IntegerValidator typeValidator = new IntegerValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    //-- initialize element descriptors
+
+    //-- _seqList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.
+        Integer.TYPE, "_seqList", "seq", org.exolab.castor.xml.NodeType.Element);
+    handler = (new org.exolab.castor.xml.XMLFieldHandler()
     {
-        return xmlName;
-    } //-- java.lang.String getXMLName() 
+      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;
+          // ignore null values for non optional primitives
+          if (value == null)
+          {
+            return;
+          }
+
+          target.addSeq( ( (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.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
+      IntegerValidator typeValidator = new IntegerValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+  } //-- jalview.schemabinding.version2.JGroupDescriptor()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Method getAccessMode
+   *
+   *
+   *
+   * @return AccessMode
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
+
+  /**
+   * Method getExtends
+   *
+   *
+   *
+   * @return ClassDescriptor
+   */
+  public org.exolab.castor.mapping.ClassDescriptor getExtends()
+  {
+    return null;
+  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
+
+  /**
+   * Method getIdentity
+   *
+   *
+   *
+   * @return FieldDescriptor
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return identity;
+  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
+
+  /**
+   * Method getJavaClass
+   *
+   *
+   *
+   * @return Class
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.JGroup.class;
+  } //-- java.lang.Class getJavaClass()
+
+  /**
+   * Method getNameSpacePrefix
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return nsPrefix;
+  } //-- java.lang.String getNameSpacePrefix()
+
+  /**
+   * Method getNameSpaceURI
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return nsURI;
+  } //-- java.lang.String getNameSpaceURI()
+
+  /**
+   * Method getValidator
+   *
+   *
+   *
+   * @return TypeValidator
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  } //-- org.exolab.castor.xml.TypeValidator getValidator()
+
+  /**
+   * Method getXMLName
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getXMLName()
+  {
+    return xmlName;
+  } //-- java.lang.String getXMLName()
 
 }
diff --git a/src/jalview/schemabinding/version2/JSeq.java b/src/jalview/schemabinding/version2/JSeq.java
index 19e2e6d..29221ad 100755
--- a/src/jalview/schemabinding/version2/JSeq.java
+++ b/src/jalview/schemabinding/version2/JSeq.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,835 +7,861 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
 //---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import java.util.*;
 
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import java.util.Enumeration;
-import java.util.Vector;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
+import org.exolab.castor.xml.*;
 
 /**
  * Class JSeq.
- * 
+ *
  * @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 _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();
-        _featuresList = new Vector();
-        _pdbidsList = new Vector();
-        _hiddenSequencesList = new Vector();
-    } //-- jalview.schemabinding.version2.JSeq()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method addFeatures
-     * 
-     * 
-     * 
-     * @param vFeatures
-     */
-    public void addFeatures(jalview.schemabinding.version2.Features vFeatures)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _featuresList.addElement(vFeatures);
-    } //-- void addFeatures(jalview.schemabinding.version2.Features) 
-
-    /**
-     * Method addFeatures
-     * 
-     * 
-     * 
-     * @param index
-     * @param vFeatures
-     */
-    public void addFeatures(int index, jalview.schemabinding.version2.Features vFeatures)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _featuresList.insertElementAt(vFeatures, index);
-    } //-- void addFeatures(int, jalview.schemabinding.version2.Features) 
-
-    /**
-     * Method addHiddenSequences
-     * 
-     * 
-     * 
-     * @param vHiddenSequences
-     */
-    public void addHiddenSequences(int vHiddenSequences)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _hiddenSequencesList.addElement(new java.lang.Integer(vHiddenSequences));
-    } //-- void addHiddenSequences(int) 
-
-    /**
-     * Method addHiddenSequences
-     * 
-     * 
-     * 
-     * @param index
-     * @param vHiddenSequences
-     */
-    public void addHiddenSequences(int index, int vHiddenSequences)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _hiddenSequencesList.insertElementAt(new java.lang.Integer(vHiddenSequences), index);
-    } //-- void addHiddenSequences(int, int) 
-
-    /**
-     * Method addPdbids
-     * 
-     * 
-     * 
-     * @param vPdbids
-     */
-    public void addPdbids(jalview.schemabinding.version2.Pdbids vPdbids)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _pdbidsList.addElement(vPdbids);
-    } //-- void addPdbids(jalview.schemabinding.version2.Pdbids) 
-
-    /**
-     * Method addPdbids
-     * 
-     * 
-     * 
-     * @param index
-     * @param vPdbids
-     */
-    public void addPdbids(int index, jalview.schemabinding.version2.Pdbids vPdbids)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _pdbidsList.insertElementAt(vPdbids, index);
-    } //-- void addPdbids(int, jalview.schemabinding.version2.Pdbids) 
-
-    /**
-     * Method deleteColour
-     * 
-     */
-    public void deleteColour()
-    {
-        this._has_colour= false;
-    } //-- void deleteColour() 
-
-    /**
-     * Method deleteEnd
-     * 
-     */
-    public void deleteEnd()
-    {
-        this._has_end= false;
-    } //-- void deleteEnd() 
-
-    /**
-     * Method deleteHidden
-     * 
-     */
-    public void deleteHidden()
-    {
-        this._has_hidden= false;
-    } //-- void deleteHidden() 
-
-    /**
-     * Method deleteId
-     * 
-     */
-    public void deleteId()
-    {
-        this._has_id= false;
-    } //-- void deleteId() 
-
-    /**
-     * Method deleteStart
-     * 
-     */
-    public void deleteStart()
-    {
-        this._has_start= false;
-    } //-- void deleteStart() 
-
-    /**
-     * Method enumerateFeatures
-     * 
-     * 
-     * 
-     * @return Enumeration
-     */
-    public java.util.Enumeration enumerateFeatures()
-    {
-        return _featuresList.elements();
-    } //-- java.util.Enumeration enumerateFeatures() 
-
-    /**
-     * Method enumerateHiddenSequences
-     * 
-     * 
-     * 
-     * @return Enumeration
-     */
-    public java.util.Enumeration enumerateHiddenSequences()
-    {
-        return _hiddenSequencesList.elements();
-    } //-- java.util.Enumeration enumerateHiddenSequences() 
-
-    /**
-     * Method enumeratePdbids
-     * 
-     * 
-     * 
-     * @return Enumeration
-     */
-    public java.util.Enumeration enumeratePdbids()
-    {
-        return _pdbidsList.elements();
-    } //-- java.util.Enumeration enumeratePdbids() 
-
-    /**
-     * Returns the value of field 'colour'.
-     * 
-     * @return int
-     * @return the value of field 'colour'.
-     */
-    public int getColour()
-    {
-        return this._colour;
-    } //-- int getColour() 
-
-    /**
-     * Returns the value of field 'end'.
-     * 
-     * @return int
-     * @return the value of field 'end'.
-     */
-    public int getEnd()
-    {
-        return this._end;
-    } //-- int getEnd() 
-
-    /**
-     * Method getFeatures
-     * 
-     * 
-     * 
-     * @param index
-     * @return Features
-     */
-    public jalview.schemabinding.version2.Features getFeatures(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _featuresList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        
-        return (jalview.schemabinding.version2.Features) _featuresList.elementAt(index);
-    } //-- jalview.schemabinding.version2.Features getFeatures(int) 
-
-    /**
-     * Method getFeatures
-     * 
-     * 
-     * 
-     * @return Features
-     */
-    public jalview.schemabinding.version2.Features[] getFeatures()
-    {
-        int size = _featuresList.size();
-        jalview.schemabinding.version2.Features[] mArray = new jalview.schemabinding.version2.Features[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = (jalview.schemabinding.version2.Features) _featuresList.elementAt(index);
-        }
-        return mArray;
-    } //-- jalview.schemabinding.version2.Features[] getFeatures() 
-
-    /**
-     * Method getFeaturesCount
-     * 
-     * 
-     * 
-     * @return int
-     */
-    public int getFeaturesCount()
-    {
-        return _featuresList.size();
-    } //-- int getFeaturesCount() 
-
-    /**
-     * Returns the value of field 'hidden'.
-     * 
-     * @return boolean
-     * @return the value of field 'hidden'.
-     */
-    public boolean getHidden()
-    {
-        return this._hidden;
-    } //-- boolean getHidden() 
-
-    /**
-     * Method getHiddenSequences
-     * 
-     * 
-     * 
-     * @param index
-     * @return int
-     */
-    public int getHiddenSequences(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _hiddenSequencesList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        
-        return ((java.lang.Integer)_hiddenSequencesList.elementAt(index)).intValue();
-    } //-- int getHiddenSequences(int) 
-
-    /**
-     * Method getHiddenSequences
-     * 
-     * 
-     * 
-     * @return int
-     */
-    public int[] getHiddenSequences()
-    {
-        int size = _hiddenSequencesList.size();
-        int[] mArray = new int[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = ((java.lang.Integer)_hiddenSequencesList.elementAt(index)).intValue();
-        }
-        return mArray;
-    } //-- int[] getHiddenSequences() 
-
-    /**
-     * Method getHiddenSequencesCount
-     * 
-     * 
-     * 
-     * @return int
-     */
-    public int getHiddenSequencesCount()
-    {
-        return _hiddenSequencesList.size();
-    } //-- int getHiddenSequencesCount() 
-
-    /**
-     * Returns the value of field 'id'.
-     * 
-     * @return int
-     * @return the value of field 'id'.
-     */
-    public int getId()
-    {
-        return this._id;
-    } //-- int getId() 
-
-    /**
-     * Method getPdbids
-     * 
-     * 
-     * 
-     * @param index
-     * @return Pdbids
-     */
-    public jalview.schemabinding.version2.Pdbids getPdbids(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _pdbidsList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        
-        return (jalview.schemabinding.version2.Pdbids) _pdbidsList.elementAt(index);
-    } //-- jalview.schemabinding.version2.Pdbids getPdbids(int) 
-
-    /**
-     * Method getPdbids
-     * 
-     * 
-     * 
-     * @return Pdbids
-     */
-    public jalview.schemabinding.version2.Pdbids[] getPdbids()
-    {
-        int size = _pdbidsList.size();
-        jalview.schemabinding.version2.Pdbids[] mArray = new jalview.schemabinding.version2.Pdbids[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = (jalview.schemabinding.version2.Pdbids) _pdbidsList.elementAt(index);
-        }
-        return mArray;
-    } //-- jalview.schemabinding.version2.Pdbids[] getPdbids() 
-
-    /**
-     * Method getPdbidsCount
-     * 
-     * 
-     * 
-     * @return int
-     */
-    public int getPdbidsCount()
-    {
-        return _pdbidsList.size();
-    } //-- int getPdbidsCount() 
-
-    /**
-     * Returns the value of field 'start'.
-     * 
-     * @return int
-     * @return the value of field 'start'.
-     */
-    public int getStart()
-    {
-        return this._start;
-    } //-- int getStart() 
-
-    /**
-     * Method hasColour
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasColour()
-    {
-        return this._has_colour;
-    } //-- boolean hasColour() 
-
-    /**
-     * Method hasEnd
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasEnd()
-    {
-        return this._has_end;
-    } //-- boolean hasEnd() 
-
-    /**
-     * Method hasHidden
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasHidden()
-    {
-        return this._has_hidden;
-    } //-- boolean hasHidden() 
-
-    /**
-     * Method hasId
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasId()
-    {
-        return this._has_id;
-    } //-- boolean hasId() 
-
-    /**
-     * Method hasStart
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasStart()
-    {
-        return this._has_start;
-    } //-- boolean hasStart() 
-
-    /**
-     * Method isValid
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean isValid()
-    {
-        try {
-            validate();
-        }
-        catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    } //-- boolean isValid() 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param out
-     */
-    public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, out);
-    } //-- void marshal(java.io.Writer) 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param handler
-     */
-    public void marshal(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, handler);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
-
-    /**
-     * Method removeAllFeatures
-     * 
-     */
-    public void removeAllFeatures()
-    {
-        _featuresList.removeAllElements();
-    } //-- void removeAllFeatures() 
-
-    /**
-     * Method removeAllHiddenSequences
-     * 
-     */
-    public void removeAllHiddenSequences()
-    {
-        _hiddenSequencesList.removeAllElements();
-    } //-- void removeAllHiddenSequences() 
-
-    /**
-     * Method removeAllPdbids
-     * 
-     */
-    public void removeAllPdbids()
-    {
-        _pdbidsList.removeAllElements();
-    } //-- void removeAllPdbids() 
-
-    /**
-     * Method removeFeatures
-     * 
-     * 
-     * 
-     * @param index
-     * @return Features
-     */
-    public jalview.schemabinding.version2.Features removeFeatures(int index)
-    {
-        java.lang.Object obj = _featuresList.elementAt(index);
-        _featuresList.removeElementAt(index);
-        return (jalview.schemabinding.version2.Features) obj;
-    } //-- jalview.schemabinding.version2.Features removeFeatures(int) 
-
-    /**
-     * Method removeHiddenSequences
-     * 
-     * 
-     * 
-     * @param index
-     * @return int
-     */
-    public int removeHiddenSequences(int index)
-    {
-        java.lang.Object obj = _hiddenSequencesList.elementAt(index);
-        _hiddenSequencesList.removeElementAt(index);
-        return ((java.lang.Integer)obj).intValue();
-    } //-- int removeHiddenSequences(int) 
-
-    /**
-     * Method removePdbids
-     * 
-     * 
-     * 
-     * @param index
-     * @return Pdbids
-     */
-    public jalview.schemabinding.version2.Pdbids removePdbids(int index)
-    {
-        java.lang.Object obj = _pdbidsList.elementAt(index);
-        _pdbidsList.removeElementAt(index);
-        return (jalview.schemabinding.version2.Pdbids) obj;
-    } //-- jalview.schemabinding.version2.Pdbids removePdbids(int) 
-
-    /**
-     * Sets the value of field 'colour'.
-     * 
-     * @param colour the value of field 'colour'.
-     */
-    public void setColour(int colour)
-    {
-        this._colour = colour;
-        this._has_colour = true;
-    } //-- void setColour(int) 
-
-    /**
-     * Sets the value of field 'end'.
-     * 
-     * @param end the value of field 'end'.
-     */
-    public void setEnd(int end)
-    {
-        this._end = end;
-        this._has_end = true;
-    } //-- void setEnd(int) 
-
-    /**
-     * Method setFeatures
-     * 
-     * 
-     * 
-     * @param index
-     * @param vFeatures
-     */
-    public void setFeatures(int index, jalview.schemabinding.version2.Features vFeatures)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _featuresList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        _featuresList.setElementAt(vFeatures, index);
-    } //-- void setFeatures(int, jalview.schemabinding.version2.Features) 
-
-    /**
-     * Method setFeatures
-     * 
-     * 
-     * 
-     * @param featuresArray
-     */
-    public void setFeatures(jalview.schemabinding.version2.Features[] featuresArray)
-    {
-        //-- copy array
-        _featuresList.removeAllElements();
-        for (int i = 0; i < featuresArray.length; i++) {
-            _featuresList.addElement(featuresArray[i]);
-        }
-    } //-- void setFeatures(jalview.schemabinding.version2.Features) 
-
-    /**
-     * Sets the value of field 'hidden'.
-     * 
-     * @param hidden the value of field 'hidden'.
-     */
-    public void setHidden(boolean hidden)
-    {
-        this._hidden = hidden;
-        this._has_hidden = true;
-    } //-- void setHidden(boolean) 
-
-    /**
-     * Method setHiddenSequences
-     * 
-     * 
-     * 
-     * @param index
-     * @param vHiddenSequences
-     */
-    public void setHiddenSequences(int index, int vHiddenSequences)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _hiddenSequencesList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        _hiddenSequencesList.setElementAt(new java.lang.Integer(vHiddenSequences), index);
-    } //-- void setHiddenSequences(int, int) 
-
-    /**
-     * Method setHiddenSequences
-     * 
-     * 
-     * 
-     * @param hiddenSequencesArray
-     */
-    public void setHiddenSequences(int[] hiddenSequencesArray)
-    {
-        //-- copy array
-        _hiddenSequencesList.removeAllElements();
-        for (int i = 0; i < hiddenSequencesArray.length; i++) {
-            _hiddenSequencesList.addElement(new java.lang.Integer(hiddenSequencesArray[i]));
-        }
-    } //-- void setHiddenSequences(int) 
-
-    /**
-     * Sets the value of field 'id'.
-     * 
-     * @param id the value of field 'id'.
-     */
-    public void setId(int id)
-    {
-        this._id = id;
-        this._has_id = true;
-    } //-- void setId(int) 
-
-    /**
-     * Method setPdbids
-     * 
-     * 
-     * 
-     * @param index
-     * @param vPdbids
-     */
-    public void setPdbids(int index, jalview.schemabinding.version2.Pdbids vPdbids)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _pdbidsList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        _pdbidsList.setElementAt(vPdbids, index);
-    } //-- void setPdbids(int, jalview.schemabinding.version2.Pdbids) 
-
-    /**
-     * Method setPdbids
-     * 
-     * 
-     * 
-     * @param pdbidsArray
-     */
-    public void setPdbids(jalview.schemabinding.version2.Pdbids[] pdbidsArray)
-    {
-        //-- copy array
-        _pdbidsList.removeAllElements();
-        for (int i = 0; i < pdbidsArray.length; i++) {
-            _pdbidsList.addElement(pdbidsArray[i]);
-        }
-    } //-- void setPdbids(jalview.schemabinding.version2.Pdbids) 
-
-    /**
-     * Sets the value of field 'start'.
-     * 
-     * @param start the value of field 'start'.
-     */
-    public void setStart(int start)
-    {
-        this._start = start;
-        this._has_start = true;
-    } //-- void setStart(int) 
-
-    /**
-     * Method unmarshal
-     * 
-     * 
-     * 
-     * @param reader
-     * @return Object
-     */
-    public static java.lang.Object unmarshal(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);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
-
-    /**
-     * Method validate
-     * 
-     */
-    public void validate()
-        throws org.exolab.castor.xml.ValidationException
-    {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    } //-- void validate() 
+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 _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();
+    _featuresList = new Vector();
+    _pdbidsList = new Vector();
+    _hiddenSequencesList = new Vector();
+  } //-- jalview.schemabinding.version2.JSeq()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Method addFeatures
+   *
+   *
+   *
+   * @param vFeatures
+   */
+  public void addFeatures(jalview.schemabinding.version2.Features vFeatures)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _featuresList.addElement(vFeatures);
+  } //-- void addFeatures(jalview.schemabinding.version2.Features)
+
+  /**
+   * Method addFeatures
+   *
+   *
+   *
+   * @param index
+   * @param vFeatures
+   */
+  public void addFeatures(int index,
+                          jalview.schemabinding.version2.Features vFeatures)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _featuresList.insertElementAt(vFeatures, index);
+  } //-- void addFeatures(int, jalview.schemabinding.version2.Features)
+
+  /**
+   * Method addHiddenSequences
+   *
+   *
+   *
+   * @param vHiddenSequences
+   */
+  public void addHiddenSequences(int vHiddenSequences)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _hiddenSequencesList.addElement(new java.lang.Integer(vHiddenSequences));
+  } //-- void addHiddenSequences(int)
+
+  /**
+   * Method addHiddenSequences
+   *
+   *
+   *
+   * @param index
+   * @param vHiddenSequences
+   */
+  public void addHiddenSequences(int index, int vHiddenSequences)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _hiddenSequencesList.insertElementAt(new java.lang.Integer(vHiddenSequences),
+                                         index);
+  } //-- void addHiddenSequences(int, int)
+
+  /**
+   * Method addPdbids
+   *
+   *
+   *
+   * @param vPdbids
+   */
+  public void addPdbids(jalview.schemabinding.version2.Pdbids vPdbids)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _pdbidsList.addElement(vPdbids);
+  } //-- void addPdbids(jalview.schemabinding.version2.Pdbids)
+
+  /**
+   * Method addPdbids
+   *
+   *
+   *
+   * @param index
+   * @param vPdbids
+   */
+  public void addPdbids(int index,
+                        jalview.schemabinding.version2.Pdbids vPdbids)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _pdbidsList.insertElementAt(vPdbids, index);
+  } //-- void addPdbids(int, jalview.schemabinding.version2.Pdbids)
+
+  /**
+   * Method deleteColour
+   *
+   */
+  public void deleteColour()
+  {
+    this._has_colour = false;
+  } //-- void deleteColour()
+
+  /**
+   * Method deleteEnd
+   *
+   */
+  public void deleteEnd()
+  {
+    this._has_end = false;
+  } //-- void deleteEnd()
+
+  /**
+   * Method deleteHidden
+   *
+   */
+  public void deleteHidden()
+  {
+    this._has_hidden = false;
+  } //-- void deleteHidden()
+
+  /**
+   * Method deleteId
+   *
+   */
+  public void deleteId()
+  {
+    this._has_id = false;
+  } //-- void deleteId()
+
+  /**
+   * Method deleteStart
+   *
+   */
+  public void deleteStart()
+  {
+    this._has_start = false;
+  } //-- void deleteStart()
+
+  /**
+   * Method enumerateFeatures
+   *
+   *
+   *
+   * @return Enumeration
+   */
+  public java.util.Enumeration enumerateFeatures()
+  {
+    return _featuresList.elements();
+  } //-- java.util.Enumeration enumerateFeatures()
+
+  /**
+   * Method enumerateHiddenSequences
+   *
+   *
+   *
+   * @return Enumeration
+   */
+  public java.util.Enumeration enumerateHiddenSequences()
+  {
+    return _hiddenSequencesList.elements();
+  } //-- java.util.Enumeration enumerateHiddenSequences()
+
+  /**
+   * Method enumeratePdbids
+   *
+   *
+   *
+   * @return Enumeration
+   */
+  public java.util.Enumeration enumeratePdbids()
+  {
+    return _pdbidsList.elements();
+  } //-- java.util.Enumeration enumeratePdbids()
+
+  /**
+   * Returns the value of field 'colour'.
+   *
+   * @return int
+   * @return the value of field 'colour'.
+   */
+  public int getColour()
+  {
+    return this._colour;
+  } //-- int getColour()
+
+  /**
+   * Returns the value of field 'end'.
+   *
+   * @return int
+   * @return the value of field 'end'.
+   */
+  public int getEnd()
+  {
+    return this._end;
+  } //-- int getEnd()
+
+  /**
+   * Method getFeatures
+   *
+   *
+   *
+   * @param index
+   * @return Features
+   */
+  public jalview.schemabinding.version2.Features getFeatures(int index)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _featuresList.size()))
+    {
+      throw new IndexOutOfBoundsException();
+    }
+
+    return (jalview.schemabinding.version2.Features) _featuresList.elementAt(
+        index);
+  } //-- jalview.schemabinding.version2.Features getFeatures(int)
+
+  /**
+   * Method getFeatures
+   *
+   *
+   *
+   * @return Features
+   */
+  public jalview.schemabinding.version2.Features[] getFeatures()
+  {
+    int size = _featuresList.size();
+    jalview.schemabinding.version2.Features[] mArray = new jalview.
+        schemabinding.version2.Features[size];
+    for (int index = 0; index < size; index++)
+    {
+      mArray[index] = (jalview.schemabinding.version2.Features) _featuresList.
+          elementAt(index);
+    }
+    return mArray;
+  } //-- jalview.schemabinding.version2.Features[] getFeatures()
+
+  /**
+   * Method getFeaturesCount
+   *
+   *
+   *
+   * @return int
+   */
+  public int getFeaturesCount()
+  {
+    return _featuresList.size();
+  } //-- int getFeaturesCount()
+
+  /**
+   * Returns the value of field 'hidden'.
+   *
+   * @return boolean
+   * @return the value of field 'hidden'.
+   */
+  public boolean getHidden()
+  {
+    return this._hidden;
+  } //-- boolean getHidden()
+
+  /**
+   * Method getHiddenSequences
+   *
+   *
+   *
+   * @param index
+   * @return int
+   */
+  public int getHiddenSequences(int index)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _hiddenSequencesList.size()))
+    {
+      throw new IndexOutOfBoundsException();
+    }
+
+    return ( (java.lang.Integer) _hiddenSequencesList.elementAt(index)).
+        intValue();
+  } //-- int getHiddenSequences(int)
+
+  /**
+   * Method getHiddenSequences
+   *
+   *
+   *
+   * @return int
+   */
+  public int[] getHiddenSequences()
+  {
+    int size = _hiddenSequencesList.size();
+    int[] mArray = new int[size];
+    for (int index = 0; index < size; index++)
+    {
+      mArray[index] = ( (java.lang.Integer) _hiddenSequencesList.elementAt(
+          index)).intValue();
+    }
+    return mArray;
+  } //-- int[] getHiddenSequences()
+
+  /**
+   * Method getHiddenSequencesCount
+   *
+   *
+   *
+   * @return int
+   */
+  public int getHiddenSequencesCount()
+  {
+    return _hiddenSequencesList.size();
+  } //-- int getHiddenSequencesCount()
+
+  /**
+   * Returns the value of field 'id'.
+   *
+   * @return int
+   * @return the value of field 'id'.
+   */
+  public int getId()
+  {
+    return this._id;
+  } //-- int getId()
+
+  /**
+   * Method getPdbids
+   *
+   *
+   *
+   * @param index
+   * @return Pdbids
+   */
+  public jalview.schemabinding.version2.Pdbids getPdbids(int index)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _pdbidsList.size()))
+    {
+      throw new IndexOutOfBoundsException();
+    }
+
+    return (jalview.schemabinding.version2.Pdbids) _pdbidsList.elementAt(index);
+  } //-- jalview.schemabinding.version2.Pdbids getPdbids(int)
+
+  /**
+   * Method getPdbids
+   *
+   *
+   *
+   * @return Pdbids
+   */
+  public jalview.schemabinding.version2.Pdbids[] getPdbids()
+  {
+    int size = _pdbidsList.size();
+    jalview.schemabinding.version2.Pdbids[] mArray = new jalview.schemabinding.
+        version2.Pdbids[size];
+    for (int index = 0; index < size; index++)
+    {
+      mArray[index] = (jalview.schemabinding.version2.Pdbids) _pdbidsList.
+          elementAt(index);
+    }
+    return mArray;
+  } //-- jalview.schemabinding.version2.Pdbids[] getPdbids()
+
+  /**
+   * Method getPdbidsCount
+   *
+   *
+   *
+   * @return int
+   */
+  public int getPdbidsCount()
+  {
+    return _pdbidsList.size();
+  } //-- int getPdbidsCount()
+
+  /**
+   * Returns the value of field 'start'.
+   *
+   * @return int
+   * @return the value of field 'start'.
+   */
+  public int getStart()
+  {
+    return this._start;
+  } //-- int getStart()
+
+  /**
+   * Method hasColour
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasColour()
+  {
+    return this._has_colour;
+  } //-- boolean hasColour()
+
+  /**
+   * Method hasEnd
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasEnd()
+  {
+    return this._has_end;
+  } //-- boolean hasEnd()
+
+  /**
+   * Method hasHidden
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasHidden()
+  {
+    return this._has_hidden;
+  } //-- boolean hasHidden()
+
+  /**
+   * Method hasId
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasId()
+  {
+    return this._has_id;
+  } //-- boolean hasId()
+
+  /**
+   * Method hasStart
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasStart()
+  {
+    return this._has_start;
+  } //-- boolean hasStart()
+
+  /**
+   * Method isValid
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    }
+    catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  } //-- boolean isValid()
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param out
+   */
+  public void marshal(java.io.Writer out)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, out);
+  } //-- void marshal(java.io.Writer)
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param handler
+   */
+  public void marshal(org.xml.sax.ContentHandler handler)
+      throws java.io.IOException, org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, handler);
+  } //-- void marshal(org.xml.sax.ContentHandler)
+
+  /**
+   * Method removeAllFeatures
+   *
+   */
+  public void removeAllFeatures()
+  {
+    _featuresList.removeAllElements();
+  } //-- void removeAllFeatures()
+
+  /**
+   * Method removeAllHiddenSequences
+   *
+   */
+  public void removeAllHiddenSequences()
+  {
+    _hiddenSequencesList.removeAllElements();
+  } //-- void removeAllHiddenSequences()
+
+  /**
+   * Method removeAllPdbids
+   *
+   */
+  public void removeAllPdbids()
+  {
+    _pdbidsList.removeAllElements();
+  } //-- void removeAllPdbids()
+
+  /**
+   * Method removeFeatures
+   *
+   *
+   *
+   * @param index
+   * @return Features
+   */
+  public jalview.schemabinding.version2.Features removeFeatures(int index)
+  {
+    java.lang.Object obj = _featuresList.elementAt(index);
+    _featuresList.removeElementAt(index);
+    return (jalview.schemabinding.version2.Features) obj;
+  } //-- jalview.schemabinding.version2.Features removeFeatures(int)
+
+  /**
+   * Method removeHiddenSequences
+   *
+   *
+   *
+   * @param index
+   * @return int
+   */
+  public int removeHiddenSequences(int index)
+  {
+    java.lang.Object obj = _hiddenSequencesList.elementAt(index);
+    _hiddenSequencesList.removeElementAt(index);
+    return ( (java.lang.Integer) obj).intValue();
+  } //-- int removeHiddenSequences(int)
+
+  /**
+   * Method removePdbids
+   *
+   *
+   *
+   * @param index
+   * @return Pdbids
+   */
+  public jalview.schemabinding.version2.Pdbids removePdbids(int index)
+  {
+    java.lang.Object obj = _pdbidsList.elementAt(index);
+    _pdbidsList.removeElementAt(index);
+    return (jalview.schemabinding.version2.Pdbids) obj;
+  } //-- jalview.schemabinding.version2.Pdbids removePdbids(int)
+
+  /**
+   * Sets the value of field 'colour'.
+   *
+   * @param colour the value of field 'colour'.
+   */
+  public void setColour(int colour)
+  {
+    this._colour = colour;
+    this._has_colour = true;
+  } //-- void setColour(int)
+
+  /**
+   * Sets the value of field 'end'.
+   *
+   * @param end the value of field 'end'.
+   */
+  public void setEnd(int end)
+  {
+    this._end = end;
+    this._has_end = true;
+  } //-- void setEnd(int)
+
+  /**
+   * Method setFeatures
+   *
+   *
+   *
+   * @param index
+   * @param vFeatures
+   */
+  public void setFeatures(int index,
+                          jalview.schemabinding.version2.Features vFeatures)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _featuresList.size()))
+    {
+      throw new IndexOutOfBoundsException();
+    }
+    _featuresList.setElementAt(vFeatures, index);
+  } //-- void setFeatures(int, jalview.schemabinding.version2.Features)
+
+  /**
+   * Method setFeatures
+   *
+   *
+   *
+   * @param featuresArray
+   */
+  public void setFeatures(jalview.schemabinding.version2.Features[]
+                          featuresArray)
+  {
+    //-- copy array
+    _featuresList.removeAllElements();
+    for (int i = 0; i < featuresArray.length; i++)
+    {
+      _featuresList.addElement(featuresArray[i]);
+    }
+  } //-- void setFeatures(jalview.schemabinding.version2.Features)
+
+  /**
+   * Sets the value of field 'hidden'.
+   *
+   * @param hidden the value of field 'hidden'.
+   */
+  public void setHidden(boolean hidden)
+  {
+    this._hidden = hidden;
+    this._has_hidden = true;
+  } //-- void setHidden(boolean)
+
+  /**
+   * Method setHiddenSequences
+   *
+   *
+   *
+   * @param index
+   * @param vHiddenSequences
+   */
+  public void setHiddenSequences(int index, int vHiddenSequences)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _hiddenSequencesList.size()))
+    {
+      throw new IndexOutOfBoundsException();
+    }
+    _hiddenSequencesList.setElementAt(new java.lang.Integer(vHiddenSequences),
+                                      index);
+  } //-- void setHiddenSequences(int, int)
+
+  /**
+   * Method setHiddenSequences
+   *
+   *
+   *
+   * @param hiddenSequencesArray
+   */
+  public void setHiddenSequences(int[] hiddenSequencesArray)
+  {
+    //-- copy array
+    _hiddenSequencesList.removeAllElements();
+    for (int i = 0; i < hiddenSequencesArray.length; i++)
+    {
+      _hiddenSequencesList.addElement(new java.lang.Integer(
+          hiddenSequencesArray[i]));
+    }
+  } //-- void setHiddenSequences(int)
+
+  /**
+   * Sets the value of field 'id'.
+   *
+   * @param id the value of field 'id'.
+   */
+  public void setId(int id)
+  {
+    this._id = id;
+    this._has_id = true;
+  } //-- void setId(int)
+
+  /**
+   * Method setPdbids
+   *
+   *
+   *
+   * @param index
+   * @param vPdbids
+   */
+  public void setPdbids(int index,
+                        jalview.schemabinding.version2.Pdbids vPdbids)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _pdbidsList.size()))
+    {
+      throw new IndexOutOfBoundsException();
+    }
+    _pdbidsList.setElementAt(vPdbids, index);
+  } //-- void setPdbids(int, jalview.schemabinding.version2.Pdbids)
+
+  /**
+   * Method setPdbids
+   *
+   *
+   *
+   * @param pdbidsArray
+   */
+  public void setPdbids(jalview.schemabinding.version2.Pdbids[] pdbidsArray)
+  {
+    //-- copy array
+    _pdbidsList.removeAllElements();
+    for (int i = 0; i < pdbidsArray.length; i++)
+    {
+      _pdbidsList.addElement(pdbidsArray[i]);
+    }
+  } //-- void setPdbids(jalview.schemabinding.version2.Pdbids)
+
+  /**
+   * Sets the value of field 'start'.
+   *
+   * @param start the value of field 'start'.
+   */
+  public void setStart(int start)
+  {
+    this._start = start;
+    this._has_start = true;
+  } //-- void setStart(int)
+
+  /**
+   * Method unmarshal
+   *
+   *
+   *
+   * @param reader
+   * @return Object
+   */
+  public static java.lang.Object unmarshal(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);
+  } //-- java.lang.Object unmarshal(java.io.Reader)
+
+  /**
+   * Method validate
+   *
+   */
+  public void validate()
+      throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.
+        Validator();
+    validator.validate(this);
+  } //-- void validate()
 
 }
diff --git a/src/jalview/schemabinding/version2/JSeqDescriptor.java b/src/jalview/schemabinding/version2/JSeqDescriptor.java
index eef74d2..9280390 100755
--- a/src/jalview/schemabinding/version2/JSeqDescriptor.java
+++ b/src/jalview/schemabinding/version2/JSeqDescriptor.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,482 +7,566 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
-import org.exolab.castor.mapping.AccessMode;
-import org.exolab.castor.xml.TypeValidator;
-import org.exolab.castor.xml.XMLFieldDescriptor;
 import org.exolab.castor.xml.validators.*;
 
 /**
  * Class JSeqDescriptor.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class JSeqDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field nsPrefix
-     */
-    private java.lang.String nsPrefix;
-
-    /**
-     * Field nsURI
-     */
-    private java.lang.String nsURI;
-
-    /**
-     * Field xmlName
-     */
-    private java.lang.String xmlName;
-
-    /**
-     * Field identity
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor identity;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public JSeqDescriptor() {
-        super();
-        nsURI = "www.jalview.org";
-        xmlName = "JSeq";
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.xml.XMLFieldHandler              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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _colour
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            IntegerValidator typeValidator= new IntegerValidator();
-            fieldValidator.setValidator(typeValidator);
+public class JSeqDescriptor
+    extends org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  //--------------------------/
+  //- Class/Member Variables -/
+  //--------------------------/
+
+  /**
+   * Field nsPrefix
+   */
+  private java.lang.String nsPrefix;
+
+  /**
+   * Field nsURI
+   */
+  private java.lang.String nsURI;
+
+  /**
+   * Field xmlName
+   */
+  private java.lang.String xmlName;
+
+  /**
+   * Field identity
+   */
+  private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+  //----------------/
+  //- Constructors -/
+  //----------------/
+
+  public JSeqDescriptor()
+  {
+    super();
+    nsURI = "www.jalview.org";
+    xmlName = "JSeq";
+
+    //-- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.xml.XMLFieldHandler 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);
-        //-- _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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _start
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            IntegerValidator typeValidator= new IntegerValidator();
-            fieldValidator.setValidator(typeValidator);
+        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());
         }
-        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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _end
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            IntegerValidator typeValidator= new IntegerValidator();
-            fieldValidator.setValidator(typeValidator);
+        catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- _id
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_id", "id", 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.hasId())
-                    return null;
-                return new java.lang.Integer(target.getId());
-            }
-            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.setId( ((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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _id
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            IntegerValidator typeValidator= new IntegerValidator();
-            fieldValidator.setValidator(typeValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    });
+    desc.setHandler(handler);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _colour
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      IntegerValidator typeValidator = new IntegerValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    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());
         }
-        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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _hidden
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            BooleanValidator typeValidator = new BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+        catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        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 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
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    });
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _start
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { //-- local scope
+      IntegerValidator typeValidator = new IntegerValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    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;
         }
-        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 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
+        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());
         }
-        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 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
-            IntegerValidator typeValidator= new IntegerValidator();
-            fieldValidator.setValidator(typeValidator);
+        catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-    } //-- jalview.schemabinding.version2.JSeqDescriptor()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method getAccessMode
-     * 
-     * 
-     * 
-     * @return AccessMode
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode()
-    {
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
-
-    /**
-     * Method getExtends
-     * 
-     * 
-     * 
-     * @return ClassDescriptor
-     */
-    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+      }
+    });
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _end
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { //-- local scope
+      IntegerValidator typeValidator = new IntegerValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    //-- _id
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.
+        Integer.TYPE, "_id", "id", 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.hasId())
+        {
+          return null;
+        }
+        return new java.lang.Integer(target.getId());
+      }
+
+      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.setId( ( (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;
-    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
-
-    /**
-     * Method getIdentity
-     * 
-     * 
-     * 
-     * @return FieldDescriptor
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
-    {
-        return identity;
-    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
-
-    /**
-     * Method getJavaClass
-     * 
-     * 
-     * 
-     * @return Class
-     */
-    public java.lang.Class getJavaClass()
-    {
-        return jalview.schemabinding.version2.JSeq.class;
-    } //-- java.lang.Class getJavaClass() 
-
-    /**
-     * Method getNameSpacePrefix
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpacePrefix()
+      }
+    });
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _id
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { //-- local scope
+      IntegerValidator typeValidator = new IntegerValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    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()
     {
-        return nsPrefix;
-    } //-- java.lang.String getNameSpacePrefix() 
-
-    /**
-     * Method getNameSpaceURI
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpaceURI()
+      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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _hidden
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      BooleanValidator typeValidator = new 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()
     {
-        return nsURI;
-    } //-- java.lang.String getNameSpaceURI() 
-
-    /**
-     * Method getValidator
-     * 
-     * 
-     * 
-     * @return TypeValidator
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator()
+      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 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()
     {
-        return this;
-    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
-
-    /**
-     * Method getXMLName
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getXMLName()
+      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 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
+    }
+    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()
     {
-        return xmlName;
-    } //-- java.lang.String getXMLName() 
+      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 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
+      IntegerValidator typeValidator = new IntegerValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+  } //-- jalview.schemabinding.version2.JSeqDescriptor()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Method getAccessMode
+   *
+   *
+   *
+   * @return AccessMode
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
+
+  /**
+   * Method getExtends
+   *
+   *
+   *
+   * @return ClassDescriptor
+   */
+  public org.exolab.castor.mapping.ClassDescriptor getExtends()
+  {
+    return null;
+  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
+
+  /**
+   * Method getIdentity
+   *
+   *
+   *
+   * @return FieldDescriptor
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return identity;
+  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
+
+  /**
+   * Method getJavaClass
+   *
+   *
+   *
+   * @return Class
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.JSeq.class;
+  } //-- java.lang.Class getJavaClass()
+
+  /**
+   * Method getNameSpacePrefix
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return nsPrefix;
+  } //-- java.lang.String getNameSpacePrefix()
+
+  /**
+   * Method getNameSpaceURI
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return nsURI;
+  } //-- java.lang.String getNameSpaceURI()
+
+  /**
+   * Method getValidator
+   *
+   *
+   *
+   * @return TypeValidator
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  } //-- org.exolab.castor.xml.TypeValidator getValidator()
+
+  /**
+   * Method getXMLName
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getXMLName()
+  {
+    return xmlName;
+  } //-- java.lang.String getXMLName()
 
 }
diff --git a/src/jalview/schemabinding/version2/JalviewModel.java b/src/jalview/schemabinding/version2/JalviewModel.java
index fe8deef..11f6e38 100755
--- a/src/jalview/schemabinding/version2/JalviewModel.java
+++ b/src/jalview/schemabinding/version2/JalviewModel.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,221 +7,223 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import java.util.Date;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
+import org.exolab.castor.xml.*;
 
 /**
  * Class JalviewModel.
- * 
+ *
  * @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();
-    } //-- jalview.schemabinding.version2.JalviewModel()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Returns the value of field 'creationDate'.
-     * 
-     * @return Date
-     * @return the value of field 'creationDate'.
-     */
-    public java.util.Date getCreationDate()
-    {
-        return this._creationDate;
-    } //-- java.util.Date getCreationDate() 
-
-    /**
-     * Returns the value of field 'jalviewModelSequence'.
-     * 
-     * @return JalviewModelSequence
-     * @return the value of field 'jalviewModelSequence'.
-     */
-    public jalview.schemabinding.version2.JalviewModelSequence getJalviewModelSequence()
-    {
-        return this._jalviewModelSequence;
-    } //-- jalview.schemabinding.version2.JalviewModelSequence getJalviewModelSequence() 
-
-    /**
-     * Returns the value of field 'vamsasModel'.
-     * 
-     * @return VamsasModel
-     * @return the value of field 'vamsasModel'.
-     */
-    public jalview.schemabinding.version2.VamsasModel getVamsasModel()
-    {
-        return this._vamsasModel;
-    } //-- jalview.schemabinding.version2.VamsasModel getVamsasModel() 
-
-    /**
-     * Returns the value of field 'version'.
-     * 
-     * @return String
-     * @return the value of field 'version'.
-     */
-    public java.lang.String getVersion()
-    {
-        return this._version;
-    } //-- java.lang.String getVersion() 
-
-    /**
-     * Method isValid
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean isValid()
-    {
-        try {
-            validate();
-        }
-        catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    } //-- boolean isValid() 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param out
-     */
-    public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, out);
-    } //-- void marshal(java.io.Writer) 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param handler
-     */
-    public void marshal(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, handler);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
-
-    /**
-     * Sets the value of field 'creationDate'.
-     * 
-     * @param creationDate the value of field 'creationDate'.
-     */
-    public void setCreationDate(java.util.Date creationDate)
-    {
-        this._creationDate = creationDate;
-    } //-- void setCreationDate(java.util.Date) 
-
-    /**
-     * Sets the value of field 'jalviewModelSequence'.
-     * 
-     * @param jalviewModelSequence the value of field
-     * 'jalviewModelSequence'.
-     */
-    public void setJalviewModelSequence(jalview.schemabinding.version2.JalviewModelSequence jalviewModelSequence)
-    {
-        this._jalviewModelSequence = jalviewModelSequence;
-    } //-- void setJalviewModelSequence(jalview.schemabinding.version2.JalviewModelSequence) 
-
-    /**
-     * Sets the value of field 'vamsasModel'.
-     * 
-     * @param vamsasModel the value of field 'vamsasModel'.
-     */
-    public void setVamsasModel(jalview.schemabinding.version2.VamsasModel vamsasModel)
-    {
-        this._vamsasModel = vamsasModel;
-    } //-- void setVamsasModel(jalview.schemabinding.version2.VamsasModel) 
-
-    /**
-     * Sets the value of field 'version'.
-     * 
-     * @param version the value of field 'version'.
-     */
-    public void setVersion(java.lang.String version)
-    {
-        this._version = version;
-    } //-- void setVersion(java.lang.String) 
-
-    /**
-     * Method unmarshal
-     * 
-     * 
-     * 
-     * @param reader
-     * @return Object
-     */
-    public static java.lang.Object unmarshal(java.io.Reader reader)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+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();
+  } //-- jalview.schemabinding.version2.JalviewModel()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Returns the value of field 'creationDate'.
+   *
+   * @return Date
+   * @return the value of field 'creationDate'.
+   */
+  public java.util.Date getCreationDate()
+  {
+    return this._creationDate;
+  } //-- java.util.Date getCreationDate()
+
+  /**
+   * Returns the value of field 'jalviewModelSequence'.
+   *
+   * @return JalviewModelSequence
+   * @return the value of field 'jalviewModelSequence'.
+   */
+  public jalview.schemabinding.version2.JalviewModelSequence
+      getJalviewModelSequence()
+  {
+    return this._jalviewModelSequence;
+  } //-- jalview.schemabinding.version2.JalviewModelSequence getJalviewModelSequence()
+
+  /**
+   * Returns the value of field 'vamsasModel'.
+   *
+   * @return VamsasModel
+   * @return the value of field 'vamsasModel'.
+   */
+  public jalview.schemabinding.version2.VamsasModel getVamsasModel()
+  {
+    return this._vamsasModel;
+  } //-- jalview.schemabinding.version2.VamsasModel getVamsasModel()
+
+  /**
+   * Returns the value of field 'version'.
+   *
+   * @return String
+   * @return the value of field 'version'.
+   */
+  public java.lang.String getVersion()
+  {
+    return this._version;
+  } //-- java.lang.String getVersion()
+
+  /**
+   * Method isValid
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean isValid()
+  {
+    try
     {
-        return (jalview.schemabinding.version2.JalviewModel) Unmarshaller.unmarshal(jalview.schemabinding.version2.JalviewModel.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
-
-    /**
-     * Method validate
-     * 
-     */
-    public void validate()
-        throws org.exolab.castor.xml.ValidationException
+      validate();
+    }
+    catch (org.exolab.castor.xml.ValidationException vex)
     {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    } //-- void validate() 
+      return false;
+    }
+    return true;
+  } //-- boolean isValid()
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param out
+   */
+  public void marshal(java.io.Writer out)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, out);
+  } //-- void marshal(java.io.Writer)
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param handler
+   */
+  public void marshal(org.xml.sax.ContentHandler handler)
+      throws java.io.IOException, org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, handler);
+  } //-- void marshal(org.xml.sax.ContentHandler)
+
+  /**
+   * Sets the value of field 'creationDate'.
+   *
+   * @param creationDate the value of field 'creationDate'.
+   */
+  public void setCreationDate(java.util.Date creationDate)
+  {
+    this._creationDate = creationDate;
+  } //-- void setCreationDate(java.util.Date)
+
+  /**
+   * Sets the value of field 'jalviewModelSequence'.
+   *
+   * @param jalviewModelSequence the value of field
+   * 'jalviewModelSequence'.
+   */
+  public void setJalviewModelSequence(jalview.schemabinding.version2.
+                                      JalviewModelSequence jalviewModelSequence)
+  {
+    this._jalviewModelSequence = jalviewModelSequence;
+  } //-- void setJalviewModelSequence(jalview.schemabinding.version2.JalviewModelSequence)
+
+  /**
+   * Sets the value of field 'vamsasModel'.
+   *
+   * @param vamsasModel the value of field 'vamsasModel'.
+   */
+  public void setVamsasModel(jalview.schemabinding.version2.VamsasModel
+                             vamsasModel)
+  {
+    this._vamsasModel = vamsasModel;
+  } //-- void setVamsasModel(jalview.schemabinding.version2.VamsasModel)
+
+  /**
+   * Sets the value of field 'version'.
+   *
+   * @param version the value of field 'version'.
+   */
+  public void setVersion(java.lang.String version)
+  {
+    this._version = version;
+  } //-- void setVersion(java.lang.String)
+
+  /**
+   * Method unmarshal
+   *
+   *
+   *
+   * @param reader
+   * @return Object
+   */
+  public static java.lang.Object unmarshal(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);
+  } //-- java.lang.Object unmarshal(java.io.Reader)
+
+  /**
+   * Method validate
+   *
+   */
+  public void validate()
+      throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.
+        Validator();
+    validator.validate(this);
+  } //-- void validate()
 
 }
diff --git a/src/jalview/schemabinding/version2/JalviewModelDescriptor.java b/src/jalview/schemabinding/version2/JalviewModelDescriptor.java
index ad2dc13..a9440e5 100755
--- a/src/jalview/schemabinding/version2/JalviewModelDescriptor.java
+++ b/src/jalview/schemabinding/version2/JalviewModelDescriptor.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,318 +7,350 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
-import org.exolab.castor.mapping.AccessMode;
-import org.exolab.castor.xml.TypeValidator;
-import org.exolab.castor.xml.XMLFieldDescriptor;
 import org.exolab.castor.xml.validators.*;
 
 /**
  * Class JalviewModelDescriptor.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class JalviewModelDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field nsPrefix
-     */
-    private java.lang.String nsPrefix;
-
-    /**
-     * Field nsURI
-     */
-    private java.lang.String nsURI;
-
-    /**
-     * Field xmlName
-     */
-    private java.lang.String xmlName;
-
-    /**
-     * Field identity
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor identity;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public JalviewModelDescriptor() {
-        super();
-        nsURI = "www.jalview.org";
-        xmlName = "JalviewModel";
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.xml.XMLFieldHandler              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();
-            }
-        } );
-        desc.setHandler( new org.exolab.castor.xml.handlers.DateFieldHandler(handler));
-        desc.setImmutable(true);
-        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
+public class JalviewModelDescriptor
+    extends org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  //--------------------------/
+  //- Class/Member Variables -/
+  //--------------------------/
+
+  /**
+   * Field nsPrefix
+   */
+  private java.lang.String nsPrefix;
+
+  /**
+   * Field nsURI
+   */
+  private java.lang.String nsURI;
+
+  /**
+   * Field xmlName
+   */
+  private java.lang.String xmlName;
+
+  /**
+   * Field identity
+   */
+  private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+  //----------------/
+  //- Constructors -/
+  //----------------/
+
+  public JalviewModelDescriptor()
+  {
+    super();
+    nsURI = "www.jalview.org";
+    xmlName = "JalviewModel";
+
+    //-- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.xml.XMLFieldHandler 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);
         }
-        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
-            StringValidator typeValidator = new StringValidator();
-            typeValidator.setWhiteSpace("preserve");
-            fieldValidator.setValidator(typeValidator);
+        catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        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
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new java.util.Date();
+      }
+    });
+    desc.setHandler(new org.exolab.castor.xml.handlers.DateFieldHandler(handler));
+    desc.setImmutable(true);
+    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
+    }
+    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);
         }
-        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.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
+        catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-    } //-- jalview.schemabinding.version2.JalviewModelDescriptor()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method getAccessMode
-     * 
-     * 
-     * 
-     * @return AccessMode
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode()
-    {
-        return null;
-    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
-
-    /**
-     * Method getExtends
-     * 
-     * 
-     * 
-     * @return ClassDescriptor
-     */
-    public org.exolab.castor.mapping.ClassDescriptor getExtends()
-    {
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
-
-    /**
-     * Method getIdentity
-     * 
-     * 
-     * 
-     * @return FieldDescriptor
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
-    {
-        return identity;
-    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
-
-    /**
-     * Method getJavaClass
-     * 
-     * 
-     * 
-     * @return Class
-     */
-    public java.lang.Class getJavaClass()
-    {
-        return jalview.schemabinding.version2.JalviewModel.class;
-    } //-- java.lang.Class getJavaClass() 
-
-    /**
-     * Method getNameSpacePrefix
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpacePrefix()
-    {
-        return nsPrefix;
-    } //-- java.lang.String getNameSpacePrefix() 
-
-    /**
-     * Method getNameSpaceURI
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpaceURI()
-    {
-        return nsURI;
-    } //-- java.lang.String getNameSpaceURI() 
-
-    /**
-     * Method getValidator
-     * 
-     * 
-     * 
-     * @return TypeValidator
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator()
+      }
+    });
+    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
+      StringValidator typeValidator = new StringValidator();
+      typeValidator.setWhiteSpace("preserve");
+      fieldValidator.setValidator(typeValidator);
+    }
+    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()
     {
-        return this;
-    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
-
-    /**
-     * Method getXMLName
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getXMLName()
+      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()
     {
-        return xmlName;
-    } //-- java.lang.String getXMLName() 
+      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.
+                            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
+    }
+    desc.setValidator(fieldValidator);
+  } //-- jalview.schemabinding.version2.JalviewModelDescriptor()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Method getAccessMode
+   *
+   *
+   *
+   * @return AccessMode
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
+
+  /**
+   * Method getExtends
+   *
+   *
+   *
+   * @return ClassDescriptor
+   */
+  public org.exolab.castor.mapping.ClassDescriptor getExtends()
+  {
+    return null;
+  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
+
+  /**
+   * Method getIdentity
+   *
+   *
+   *
+   * @return FieldDescriptor
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return identity;
+  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
+
+  /**
+   * Method getJavaClass
+   *
+   *
+   *
+   * @return Class
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.JalviewModel.class;
+  } //-- java.lang.Class getJavaClass()
+
+  /**
+   * Method getNameSpacePrefix
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return nsPrefix;
+  } //-- java.lang.String getNameSpacePrefix()
+
+  /**
+   * Method getNameSpaceURI
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return nsURI;
+  } //-- java.lang.String getNameSpaceURI()
+
+  /**
+   * Method getValidator
+   *
+   *
+   *
+   * @return TypeValidator
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  } //-- org.exolab.castor.xml.TypeValidator getValidator()
+
+  /**
+   * Method getXMLName
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getXMLName()
+  {
+    return xmlName;
+  } //-- java.lang.String getXMLName()
 
 }
diff --git a/src/jalview/schemabinding/version2/JalviewModelSequence.java b/src/jalview/schemabinding/version2/JalviewModelSequence.java
index 45f486b..ba0c4c8 100755
--- a/src/jalview/schemabinding/version2/JalviewModelSequence.java
+++ b/src/jalview/schemabinding/version2/JalviewModelSequence.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,898 +7,942 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
 //---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import java.util.*;
 
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import java.util.Enumeration;
-import java.util.Vector;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
+import org.exolab.castor.xml.*;
 
 /**
  * Class JalviewModelSequence.
- * 
+ *
  * @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();
-        _JSeqList = new Vector();
-        _JGroupList = new Vector();
-        _viewportList = new Vector();
-        _userColoursList = new Vector();
-        _treeList = new Vector();
-    } //-- jalview.schemabinding.version2.JalviewModelSequence()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method addJGroup
-     * 
-     * 
-     * 
-     * @param vJGroup
-     */
-    public void addJGroup(jalview.schemabinding.version2.JGroup vJGroup)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _JGroupList.addElement(vJGroup);
-    } //-- void addJGroup(jalview.schemabinding.version2.JGroup) 
-
-    /**
-     * Method addJGroup
-     * 
-     * 
-     * 
-     * @param index
-     * @param vJGroup
-     */
-    public void addJGroup(int index, jalview.schemabinding.version2.JGroup vJGroup)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _JGroupList.insertElementAt(vJGroup, index);
-    } //-- void addJGroup(int, jalview.schemabinding.version2.JGroup) 
-
-    /**
-     * Method addJSeq
-     * 
-     * 
-     * 
-     * @param vJSeq
-     */
-    public void addJSeq(jalview.schemabinding.version2.JSeq vJSeq)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _JSeqList.addElement(vJSeq);
-    } //-- void addJSeq(jalview.schemabinding.version2.JSeq) 
-
-    /**
-     * Method addJSeq
-     * 
-     * 
-     * 
-     * @param index
-     * @param vJSeq
-     */
-    public void addJSeq(int index, jalview.schemabinding.version2.JSeq vJSeq)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _JSeqList.insertElementAt(vJSeq, index);
-    } //-- void addJSeq(int, jalview.schemabinding.version2.JSeq) 
-
-    /**
-     * Method addTree
-     * 
-     * 
-     * 
-     * @param vTree
-     */
-    public void addTree(jalview.schemabinding.version2.Tree vTree)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _treeList.addElement(vTree);
-    } //-- void addTree(jalview.schemabinding.version2.Tree) 
-
-    /**
-     * Method addTree
-     * 
-     * 
-     * 
-     * @param index
-     * @param vTree
-     */
-    public void addTree(int index, jalview.schemabinding.version2.Tree vTree)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _treeList.insertElementAt(vTree, index);
-    } //-- void addTree(int, jalview.schemabinding.version2.Tree) 
-
-    /**
-     * Method addUserColours
-     * 
-     * 
-     * 
-     * @param vUserColours
-     */
-    public void addUserColours(jalview.schemabinding.version2.UserColours vUserColours)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _userColoursList.addElement(vUserColours);
-    } //-- void addUserColours(jalview.schemabinding.version2.UserColours) 
-
-    /**
-     * Method addUserColours
-     * 
-     * 
-     * 
-     * @param index
-     * @param vUserColours
-     */
-    public void addUserColours(int index, jalview.schemabinding.version2.UserColours vUserColours)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _userColoursList.insertElementAt(vUserColours, index);
-    } //-- void addUserColours(int, jalview.schemabinding.version2.UserColours) 
-
-    /**
-     * Method addViewport
-     * 
-     * 
-     * 
-     * @param vViewport
-     */
-    public void addViewport(jalview.schemabinding.version2.Viewport vViewport)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _viewportList.addElement(vViewport);
-    } //-- void addViewport(jalview.schemabinding.version2.Viewport) 
-
-    /**
-     * Method addViewport
-     * 
-     * 
-     * 
-     * @param index
-     * @param vViewport
-     */
-    public void addViewport(int index, jalview.schemabinding.version2.Viewport vViewport)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _viewportList.insertElementAt(vViewport, index);
-    } //-- void addViewport(int, jalview.schemabinding.version2.Viewport) 
-
-    /**
-     * Method enumerateJGroup
-     * 
-     * 
-     * 
-     * @return Enumeration
-     */
-    public java.util.Enumeration enumerateJGroup()
-    {
-        return _JGroupList.elements();
-    } //-- java.util.Enumeration enumerateJGroup() 
-
-    /**
-     * Method enumerateJSeq
-     * 
-     * 
-     * 
-     * @return Enumeration
-     */
-    public java.util.Enumeration enumerateJSeq()
-    {
-        return _JSeqList.elements();
-    } //-- java.util.Enumeration enumerateJSeq() 
-
-    /**
-     * Method enumerateTree
-     * 
-     * 
-     * 
-     * @return Enumeration
-     */
-    public java.util.Enumeration enumerateTree()
-    {
-        return _treeList.elements();
-    } //-- java.util.Enumeration enumerateTree() 
-
-    /**
-     * Method enumerateUserColours
-     * 
-     * 
-     * 
-     * @return Enumeration
-     */
-    public java.util.Enumeration enumerateUserColours()
-    {
-        return _userColoursList.elements();
-    } //-- java.util.Enumeration enumerateUserColours() 
-
-    /**
-     * Method enumerateViewport
-     * 
-     * 
-     * 
-     * @return Enumeration
-     */
-    public java.util.Enumeration enumerateViewport()
-    {
-        return _viewportList.elements();
-    } //-- java.util.Enumeration enumerateViewport() 
-
-    /**
-     * Returns the value of field 'featureSettings'.
-     * 
-     * @return FeatureSettings
-     * @return the value of field 'featureSettings'.
-     */
-    public jalview.schemabinding.version2.FeatureSettings getFeatureSettings()
-    {
-        return this._featureSettings;
-    } //-- jalview.schemabinding.version2.FeatureSettings getFeatureSettings() 
-
-    /**
-     * Method getJGroup
-     * 
-     * 
-     * 
-     * @param index
-     * @return JGroup
-     */
-    public jalview.schemabinding.version2.JGroup getJGroup(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _JGroupList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        
-        return (jalview.schemabinding.version2.JGroup) _JGroupList.elementAt(index);
-    } //-- jalview.schemabinding.version2.JGroup getJGroup(int) 
-
-    /**
-     * Method getJGroup
-     * 
-     * 
-     * 
-     * @return JGroup
-     */
-    public jalview.schemabinding.version2.JGroup[] getJGroup()
-    {
-        int size = _JGroupList.size();
-        jalview.schemabinding.version2.JGroup[] mArray = new jalview.schemabinding.version2.JGroup[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = (jalview.schemabinding.version2.JGroup) _JGroupList.elementAt(index);
-        }
-        return mArray;
-    } //-- jalview.schemabinding.version2.JGroup[] getJGroup() 
-
-    /**
-     * Method getJGroupCount
-     * 
-     * 
-     * 
-     * @return int
-     */
-    public int getJGroupCount()
-    {
-        return _JGroupList.size();
-    } //-- int getJGroupCount() 
-
-    /**
-     * Method getJSeq
-     * 
-     * 
-     * 
-     * @param index
-     * @return JSeq
-     */
-    public jalview.schemabinding.version2.JSeq getJSeq(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _JSeqList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        
-        return (jalview.schemabinding.version2.JSeq) _JSeqList.elementAt(index);
-    } //-- jalview.schemabinding.version2.JSeq getJSeq(int) 
-
-    /**
-     * Method getJSeq
-     * 
-     * 
-     * 
-     * @return JSeq
-     */
-    public jalview.schemabinding.version2.JSeq[] getJSeq()
-    {
-        int size = _JSeqList.size();
-        jalview.schemabinding.version2.JSeq[] mArray = new jalview.schemabinding.version2.JSeq[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = (jalview.schemabinding.version2.JSeq) _JSeqList.elementAt(index);
-        }
-        return mArray;
-    } //-- jalview.schemabinding.version2.JSeq[] getJSeq() 
-
-    /**
-     * Method getJSeqCount
-     * 
-     * 
-     * 
-     * @return int
-     */
-    public int getJSeqCount()
-    {
-        return _JSeqList.size();
-    } //-- int getJSeqCount() 
-
-    /**
-     * Method getTree
-     * 
-     * 
-     * 
-     * @param index
-     * @return Tree
-     */
-    public jalview.schemabinding.version2.Tree getTree(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _treeList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        
-        return (jalview.schemabinding.version2.Tree) _treeList.elementAt(index);
-    } //-- jalview.schemabinding.version2.Tree getTree(int) 
-
-    /**
-     * Method getTree
-     * 
-     * 
-     * 
-     * @return Tree
-     */
-    public jalview.schemabinding.version2.Tree[] getTree()
-    {
-        int size = _treeList.size();
-        jalview.schemabinding.version2.Tree[] mArray = new jalview.schemabinding.version2.Tree[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = (jalview.schemabinding.version2.Tree) _treeList.elementAt(index);
-        }
-        return mArray;
-    } //-- jalview.schemabinding.version2.Tree[] getTree() 
-
-    /**
-     * Method getTreeCount
-     * 
-     * 
-     * 
-     * @return int
-     */
-    public int getTreeCount()
-    {
-        return _treeList.size();
-    } //-- int getTreeCount() 
-
-    /**
-     * Method getUserColours
-     * 
-     * 
-     * 
-     * @param index
-     * @return UserColours
-     */
-    public jalview.schemabinding.version2.UserColours getUserColours(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _userColoursList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        
-        return (jalview.schemabinding.version2.UserColours) _userColoursList.elementAt(index);
-    } //-- jalview.schemabinding.version2.UserColours getUserColours(int) 
-
-    /**
-     * Method getUserColours
-     * 
-     * 
-     * 
-     * @return UserColours
-     */
-    public jalview.schemabinding.version2.UserColours[] getUserColours()
-    {
-        int size = _userColoursList.size();
-        jalview.schemabinding.version2.UserColours[] mArray = new jalview.schemabinding.version2.UserColours[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = (jalview.schemabinding.version2.UserColours) _userColoursList.elementAt(index);
-        }
-        return mArray;
-    } //-- jalview.schemabinding.version2.UserColours[] getUserColours() 
-
-    /**
-     * Method getUserColoursCount
-     * 
-     * 
-     * 
-     * @return int
-     */
-    public int getUserColoursCount()
-    {
-        return _userColoursList.size();
-    } //-- int getUserColoursCount() 
-
-    /**
-     * Method getViewport
-     * 
-     * 
-     * 
-     * @param index
-     * @return Viewport
-     */
-    public jalview.schemabinding.version2.Viewport getViewport(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _viewportList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        
-        return (jalview.schemabinding.version2.Viewport) _viewportList.elementAt(index);
-    } //-- jalview.schemabinding.version2.Viewport getViewport(int) 
-
-    /**
-     * Method getViewport
-     * 
-     * 
-     * 
-     * @return Viewport
-     */
-    public jalview.schemabinding.version2.Viewport[] getViewport()
-    {
-        int size = _viewportList.size();
-        jalview.schemabinding.version2.Viewport[] mArray = new jalview.schemabinding.version2.Viewport[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = (jalview.schemabinding.version2.Viewport) _viewportList.elementAt(index);
-        }
-        return mArray;
-    } //-- jalview.schemabinding.version2.Viewport[] getViewport() 
-
-    /**
-     * Method getViewportCount
-     * 
-     * 
-     * 
-     * @return int
-     */
-    public int getViewportCount()
-    {
-        return _viewportList.size();
-    } //-- int getViewportCount() 
-
-    /**
-     * Method isValid
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean isValid()
-    {
-        try {
-            validate();
-        }
-        catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    } //-- boolean isValid() 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param out
-     */
-    public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, out);
-    } //-- void marshal(java.io.Writer) 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param handler
-     */
-    public void marshal(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, handler);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
-
-    /**
-     * Method removeAllJGroup
-     * 
-     */
-    public void removeAllJGroup()
-    {
-        _JGroupList.removeAllElements();
-    } //-- void removeAllJGroup() 
-
-    /**
-     * Method removeAllJSeq
-     * 
-     */
-    public void removeAllJSeq()
-    {
-        _JSeqList.removeAllElements();
-    } //-- void removeAllJSeq() 
-
-    /**
-     * Method removeAllTree
-     * 
-     */
-    public void removeAllTree()
-    {
-        _treeList.removeAllElements();
-    } //-- void removeAllTree() 
-
-    /**
-     * Method removeAllUserColours
-     * 
-     */
-    public void removeAllUserColours()
-    {
-        _userColoursList.removeAllElements();
-    } //-- void removeAllUserColours() 
-
-    /**
-     * Method removeAllViewport
-     * 
-     */
-    public void removeAllViewport()
-    {
-        _viewportList.removeAllElements();
-    } //-- void removeAllViewport() 
-
-    /**
-     * Method removeJGroup
-     * 
-     * 
-     * 
-     * @param index
-     * @return JGroup
-     */
-    public jalview.schemabinding.version2.JGroup removeJGroup(int index)
-    {
-        java.lang.Object obj = _JGroupList.elementAt(index);
-        _JGroupList.removeElementAt(index);
-        return (jalview.schemabinding.version2.JGroup) obj;
-    } //-- jalview.schemabinding.version2.JGroup removeJGroup(int) 
-
-    /**
-     * Method removeJSeq
-     * 
-     * 
-     * 
-     * @param index
-     * @return JSeq
-     */
-    public jalview.schemabinding.version2.JSeq removeJSeq(int index)
-    {
-        java.lang.Object obj = _JSeqList.elementAt(index);
-        _JSeqList.removeElementAt(index);
-        return (jalview.schemabinding.version2.JSeq) obj;
-    } //-- jalview.schemabinding.version2.JSeq removeJSeq(int) 
-
-    /**
-     * Method removeTree
-     * 
-     * 
-     * 
-     * @param index
-     * @return Tree
-     */
-    public jalview.schemabinding.version2.Tree removeTree(int index)
-    {
-        java.lang.Object obj = _treeList.elementAt(index);
-        _treeList.removeElementAt(index);
-        return (jalview.schemabinding.version2.Tree) obj;
-    } //-- jalview.schemabinding.version2.Tree removeTree(int) 
-
-    /**
-     * Method removeUserColours
-     * 
-     * 
-     * 
-     * @param index
-     * @return UserColours
-     */
-    public jalview.schemabinding.version2.UserColours removeUserColours(int index)
-    {
-        java.lang.Object obj = _userColoursList.elementAt(index);
-        _userColoursList.removeElementAt(index);
-        return (jalview.schemabinding.version2.UserColours) obj;
-    } //-- jalview.schemabinding.version2.UserColours removeUserColours(int) 
-
-    /**
-     * Method removeViewport
-     * 
-     * 
-     * 
-     * @param index
-     * @return Viewport
-     */
-    public jalview.schemabinding.version2.Viewport removeViewport(int index)
-    {
-        java.lang.Object obj = _viewportList.elementAt(index);
-        _viewportList.removeElementAt(index);
-        return (jalview.schemabinding.version2.Viewport) obj;
-    } //-- jalview.schemabinding.version2.Viewport removeViewport(int) 
-
-    /**
-     * Sets the value of field 'featureSettings'.
-     * 
-     * @param featureSettings the value of field 'featureSettings'.
-     */
-    public void setFeatureSettings(jalview.schemabinding.version2.FeatureSettings featureSettings)
-    {
-        this._featureSettings = featureSettings;
-    } //-- void setFeatureSettings(jalview.schemabinding.version2.FeatureSettings) 
-
-    /**
-     * Method setJGroup
-     * 
-     * 
-     * 
-     * @param index
-     * @param vJGroup
-     */
-    public void setJGroup(int index, jalview.schemabinding.version2.JGroup vJGroup)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _JGroupList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        _JGroupList.setElementAt(vJGroup, index);
-    } //-- void setJGroup(int, jalview.schemabinding.version2.JGroup) 
-
-    /**
-     * Method setJGroup
-     * 
-     * 
-     * 
-     * @param JGroupArray
-     */
-    public void setJGroup(jalview.schemabinding.version2.JGroup[] JGroupArray)
-    {
-        //-- copy array
-        _JGroupList.removeAllElements();
-        for (int i = 0; i < JGroupArray.length; i++) {
-            _JGroupList.addElement(JGroupArray[i]);
-        }
-    } //-- void setJGroup(jalview.schemabinding.version2.JGroup) 
-
-    /**
-     * Method setJSeq
-     * 
-     * 
-     * 
-     * @param index
-     * @param vJSeq
-     */
-    public void setJSeq(int index, jalview.schemabinding.version2.JSeq vJSeq)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _JSeqList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        _JSeqList.setElementAt(vJSeq, index);
-    } //-- void setJSeq(int, jalview.schemabinding.version2.JSeq) 
-
-    /**
-     * Method setJSeq
-     * 
-     * 
-     * 
-     * @param JSeqArray
-     */
-    public void setJSeq(jalview.schemabinding.version2.JSeq[] JSeqArray)
-    {
-        //-- copy array
-        _JSeqList.removeAllElements();
-        for (int i = 0; i < JSeqArray.length; i++) {
-            _JSeqList.addElement(JSeqArray[i]);
-        }
-    } //-- void setJSeq(jalview.schemabinding.version2.JSeq) 
-
-    /**
-     * Method setTree
-     * 
-     * 
-     * 
-     * @param index
-     * @param vTree
-     */
-    public void setTree(int index, jalview.schemabinding.version2.Tree vTree)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _treeList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        _treeList.setElementAt(vTree, index);
-    } //-- void setTree(int, jalview.schemabinding.version2.Tree) 
-
-    /**
-     * Method setTree
-     * 
-     * 
-     * 
-     * @param treeArray
-     */
-    public void setTree(jalview.schemabinding.version2.Tree[] treeArray)
-    {
-        //-- copy array
-        _treeList.removeAllElements();
-        for (int i = 0; i < treeArray.length; i++) {
-            _treeList.addElement(treeArray[i]);
-        }
-    } //-- void setTree(jalview.schemabinding.version2.Tree) 
-
-    /**
-     * Method setUserColours
-     * 
-     * 
-     * 
-     * @param index
-     * @param vUserColours
-     */
-    public void setUserColours(int index, jalview.schemabinding.version2.UserColours vUserColours)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _userColoursList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        _userColoursList.setElementAt(vUserColours, index);
-    } //-- void setUserColours(int, jalview.schemabinding.version2.UserColours) 
-
-    /**
-     * Method setUserColours
-     * 
-     * 
-     * 
-     * @param userColoursArray
-     */
-    public void setUserColours(jalview.schemabinding.version2.UserColours[] userColoursArray)
-    {
-        //-- copy array
-        _userColoursList.removeAllElements();
-        for (int i = 0; i < userColoursArray.length; i++) {
-            _userColoursList.addElement(userColoursArray[i]);
-        }
-    } //-- void setUserColours(jalview.schemabinding.version2.UserColours) 
-
-    /**
-     * Method setViewport
-     * 
-     * 
-     * 
-     * @param index
-     * @param vViewport
-     */
-    public void setViewport(int index, jalview.schemabinding.version2.Viewport vViewport)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _viewportList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        _viewportList.setElementAt(vViewport, index);
-    } //-- void setViewport(int, jalview.schemabinding.version2.Viewport) 
-
-    /**
-     * Method setViewport
-     * 
-     * 
-     * 
-     * @param viewportArray
-     */
-    public void setViewport(jalview.schemabinding.version2.Viewport[] viewportArray)
-    {
-        //-- copy array
-        _viewportList.removeAllElements();
-        for (int i = 0; i < viewportArray.length; i++) {
-            _viewportList.addElement(viewportArray[i]);
-        }
-    } //-- void setViewport(jalview.schemabinding.version2.Viewport) 
-
-    /**
-     * Method unmarshal
-     * 
-     * 
-     * 
-     * @param reader
-     * @return Object
-     */
-    public static java.lang.Object unmarshal(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);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
-
-    /**
-     * Method validate
-     * 
-     */
-    public void validate()
-        throws org.exolab.castor.xml.ValidationException
-    {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    } //-- void validate() 
+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();
+    _JSeqList = new Vector();
+    _JGroupList = new Vector();
+    _viewportList = new Vector();
+    _userColoursList = new Vector();
+    _treeList = new Vector();
+  } //-- jalview.schemabinding.version2.JalviewModelSequence()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Method addJGroup
+   *
+   *
+   *
+   * @param vJGroup
+   */
+  public void addJGroup(jalview.schemabinding.version2.JGroup vJGroup)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _JGroupList.addElement(vJGroup);
+  } //-- void addJGroup(jalview.schemabinding.version2.JGroup)
+
+  /**
+   * Method addJGroup
+   *
+   *
+   *
+   * @param index
+   * @param vJGroup
+   */
+  public void addJGroup(int index,
+                        jalview.schemabinding.version2.JGroup vJGroup)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _JGroupList.insertElementAt(vJGroup, index);
+  } //-- void addJGroup(int, jalview.schemabinding.version2.JGroup)
+
+  /**
+   * Method addJSeq
+   *
+   *
+   *
+   * @param vJSeq
+   */
+  public void addJSeq(jalview.schemabinding.version2.JSeq vJSeq)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _JSeqList.addElement(vJSeq);
+  } //-- void addJSeq(jalview.schemabinding.version2.JSeq)
+
+  /**
+   * Method addJSeq
+   *
+   *
+   *
+   * @param index
+   * @param vJSeq
+   */
+  public void addJSeq(int index, jalview.schemabinding.version2.JSeq vJSeq)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _JSeqList.insertElementAt(vJSeq, index);
+  } //-- void addJSeq(int, jalview.schemabinding.version2.JSeq)
+
+  /**
+   * Method addTree
+   *
+   *
+   *
+   * @param vTree
+   */
+  public void addTree(jalview.schemabinding.version2.Tree vTree)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _treeList.addElement(vTree);
+  } //-- void addTree(jalview.schemabinding.version2.Tree)
+
+  /**
+   * Method addTree
+   *
+   *
+   *
+   * @param index
+   * @param vTree
+   */
+  public void addTree(int index, jalview.schemabinding.version2.Tree vTree)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _treeList.insertElementAt(vTree, index);
+  } //-- void addTree(int, jalview.schemabinding.version2.Tree)
+
+  /**
+   * Method addUserColours
+   *
+   *
+   *
+   * @param vUserColours
+   */
+  public void addUserColours(jalview.schemabinding.version2.UserColours
+                             vUserColours)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _userColoursList.addElement(vUserColours);
+  } //-- void addUserColours(jalview.schemabinding.version2.UserColours)
+
+  /**
+   * Method addUserColours
+   *
+   *
+   *
+   * @param index
+   * @param vUserColours
+   */
+  public void addUserColours(int index,
+                             jalview.schemabinding.version2.UserColours
+                             vUserColours)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _userColoursList.insertElementAt(vUserColours, index);
+  } //-- void addUserColours(int, jalview.schemabinding.version2.UserColours)
+
+  /**
+   * Method addViewport
+   *
+   *
+   *
+   * @param vViewport
+   */
+  public void addViewport(jalview.schemabinding.version2.Viewport vViewport)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _viewportList.addElement(vViewport);
+  } //-- void addViewport(jalview.schemabinding.version2.Viewport)
+
+  /**
+   * Method addViewport
+   *
+   *
+   *
+   * @param index
+   * @param vViewport
+   */
+  public void addViewport(int index,
+                          jalview.schemabinding.version2.Viewport vViewport)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _viewportList.insertElementAt(vViewport, index);
+  } //-- void addViewport(int, jalview.schemabinding.version2.Viewport)
+
+  /**
+   * Method enumerateJGroup
+   *
+   *
+   *
+   * @return Enumeration
+   */
+  public java.util.Enumeration enumerateJGroup()
+  {
+    return _JGroupList.elements();
+  } //-- java.util.Enumeration enumerateJGroup()
+
+  /**
+   * Method enumerateJSeq
+   *
+   *
+   *
+   * @return Enumeration
+   */
+  public java.util.Enumeration enumerateJSeq()
+  {
+    return _JSeqList.elements();
+  } //-- java.util.Enumeration enumerateJSeq()
+
+  /**
+   * Method enumerateTree
+   *
+   *
+   *
+   * @return Enumeration
+   */
+  public java.util.Enumeration enumerateTree()
+  {
+    return _treeList.elements();
+  } //-- java.util.Enumeration enumerateTree()
+
+  /**
+   * Method enumerateUserColours
+   *
+   *
+   *
+   * @return Enumeration
+   */
+  public java.util.Enumeration enumerateUserColours()
+  {
+    return _userColoursList.elements();
+  } //-- java.util.Enumeration enumerateUserColours()
+
+  /**
+   * Method enumerateViewport
+   *
+   *
+   *
+   * @return Enumeration
+   */
+  public java.util.Enumeration enumerateViewport()
+  {
+    return _viewportList.elements();
+  } //-- java.util.Enumeration enumerateViewport()
+
+  /**
+   * Returns the value of field 'featureSettings'.
+   *
+   * @return FeatureSettings
+   * @return the value of field 'featureSettings'.
+   */
+  public jalview.schemabinding.version2.FeatureSettings getFeatureSettings()
+  {
+    return this._featureSettings;
+  } //-- jalview.schemabinding.version2.FeatureSettings getFeatureSettings()
+
+  /**
+   * Method getJGroup
+   *
+   *
+   *
+   * @param index
+   * @return JGroup
+   */
+  public jalview.schemabinding.version2.JGroup getJGroup(int index)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _JGroupList.size()))
+    {
+      throw new IndexOutOfBoundsException();
+    }
+
+    return (jalview.schemabinding.version2.JGroup) _JGroupList.elementAt(index);
+  } //-- jalview.schemabinding.version2.JGroup getJGroup(int)
+
+  /**
+   * Method getJGroup
+   *
+   *
+   *
+   * @return JGroup
+   */
+  public jalview.schemabinding.version2.JGroup[] getJGroup()
+  {
+    int size = _JGroupList.size();
+    jalview.schemabinding.version2.JGroup[] mArray = new jalview.schemabinding.
+        version2.JGroup[size];
+    for (int index = 0; index < size; index++)
+    {
+      mArray[index] = (jalview.schemabinding.version2.JGroup) _JGroupList.
+          elementAt(index);
+    }
+    return mArray;
+  } //-- jalview.schemabinding.version2.JGroup[] getJGroup()
+
+  /**
+   * Method getJGroupCount
+   *
+   *
+   *
+   * @return int
+   */
+  public int getJGroupCount()
+  {
+    return _JGroupList.size();
+  } //-- int getJGroupCount()
+
+  /**
+   * Method getJSeq
+   *
+   *
+   *
+   * @param index
+   * @return JSeq
+   */
+  public jalview.schemabinding.version2.JSeq getJSeq(int index)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _JSeqList.size()))
+    {
+      throw new IndexOutOfBoundsException();
+    }
+
+    return (jalview.schemabinding.version2.JSeq) _JSeqList.elementAt(index);
+  } //-- jalview.schemabinding.version2.JSeq getJSeq(int)
+
+  /**
+   * Method getJSeq
+   *
+   *
+   *
+   * @return JSeq
+   */
+  public jalview.schemabinding.version2.JSeq[] getJSeq()
+  {
+    int size = _JSeqList.size();
+    jalview.schemabinding.version2.JSeq[] mArray = new jalview.schemabinding.
+        version2.JSeq[size];
+    for (int index = 0; index < size; index++)
+    {
+      mArray[index] = (jalview.schemabinding.version2.JSeq) _JSeqList.elementAt(
+          index);
+    }
+    return mArray;
+  } //-- jalview.schemabinding.version2.JSeq[] getJSeq()
+
+  /**
+   * Method getJSeqCount
+   *
+   *
+   *
+   * @return int
+   */
+  public int getJSeqCount()
+  {
+    return _JSeqList.size();
+  } //-- int getJSeqCount()
+
+  /**
+   * Method getTree
+   *
+   *
+   *
+   * @param index
+   * @return Tree
+   */
+  public jalview.schemabinding.version2.Tree getTree(int index)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _treeList.size()))
+    {
+      throw new IndexOutOfBoundsException();
+    }
+
+    return (jalview.schemabinding.version2.Tree) _treeList.elementAt(index);
+  } //-- jalview.schemabinding.version2.Tree getTree(int)
+
+  /**
+   * Method getTree
+   *
+   *
+   *
+   * @return Tree
+   */
+  public jalview.schemabinding.version2.Tree[] getTree()
+  {
+    int size = _treeList.size();
+    jalview.schemabinding.version2.Tree[] mArray = new jalview.schemabinding.
+        version2.Tree[size];
+    for (int index = 0; index < size; index++)
+    {
+      mArray[index] = (jalview.schemabinding.version2.Tree) _treeList.elementAt(
+          index);
+    }
+    return mArray;
+  } //-- jalview.schemabinding.version2.Tree[] getTree()
+
+  /**
+   * Method getTreeCount
+   *
+   *
+   *
+   * @return int
+   */
+  public int getTreeCount()
+  {
+    return _treeList.size();
+  } //-- int getTreeCount()
+
+  /**
+   * Method getUserColours
+   *
+   *
+   *
+   * @param index
+   * @return UserColours
+   */
+  public jalview.schemabinding.version2.UserColours getUserColours(int index)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _userColoursList.size()))
+    {
+      throw new IndexOutOfBoundsException();
+    }
+
+    return (jalview.schemabinding.version2.UserColours) _userColoursList.
+        elementAt(index);
+  } //-- jalview.schemabinding.version2.UserColours getUserColours(int)
+
+  /**
+   * Method getUserColours
+   *
+   *
+   *
+   * @return UserColours
+   */
+  public jalview.schemabinding.version2.UserColours[] getUserColours()
+  {
+    int size = _userColoursList.size();
+    jalview.schemabinding.version2.UserColours[] mArray = new jalview.
+        schemabinding.version2.UserColours[size];
+    for (int index = 0; index < size; index++)
+    {
+      mArray[index] = (jalview.schemabinding.version2.UserColours)
+          _userColoursList.elementAt(index);
+    }
+    return mArray;
+  } //-- jalview.schemabinding.version2.UserColours[] getUserColours()
+
+  /**
+   * Method getUserColoursCount
+   *
+   *
+   *
+   * @return int
+   */
+  public int getUserColoursCount()
+  {
+    return _userColoursList.size();
+  } //-- int getUserColoursCount()
+
+  /**
+   * Method getViewport
+   *
+   *
+   *
+   * @param index
+   * @return Viewport
+   */
+  public jalview.schemabinding.version2.Viewport getViewport(int index)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _viewportList.size()))
+    {
+      throw new IndexOutOfBoundsException();
+    }
+
+    return (jalview.schemabinding.version2.Viewport) _viewportList.elementAt(
+        index);
+  } //-- jalview.schemabinding.version2.Viewport getViewport(int)
+
+  /**
+   * Method getViewport
+   *
+   *
+   *
+   * @return Viewport
+   */
+  public jalview.schemabinding.version2.Viewport[] getViewport()
+  {
+    int size = _viewportList.size();
+    jalview.schemabinding.version2.Viewport[] mArray = new jalview.
+        schemabinding.version2.Viewport[size];
+    for (int index = 0; index < size; index++)
+    {
+      mArray[index] = (jalview.schemabinding.version2.Viewport) _viewportList.
+          elementAt(index);
+    }
+    return mArray;
+  } //-- jalview.schemabinding.version2.Viewport[] getViewport()
+
+  /**
+   * Method getViewportCount
+   *
+   *
+   *
+   * @return int
+   */
+  public int getViewportCount()
+  {
+    return _viewportList.size();
+  } //-- int getViewportCount()
+
+  /**
+   * Method isValid
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    }
+    catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  } //-- boolean isValid()
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param out
+   */
+  public void marshal(java.io.Writer out)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, out);
+  } //-- void marshal(java.io.Writer)
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param handler
+   */
+  public void marshal(org.xml.sax.ContentHandler handler)
+      throws java.io.IOException, org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, handler);
+  } //-- void marshal(org.xml.sax.ContentHandler)
+
+  /**
+   * Method removeAllJGroup
+   *
+   */
+  public void removeAllJGroup()
+  {
+    _JGroupList.removeAllElements();
+  } //-- void removeAllJGroup()
+
+  /**
+   * Method removeAllJSeq
+   *
+   */
+  public void removeAllJSeq()
+  {
+    _JSeqList.removeAllElements();
+  } //-- void removeAllJSeq()
+
+  /**
+   * Method removeAllTree
+   *
+   */
+  public void removeAllTree()
+  {
+    _treeList.removeAllElements();
+  } //-- void removeAllTree()
+
+  /**
+   * Method removeAllUserColours
+   *
+   */
+  public void removeAllUserColours()
+  {
+    _userColoursList.removeAllElements();
+  } //-- void removeAllUserColours()
+
+  /**
+   * Method removeAllViewport
+   *
+   */
+  public void removeAllViewport()
+  {
+    _viewportList.removeAllElements();
+  } //-- void removeAllViewport()
+
+  /**
+   * Method removeJGroup
+   *
+   *
+   *
+   * @param index
+   * @return JGroup
+   */
+  public jalview.schemabinding.version2.JGroup removeJGroup(int index)
+  {
+    java.lang.Object obj = _JGroupList.elementAt(index);
+    _JGroupList.removeElementAt(index);
+    return (jalview.schemabinding.version2.JGroup) obj;
+  } //-- jalview.schemabinding.version2.JGroup removeJGroup(int)
+
+  /**
+   * Method removeJSeq
+   *
+   *
+   *
+   * @param index
+   * @return JSeq
+   */
+  public jalview.schemabinding.version2.JSeq removeJSeq(int index)
+  {
+    java.lang.Object obj = _JSeqList.elementAt(index);
+    _JSeqList.removeElementAt(index);
+    return (jalview.schemabinding.version2.JSeq) obj;
+  } //-- jalview.schemabinding.version2.JSeq removeJSeq(int)
+
+  /**
+   * Method removeTree
+   *
+   *
+   *
+   * @param index
+   * @return Tree
+   */
+  public jalview.schemabinding.version2.Tree removeTree(int index)
+  {
+    java.lang.Object obj = _treeList.elementAt(index);
+    _treeList.removeElementAt(index);
+    return (jalview.schemabinding.version2.Tree) obj;
+  } //-- jalview.schemabinding.version2.Tree removeTree(int)
+
+  /**
+   * Method removeUserColours
+   *
+   *
+   *
+   * @param index
+   * @return UserColours
+   */
+  public jalview.schemabinding.version2.UserColours removeUserColours(int index)
+  {
+    java.lang.Object obj = _userColoursList.elementAt(index);
+    _userColoursList.removeElementAt(index);
+    return (jalview.schemabinding.version2.UserColours) obj;
+  } //-- jalview.schemabinding.version2.UserColours removeUserColours(int)
+
+  /**
+   * Method removeViewport
+   *
+   *
+   *
+   * @param index
+   * @return Viewport
+   */
+  public jalview.schemabinding.version2.Viewport removeViewport(int index)
+  {
+    java.lang.Object obj = _viewportList.elementAt(index);
+    _viewportList.removeElementAt(index);
+    return (jalview.schemabinding.version2.Viewport) obj;
+  } //-- jalview.schemabinding.version2.Viewport removeViewport(int)
+
+  /**
+   * Sets the value of field 'featureSettings'.
+   *
+   * @param featureSettings the value of field 'featureSettings'.
+   */
+  public void setFeatureSettings(jalview.schemabinding.version2.FeatureSettings
+                                 featureSettings)
+  {
+    this._featureSettings = featureSettings;
+  } //-- void setFeatureSettings(jalview.schemabinding.version2.FeatureSettings)
+
+  /**
+   * Method setJGroup
+   *
+   *
+   *
+   * @param index
+   * @param vJGroup
+   */
+  public void setJGroup(int index,
+                        jalview.schemabinding.version2.JGroup vJGroup)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _JGroupList.size()))
+    {
+      throw new IndexOutOfBoundsException();
+    }
+    _JGroupList.setElementAt(vJGroup, index);
+  } //-- void setJGroup(int, jalview.schemabinding.version2.JGroup)
+
+  /**
+   * Method setJGroup
+   *
+   *
+   *
+   * @param JGroupArray
+   */
+  public void setJGroup(jalview.schemabinding.version2.JGroup[] JGroupArray)
+  {
+    //-- copy array
+    _JGroupList.removeAllElements();
+    for (int i = 0; i < JGroupArray.length; i++)
+    {
+      _JGroupList.addElement(JGroupArray[i]);
+    }
+  } //-- void setJGroup(jalview.schemabinding.version2.JGroup)
+
+  /**
+   * Method setJSeq
+   *
+   *
+   *
+   * @param index
+   * @param vJSeq
+   */
+  public void setJSeq(int index, jalview.schemabinding.version2.JSeq vJSeq)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _JSeqList.size()))
+    {
+      throw new IndexOutOfBoundsException();
+    }
+    _JSeqList.setElementAt(vJSeq, index);
+  } //-- void setJSeq(int, jalview.schemabinding.version2.JSeq)
+
+  /**
+   * Method setJSeq
+   *
+   *
+   *
+   * @param JSeqArray
+   */
+  public void setJSeq(jalview.schemabinding.version2.JSeq[] JSeqArray)
+  {
+    //-- copy array
+    _JSeqList.removeAllElements();
+    for (int i = 0; i < JSeqArray.length; i++)
+    {
+      _JSeqList.addElement(JSeqArray[i]);
+    }
+  } //-- void setJSeq(jalview.schemabinding.version2.JSeq)
+
+  /**
+   * Method setTree
+   *
+   *
+   *
+   * @param index
+   * @param vTree
+   */
+  public void setTree(int index, jalview.schemabinding.version2.Tree vTree)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _treeList.size()))
+    {
+      throw new IndexOutOfBoundsException();
+    }
+    _treeList.setElementAt(vTree, index);
+  } //-- void setTree(int, jalview.schemabinding.version2.Tree)
+
+  /**
+   * Method setTree
+   *
+   *
+   *
+   * @param treeArray
+   */
+  public void setTree(jalview.schemabinding.version2.Tree[] treeArray)
+  {
+    //-- copy array
+    _treeList.removeAllElements();
+    for (int i = 0; i < treeArray.length; i++)
+    {
+      _treeList.addElement(treeArray[i]);
+    }
+  } //-- void setTree(jalview.schemabinding.version2.Tree)
+
+  /**
+   * Method setUserColours
+   *
+   *
+   *
+   * @param index
+   * @param vUserColours
+   */
+  public void setUserColours(int index,
+                             jalview.schemabinding.version2.UserColours
+                             vUserColours)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _userColoursList.size()))
+    {
+      throw new IndexOutOfBoundsException();
+    }
+    _userColoursList.setElementAt(vUserColours, index);
+  } //-- void setUserColours(int, jalview.schemabinding.version2.UserColours)
+
+  /**
+   * Method setUserColours
+   *
+   *
+   *
+   * @param userColoursArray
+   */
+  public void setUserColours(jalview.schemabinding.version2.UserColours[]
+                             userColoursArray)
+  {
+    //-- copy array
+    _userColoursList.removeAllElements();
+    for (int i = 0; i < userColoursArray.length; i++)
+    {
+      _userColoursList.addElement(userColoursArray[i]);
+    }
+  } //-- void setUserColours(jalview.schemabinding.version2.UserColours)
+
+  /**
+   * Method setViewport
+   *
+   *
+   *
+   * @param index
+   * @param vViewport
+   */
+  public void setViewport(int index,
+                          jalview.schemabinding.version2.Viewport vViewport)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _viewportList.size()))
+    {
+      throw new IndexOutOfBoundsException();
+    }
+    _viewportList.setElementAt(vViewport, index);
+  } //-- void setViewport(int, jalview.schemabinding.version2.Viewport)
+
+  /**
+   * Method setViewport
+   *
+   *
+   *
+   * @param viewportArray
+   */
+  public void setViewport(jalview.schemabinding.version2.Viewport[]
+                          viewportArray)
+  {
+    //-- copy array
+    _viewportList.removeAllElements();
+    for (int i = 0; i < viewportArray.length; i++)
+    {
+      _viewportList.addElement(viewportArray[i]);
+    }
+  } //-- void setViewport(jalview.schemabinding.version2.Viewport)
+
+  /**
+   * Method unmarshal
+   *
+   *
+   *
+   * @param reader
+   * @return Object
+   */
+  public static java.lang.Object unmarshal(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);
+  } //-- java.lang.Object unmarshal(java.io.Reader)
+
+  /**
+   * Method validate
+   *
+   */
+  public void validate()
+      throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.
+        Validator();
+    validator.validate(this);
+  } //-- void validate()
 
 }
diff --git a/src/jalview/schemabinding/version2/JalviewModelSequenceDescriptor.java b/src/jalview/schemabinding/version2/JalviewModelSequenceDescriptor.java
index 7f5bd43..557b8fe 100755
--- a/src/jalview/schemabinding/version2/JalviewModelSequenceDescriptor.java
+++ b/src/jalview/schemabinding/version2/JalviewModelSequenceDescriptor.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,377 +7,424 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
 //---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
 
-import org.exolab.castor.mapping.AccessMode;
-import org.exolab.castor.xml.TypeValidator;
-import org.exolab.castor.xml.XMLFieldDescriptor;
-import org.exolab.castor.xml.validators.*;
 
 /**
  * Class JalviewModelSequenceDescriptor.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class JalviewModelSequenceDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field nsPrefix
-     */
-    private java.lang.String nsPrefix;
-
-    /**
-     * Field nsURI
-     */
-    private java.lang.String nsURI;
-
-    /**
-     * Field xmlName
-     */
-    private java.lang.String xmlName;
-
-    /**
-     * Field identity
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor identity;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public JalviewModelSequenceDescriptor() {
-        super();
-        nsURI = "www.jalview.org";
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.xml.XMLFieldHandler              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 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 nsPrefix
+   */
+  private java.lang.String nsPrefix;
+
+  /**
+   * Field nsURI
+   */
+  private java.lang.String nsURI;
+
+  /**
+   * Field xmlName
+   */
+  private java.lang.String xmlName;
+
+  /**
+   * Field identity
+   */
+  private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+  //----------------/
+  //- Constructors -/
+  //----------------/
+
+  public JalviewModelSequenceDescriptor()
+  {
+    super();
+    nsURI = "www.jalview.org";
+
+    //-- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.xml.XMLFieldHandler 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);
         }
-        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 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
+        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 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);
         }
-        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 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
+        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 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);
         }
-        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
+        catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-    } //-- jalview.schemabinding.version2.JalviewModelSequenceDescriptor()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method getAccessMode
-     * 
-     * 
-     * 
-     * @return AccessMode
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode()
-    {
-        return null;
-    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
-
-    /**
-     * Method getExtends
-     * 
-     * 
-     * 
-     * @return ClassDescriptor
-     */
-    public org.exolab.castor.mapping.ClassDescriptor getExtends()
-    {
-        return null;
-    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
-
-    /**
-     * Method getIdentity
-     * 
-     * 
-     * 
-     * @return FieldDescriptor
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
-    {
-        return identity;
-    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
-
-    /**
-     * Method getJavaClass
-     * 
-     * 
-     * 
-     * @return Class
-     */
-    public java.lang.Class getJavaClass()
-    {
-        return jalview.schemabinding.version2.JalviewModelSequence.class;
-    } //-- java.lang.Class getJavaClass() 
-
-    /**
-     * Method getNameSpacePrefix
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpacePrefix()
-    {
-        return nsPrefix;
-    } //-- java.lang.String getNameSpacePrefix() 
-
-    /**
-     * Method getNameSpaceURI
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpaceURI()
+      }
+
+      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()
     {
-        return nsURI;
-    } //-- java.lang.String getNameSpaceURI() 
-
-    /**
-     * Method getValidator
-     * 
-     * 
-     * 
-     * @return TypeValidator
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator()
+      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 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
+    }
+    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()
     {
-        return this;
-    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
-
-    /**
-     * Method getXMLName
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getXMLName()
+      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 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
+    }
+    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()
     {
-        return xmlName;
-    } //-- java.lang.String getXMLName() 
+      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
+    }
+    desc.setValidator(fieldValidator);
+  } //-- jalview.schemabinding.version2.JalviewModelSequenceDescriptor()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Method getAccessMode
+   *
+   *
+   *
+   * @return AccessMode
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
+
+  /**
+   * Method getExtends
+   *
+   *
+   *
+   * @return ClassDescriptor
+   */
+  public org.exolab.castor.mapping.ClassDescriptor getExtends()
+  {
+    return null;
+  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
+
+  /**
+   * Method getIdentity
+   *
+   *
+   *
+   * @return FieldDescriptor
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return identity;
+  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
+
+  /**
+   * Method getJavaClass
+   *
+   *
+   *
+   * @return Class
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.JalviewModelSequence.class;
+  } //-- java.lang.Class getJavaClass()
+
+  /**
+   * Method getNameSpacePrefix
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return nsPrefix;
+  } //-- java.lang.String getNameSpacePrefix()
+
+  /**
+   * Method getNameSpaceURI
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return nsURI;
+  } //-- java.lang.String getNameSpaceURI()
+
+  /**
+   * Method getValidator
+   *
+   *
+   *
+   * @return TypeValidator
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  } //-- org.exolab.castor.xml.TypeValidator getValidator()
+
+  /**
+   * Method getXMLName
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getXMLName()
+  {
+    return xmlName;
+  } //-- java.lang.String getXMLName()
 
 }
diff --git a/src/jalview/schemabinding/version2/JalviewUserColours.java b/src/jalview/schemabinding/version2/JalviewUserColours.java
index 7963596..5b4fb76 100755
--- a/src/jalview/schemabinding/version2/JalviewUserColours.java
+++ b/src/jalview/schemabinding/version2/JalviewUserColours.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,294 +7,302 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
 //---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import java.util.*;
 
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import java.util.Enumeration;
-import java.util.Vector;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
+import org.exolab.castor.xml.*;
 
 /**
  * Class JalviewUserColours.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class JalviewUserColours implements java.io.Serializable {
+public class JalviewUserColours
+    implements java.io.Serializable
+{
 
+  //--------------------------/
+  //- Class/Member Variables -/
+  //--------------------------/
 
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
+  /**
+   * Field _schemeName
+   */
+  private java.lang.String _schemeName;
 
-    /**
-     * Field _schemeName
-     */
-    private java.lang.String _schemeName;
+  /**
+   * Field _colourList
+   */
+  private java.util.Vector _colourList;
 
-    /**
-     * Field _colourList
-     */
-    private java.util.Vector _colourList;
+  //----------------/
+  //- Constructors -/
+  //----------------/
 
+  public JalviewUserColours()
+  {
+    super();
+    _colourList = new Vector();
+  } //-- jalview.schemabinding.version2.JalviewUserColours()
 
-      //----------------/
-     //- Constructors -/
-    //----------------/
+  //-----------/
+  //- Methods -/
+  //-----------/
 
-    public JalviewUserColours() {
-        super();
-        _colourList = new Vector();
-    } //-- jalview.schemabinding.version2.JalviewUserColours()
+  /**
+   * Method addColour
+   *
+   *
+   *
+   * @param vColour
+   */
+  public void addColour(jalview.schemabinding.version2.Colour vColour)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _colourList.addElement(vColour);
+  } //-- void addColour(jalview.schemabinding.version2.Colour)
 
+  /**
+   * Method addColour
+   *
+   *
+   *
+   * @param index
+   * @param vColour
+   */
+  public void addColour(int index,
+                        jalview.schemabinding.version2.Colour vColour)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _colourList.insertElementAt(vColour, index);
+  } //-- void addColour(int, jalview.schemabinding.version2.Colour)
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+  /**
+   * Method enumerateColour
+   *
+   *
+   *
+   * @return Enumeration
+   */
+  public java.util.Enumeration enumerateColour()
+  {
+    return _colourList.elements();
+  } //-- java.util.Enumeration enumerateColour()
 
-    /**
-     * Method addColour
-     * 
-     * 
-     * 
-     * @param vColour
-     */
-    public void addColour(jalview.schemabinding.version2.Colour vColour)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _colourList.addElement(vColour);
-    } //-- void addColour(jalview.schemabinding.version2.Colour) 
-
-    /**
-     * Method addColour
-     * 
-     * 
-     * 
-     * @param index
-     * @param vColour
-     */
-    public void addColour(int index, jalview.schemabinding.version2.Colour vColour)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _colourList.insertElementAt(vColour, index);
-    } //-- void addColour(int, jalview.schemabinding.version2.Colour) 
-
-    /**
-     * Method enumerateColour
-     * 
-     * 
-     * 
-     * @return Enumeration
-     */
-    public java.util.Enumeration enumerateColour()
-    {
-        return _colourList.elements();
-    } //-- java.util.Enumeration enumerateColour() 
-
-    /**
-     * Method getColour
-     * 
-     * 
-     * 
-     * @param index
-     * @return Colour
-     */
-    public jalview.schemabinding.version2.Colour getColour(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _colourList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        
-        return (jalview.schemabinding.version2.Colour) _colourList.elementAt(index);
-    } //-- jalview.schemabinding.version2.Colour getColour(int) 
-
-    /**
-     * Method getColour
-     * 
-     * 
-     * 
-     * @return Colour
-     */
-    public jalview.schemabinding.version2.Colour[] getColour()
-    {
-        int size = _colourList.size();
-        jalview.schemabinding.version2.Colour[] mArray = new jalview.schemabinding.version2.Colour[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = (jalview.schemabinding.version2.Colour) _colourList.elementAt(index);
-        }
-        return mArray;
-    } //-- jalview.schemabinding.version2.Colour[] getColour() 
-
-    /**
-     * Method getColourCount
-     * 
-     * 
-     * 
-     * @return int
-     */
-    public int getColourCount()
-    {
-        return _colourList.size();
-    } //-- int getColourCount() 
-
-    /**
-     * Returns the value of field 'schemeName'.
-     * 
-     * @return String
-     * @return the value of field 'schemeName'.
-     */
-    public java.lang.String getSchemeName()
+  /**
+   * Method getColour
+   *
+   *
+   *
+   * @param index
+   * @return Colour
+   */
+  public jalview.schemabinding.version2.Colour getColour(int index)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _colourList.size()))
     {
-        return this._schemeName;
-    } //-- java.lang.String getSchemeName() 
-
-    /**
-     * Method isValid
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean isValid()
-    {
-        try {
-            validate();
-        }
-        catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    } //-- boolean isValid() 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param out
-     */
-    public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, out);
-    } //-- void marshal(java.io.Writer) 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param handler
-     */
-    public void marshal(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, handler);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
-
-    /**
-     * Method removeAllColour
-     * 
-     */
-    public void removeAllColour()
-    {
-        _colourList.removeAllElements();
-    } //-- void removeAllColour() 
-
-    /**
-     * Method removeColour
-     * 
-     * 
-     * 
-     * @param index
-     * @return Colour
-     */
-    public jalview.schemabinding.version2.Colour removeColour(int index)
-    {
-        java.lang.Object obj = _colourList.elementAt(index);
-        _colourList.removeElementAt(index);
-        return (jalview.schemabinding.version2.Colour) obj;
-    } //-- jalview.schemabinding.version2.Colour removeColour(int) 
-
-    /**
-     * Method setColour
-     * 
-     * 
-     * 
-     * @param index
-     * @param vColour
-     */
-    public void setColour(int index, jalview.schemabinding.version2.Colour vColour)
-        throws java.lang.IndexOutOfBoundsException
+      throw new IndexOutOfBoundsException();
+    }
+
+    return (jalview.schemabinding.version2.Colour) _colourList.elementAt(index);
+  } //-- jalview.schemabinding.version2.Colour getColour(int)
+
+  /**
+   * Method getColour
+   *
+   *
+   *
+   * @return Colour
+   */
+  public jalview.schemabinding.version2.Colour[] getColour()
+  {
+    int size = _colourList.size();
+    jalview.schemabinding.version2.Colour[] mArray = new jalview.schemabinding.
+        version2.Colour[size];
+    for (int index = 0; index < size; index++)
     {
-        //-- check bounds for index
-        if ((index < 0) || (index > _colourList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        _colourList.setElementAt(vColour, index);
-    } //-- void setColour(int, jalview.schemabinding.version2.Colour) 
-
-    /**
-     * Method setColour
-     * 
-     * 
-     * 
-     * @param colourArray
-     */
-    public void setColour(jalview.schemabinding.version2.Colour[] colourArray)
+      mArray[index] = (jalview.schemabinding.version2.Colour) _colourList.
+          elementAt(index);
+    }
+    return mArray;
+  } //-- jalview.schemabinding.version2.Colour[] getColour()
+
+  /**
+   * Method getColourCount
+   *
+   *
+   *
+   * @return int
+   */
+  public int getColourCount()
+  {
+    return _colourList.size();
+  } //-- int getColourCount()
+
+  /**
+   * Returns the value of field 'schemeName'.
+   *
+   * @return String
+   * @return the value of field 'schemeName'.
+   */
+  public java.lang.String getSchemeName()
+  {
+    return this._schemeName;
+  } //-- java.lang.String getSchemeName()
+
+  /**
+   * Method isValid
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean isValid()
+  {
+    try
     {
-        //-- copy array
-        _colourList.removeAllElements();
-        for (int i = 0; i < colourArray.length; i++) {
-            _colourList.addElement(colourArray[i]);
-        }
-    } //-- void setColour(jalview.schemabinding.version2.Colour) 
-
-    /**
-     * Sets the value of field 'schemeName'.
-     * 
-     * @param schemeName the value of field 'schemeName'.
-     */
-    public void setSchemeName(java.lang.String schemeName)
+      validate();
+    }
+    catch (org.exolab.castor.xml.ValidationException vex)
     {
-        this._schemeName = schemeName;
-    } //-- void setSchemeName(java.lang.String) 
-
-    /**
-     * Method unmarshal
-     * 
-     * 
-     * 
-     * @param reader
-     * @return Object
-     */
-    public static java.lang.Object unmarshal(java.io.Reader reader)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+      return false;
+    }
+    return true;
+  } //-- boolean isValid()
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param out
+   */
+  public void marshal(java.io.Writer out)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, out);
+  } //-- void marshal(java.io.Writer)
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param handler
+   */
+  public void marshal(org.xml.sax.ContentHandler handler)
+      throws java.io.IOException, org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, handler);
+  } //-- void marshal(org.xml.sax.ContentHandler)
+
+  /**
+   * Method removeAllColour
+   *
+   */
+  public void removeAllColour()
+  {
+    _colourList.removeAllElements();
+  } //-- void removeAllColour()
+
+  /**
+   * Method removeColour
+   *
+   *
+   *
+   * @param index
+   * @return Colour
+   */
+  public jalview.schemabinding.version2.Colour removeColour(int index)
+  {
+    java.lang.Object obj = _colourList.elementAt(index);
+    _colourList.removeElementAt(index);
+    return (jalview.schemabinding.version2.Colour) obj;
+  } //-- jalview.schemabinding.version2.Colour removeColour(int)
+
+  /**
+   * Method setColour
+   *
+   *
+   *
+   * @param index
+   * @param vColour
+   */
+  public void setColour(int index,
+                        jalview.schemabinding.version2.Colour vColour)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _colourList.size()))
     {
-        return (jalview.schemabinding.version2.JalviewUserColours) Unmarshaller.unmarshal(jalview.schemabinding.version2.JalviewUserColours.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
-
-    /**
-     * Method validate
-     * 
-     */
-    public void validate()
-        throws org.exolab.castor.xml.ValidationException
+      throw new IndexOutOfBoundsException();
+    }
+    _colourList.setElementAt(vColour, index);
+  } //-- void setColour(int, jalview.schemabinding.version2.Colour)
+
+  /**
+   * Method setColour
+   *
+   *
+   *
+   * @param colourArray
+   */
+  public void setColour(jalview.schemabinding.version2.Colour[] colourArray)
+  {
+    //-- copy array
+    _colourList.removeAllElements();
+    for (int i = 0; i < colourArray.length; i++)
     {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    } //-- void validate() 
+      _colourList.addElement(colourArray[i]);
+    }
+  } //-- void setColour(jalview.schemabinding.version2.Colour)
+
+  /**
+   * Sets the value of field 'schemeName'.
+   *
+   * @param schemeName the value of field 'schemeName'.
+   */
+  public void setSchemeName(java.lang.String schemeName)
+  {
+    this._schemeName = schemeName;
+  } //-- void setSchemeName(java.lang.String)
+
+  /**
+   * Method unmarshal
+   *
+   *
+   *
+   * @param reader
+   * @return Object
+   */
+  public static java.lang.Object unmarshal(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);
+  } //-- java.lang.Object unmarshal(java.io.Reader)
+
+  /**
+   * Method validate
+   *
+   */
+  public void validate()
+      throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.
+        Validator();
+    validator.validate(this);
+  } //-- void validate()
 
 }
diff --git a/src/jalview/schemabinding/version2/JalviewUserColoursDescriptor.java b/src/jalview/schemabinding/version2/JalviewUserColoursDescriptor.java
index 661d102..b726902 100755
--- a/src/jalview/schemabinding/version2/JalviewUserColoursDescriptor.java
+++ b/src/jalview/schemabinding/version2/JalviewUserColoursDescriptor.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,238 +7,251 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
-import org.exolab.castor.mapping.AccessMode;
-import org.exolab.castor.xml.TypeValidator;
-import org.exolab.castor.xml.XMLFieldDescriptor;
 import org.exolab.castor.xml.validators.*;
 
 /**
  * Class JalviewUserColoursDescriptor.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class JalviewUserColoursDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field nsPrefix
-     */
-    private java.lang.String nsPrefix;
-
-    /**
-     * Field nsURI
-     */
-    private java.lang.String nsURI;
-
-    /**
-     * Field xmlName
-     */
-    private java.lang.String xmlName;
-
-    /**
-     * Field identity
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor identity;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public JalviewUserColoursDescriptor() {
-        super();
-        nsURI = "www.jalview.org/colours";
-        xmlName = "JalviewUserColours";
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.xml.XMLFieldHandler              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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _schemeName
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            StringValidator typeValidator = new StringValidator();
-            typeValidator.setWhiteSpace("preserve");
-            fieldValidator.setValidator(typeValidator);
+public class JalviewUserColoursDescriptor
+    extends org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  //--------------------------/
+  //- Class/Member Variables -/
+  //--------------------------/
+
+  /**
+   * Field nsPrefix
+   */
+  private java.lang.String nsPrefix;
+
+  /**
+   * Field nsURI
+   */
+  private java.lang.String nsURI;
+
+  /**
+   * Field xmlName
+   */
+  private java.lang.String xmlName;
+
+  /**
+   * Field identity
+   */
+  private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+  //----------------/
+  //- Constructors -/
+  //----------------/
+
+  public JalviewUserColoursDescriptor()
+  {
+    super();
+    nsURI = "www.jalview.org/colours";
+    xmlName = "JalviewUserColours";
+
+    //-- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.xml.XMLFieldHandler 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);
         }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-        //-- _colourList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.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( (jalview.schemabinding.version2.Colour) 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.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
+        catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-    } //-- jalview.schemabinding.version2.JalviewUserColoursDescriptor()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method getAccessMode
-     * 
-     * 
-     * 
-     * @return AccessMode
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode()
-    {
-        return null;
-    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
-
-    /**
-     * Method getExtends
-     * 
-     * 
-     * 
-     * @return ClassDescriptor
-     */
-    public org.exolab.castor.mapping.ClassDescriptor getExtends()
-    {
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
-
-    /**
-     * Method getIdentity
-     * 
-     * 
-     * 
-     * @return FieldDescriptor
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
-    {
-        return identity;
-    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
-
-    /**
-     * Method getJavaClass
-     * 
-     * 
-     * 
-     * @return Class
-     */
-    public java.lang.Class getJavaClass()
-    {
-        return jalview.schemabinding.version2.JalviewUserColours.class;
-    } //-- java.lang.Class getJavaClass() 
-
-    /**
-     * Method getNameSpacePrefix
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpacePrefix()
-    {
-        return nsPrefix;
-    } //-- java.lang.String getNameSpacePrefix() 
-
-    /**
-     * Method getNameSpaceURI
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpaceURI()
-    {
-        return nsURI;
-    } //-- java.lang.String getNameSpaceURI() 
-
-    /**
-     * Method getValidator
-     * 
-     * 
-     * 
-     * @return TypeValidator
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator()
-    {
-        return this;
-    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
-
-    /**
-     * Method getXMLName
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getXMLName()
+      }
+    });
+    desc.setHandler(handler);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _schemeName
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      StringValidator typeValidator = new StringValidator();
+      typeValidator.setWhiteSpace("preserve");
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    //-- initialize element descriptors
+
+    //-- _colourList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.
+        schemabinding.version2.Colour.class, "_colourList", "colour",
+        org.exolab.castor.xml.NodeType.Element);
+    handler = (new org.exolab.castor.xml.XMLFieldHandler()
     {
-        return xmlName;
-    } //-- java.lang.String getXMLName() 
+      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( (jalview.schemabinding.version2.Colour) 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.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);
+  } //-- jalview.schemabinding.version2.JalviewUserColoursDescriptor()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Method getAccessMode
+   *
+   *
+   *
+   * @return AccessMode
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
+
+  /**
+   * Method getExtends
+   *
+   *
+   *
+   * @return ClassDescriptor
+   */
+  public org.exolab.castor.mapping.ClassDescriptor getExtends()
+  {
+    return null;
+  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
+
+  /**
+   * Method getIdentity
+   *
+   *
+   *
+   * @return FieldDescriptor
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return identity;
+  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
+
+  /**
+   * Method getJavaClass
+   *
+   *
+   *
+   * @return Class
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.JalviewUserColours.class;
+  } //-- java.lang.Class getJavaClass()
+
+  /**
+   * Method getNameSpacePrefix
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return nsPrefix;
+  } //-- java.lang.String getNameSpacePrefix()
+
+  /**
+   * Method getNameSpaceURI
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return nsURI;
+  } //-- java.lang.String getNameSpaceURI()
+
+  /**
+   * Method getValidator
+   *
+   *
+   *
+   * @return TypeValidator
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  } //-- org.exolab.castor.xml.TypeValidator getValidator()
+
+  /**
+   * Method getXMLName
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getXMLName()
+  {
+    return xmlName;
+  } //-- java.lang.String getXMLName()
 
 }
diff --git a/src/jalview/schemabinding/version2/OtherData.java b/src/jalview/schemabinding/version2/OtherData.java
index 47423eb..7bf72de 100644
--- a/src/jalview/schemabinding/version2/OtherData.java
+++ b/src/jalview/schemabinding/version2/OtherData.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,167 +7,166 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
+import org.exolab.castor.xml.*;
 
 /**
  * Class OtherData.
- * 
+ *
  * @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();
-    } //-- jalview.schemabinding.version2.OtherData()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Returns the value of field 'key'.
-     * 
-     * @return String
-     * @return the value of field 'key'.
-     */
-    public java.lang.String getKey()
-    {
-        return this._key;
-    } //-- java.lang.String getKey() 
-
-    /**
-     * Returns the value of field 'value'.
-     * 
-     * @return String
-     * @return the value of field 'value'.
-     */
-    public java.lang.String getValue()
-    {
-        return this._value;
-    } //-- java.lang.String getValue() 
-
-    /**
-     * Method isValid
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean isValid()
-    {
-        try {
-            validate();
-        }
-        catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    } //-- boolean isValid() 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param out
-     */
-    public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, out);
-    } //-- void marshal(java.io.Writer) 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param handler
-     */
-    public void marshal(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, handler);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
-
-    /**
-     * Sets the value of field 'key'.
-     * 
-     * @param key the value of field 'key'.
-     */
-    public void setKey(java.lang.String key)
-    {
-        this._key = key;
-    } //-- void setKey(java.lang.String) 
-
-    /**
-     * Sets the value of field 'value'.
-     * 
-     * @param value the value of field 'value'.
-     */
-    public void setValue(java.lang.String value)
-    {
-        this._value = value;
-    } //-- void setValue(java.lang.String) 
-
-    /**
-     * Method unmarshal
-     * 
-     * 
-     * 
-     * @param reader
-     * @return Object
-     */
-    public static java.lang.Object unmarshal(java.io.Reader reader)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+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();
+  } //-- jalview.schemabinding.version2.OtherData()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Returns the value of field 'key'.
+   *
+   * @return String
+   * @return the value of field 'key'.
+   */
+  public java.lang.String getKey()
+  {
+    return this._key;
+  } //-- java.lang.String getKey()
+
+  /**
+   * Returns the value of field 'value'.
+   *
+   * @return String
+   * @return the value of field 'value'.
+   */
+  public java.lang.String getValue()
+  {
+    return this._value;
+  } //-- java.lang.String getValue()
+
+  /**
+   * Method isValid
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean isValid()
+  {
+    try
     {
-        return (jalview.schemabinding.version2.OtherData) Unmarshaller.unmarshal(jalview.schemabinding.version2.OtherData.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
-
-    /**
-     * Method validate
-     * 
-     */
-    public void validate()
-        throws org.exolab.castor.xml.ValidationException
+      validate();
+    }
+    catch (org.exolab.castor.xml.ValidationException vex)
     {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    } //-- void validate() 
+      return false;
+    }
+    return true;
+  } //-- boolean isValid()
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param out
+   */
+  public void marshal(java.io.Writer out)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, out);
+  } //-- void marshal(java.io.Writer)
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param handler
+   */
+  public void marshal(org.xml.sax.ContentHandler handler)
+      throws java.io.IOException, org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, handler);
+  } //-- void marshal(org.xml.sax.ContentHandler)
+
+  /**
+   * Sets the value of field 'key'.
+   *
+   * @param key the value of field 'key'.
+   */
+  public void setKey(java.lang.String key)
+  {
+    this._key = key;
+  } //-- void setKey(java.lang.String)
+
+  /**
+   * Sets the value of field 'value'.
+   *
+   * @param value the value of field 'value'.
+   */
+  public void setValue(java.lang.String value)
+  {
+    this._value = value;
+  } //-- void setValue(java.lang.String)
+
+  /**
+   * Method unmarshal
+   *
+   *
+   *
+   * @param reader
+   * @return Object
+   */
+  public static java.lang.Object unmarshal(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);
+  } //-- java.lang.Object unmarshal(java.io.Reader)
+
+  /**
+   * Method validate
+   *
+   */
+  public void validate()
+      throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.
+        Validator();
+    validator.validate(this);
+  } //-- void validate()
 
 }
diff --git a/src/jalview/schemabinding/version2/OtherDataDescriptor.java b/src/jalview/schemabinding/version2/OtherDataDescriptor.java
index f6ec794..f39c05d 100644
--- a/src/jalview/schemabinding/version2/OtherDataDescriptor.java
+++ b/src/jalview/schemabinding/version2/OtherDataDescriptor.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,240 +7,252 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
-import org.exolab.castor.mapping.AccessMode;
-import org.exolab.castor.xml.TypeValidator;
-import org.exolab.castor.xml.XMLFieldDescriptor;
 import org.exolab.castor.xml.validators.*;
 
 /**
  * Class OtherDataDescriptor.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class OtherDataDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field nsPrefix
-     */
-    private java.lang.String nsPrefix;
-
-    /**
-     * Field nsURI
-     */
-    private java.lang.String nsURI;
-
-    /**
-     * Field xmlName
-     */
-    private java.lang.String xmlName;
-
-    /**
-     * Field identity
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor identity;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public OtherDataDescriptor() {
-        super();
-        nsURI = "www.jalview.org";
-        xmlName = "otherData";
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.xml.XMLFieldHandler              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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _key
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            StringValidator typeValidator = new StringValidator();
-            typeValidator.setWhiteSpace("preserve");
-            fieldValidator.setValidator(typeValidator);
+public class OtherDataDescriptor
+    extends org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  //--------------------------/
+  //- Class/Member Variables -/
+  //--------------------------/
+
+  /**
+   * Field nsPrefix
+   */
+  private java.lang.String nsPrefix;
+
+  /**
+   * Field nsURI
+   */
+  private java.lang.String nsURI;
+
+  /**
+   * Field xmlName
+   */
+  private java.lang.String xmlName;
+
+  /**
+   * Field identity
+   */
+  private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+  //----------------/
+  //- Constructors -/
+  //----------------/
+
+  public OtherDataDescriptor()
+  {
+    super();
+    nsURI = "www.jalview.org";
+    xmlName = "otherData";
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.xml.XMLFieldHandler 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);
         }
-        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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _value
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            StringValidator typeValidator = new StringValidator();
-            typeValidator.setWhiteSpace("preserve");
-            fieldValidator.setValidator(typeValidator);
+        catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-    } //-- jalview.schemabinding.version2.OtherDataDescriptor()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method getAccessMode
-     * 
-     * 
-     * 
-     * @return AccessMode
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode()
-    {
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
-
-    /**
-     * Method getExtends
-     * 
-     * 
-     * 
-     * @return ClassDescriptor
-     */
-    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+      }
+    });
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _key
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { //-- local scope
+      StringValidator typeValidator = new StringValidator();
+      typeValidator.setWhiteSpace("preserve");
+      fieldValidator.setValidator(typeValidator);
+    }
+    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;
-    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
-
-    /**
-     * Method getIdentity
-     * 
-     * 
-     * 
-     * @return FieldDescriptor
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
-    {
-        return identity;
-    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
-
-    /**
-     * Method getJavaClass
-     * 
-     * 
-     * 
-     * @return Class
-     */
-    public java.lang.Class getJavaClass()
-    {
-        return jalview.schemabinding.version2.OtherData.class;
-    } //-- java.lang.Class getJavaClass() 
-
-    /**
-     * Method getNameSpacePrefix
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpacePrefix()
-    {
-        return nsPrefix;
-    } //-- java.lang.String getNameSpacePrefix() 
-
-    /**
-     * Method getNameSpaceURI
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpaceURI()
-    {
-        return nsURI;
-    } //-- java.lang.String getNameSpaceURI() 
-
-    /**
-     * Method getValidator
-     * 
-     * 
-     * 
-     * @return TypeValidator
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator()
-    {
-        return this;
-    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
-
-    /**
-     * Method getXMLName
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getXMLName()
-    {
-        return xmlName;
-    } //-- java.lang.String getXMLName() 
+      }
+    });
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _value
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { //-- local scope
+      StringValidator typeValidator = new StringValidator();
+      typeValidator.setWhiteSpace("preserve");
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    //-- initialize element descriptors
+
+  } //-- jalview.schemabinding.version2.OtherDataDescriptor()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Method getAccessMode
+   *
+   *
+   *
+   * @return AccessMode
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
+
+  /**
+   * Method getExtends
+   *
+   *
+   *
+   * @return ClassDescriptor
+   */
+  public org.exolab.castor.mapping.ClassDescriptor getExtends()
+  {
+    return null;
+  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
+
+  /**
+   * Method getIdentity
+   *
+   *
+   *
+   * @return FieldDescriptor
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return identity;
+  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
+
+  /**
+   * Method getJavaClass
+   *
+   *
+   *
+   * @return Class
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.OtherData.class;
+  } //-- java.lang.Class getJavaClass()
+
+  /**
+   * Method getNameSpacePrefix
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return nsPrefix;
+  } //-- java.lang.String getNameSpacePrefix()
+
+  /**
+   * Method getNameSpaceURI
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return nsURI;
+  } //-- java.lang.String getNameSpaceURI()
+
+  /**
+   * Method getValidator
+   *
+   *
+   *
+   * @return TypeValidator
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  } //-- org.exolab.castor.xml.TypeValidator getValidator()
+
+  /**
+   * Method getXMLName
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getXMLName()
+  {
+    return xmlName;
+  } //-- java.lang.String getXMLName()
 
 }
diff --git a/src/jalview/schemabinding/version2/Pdbentry.java b/src/jalview/schemabinding/version2/Pdbentry.java
index 93c2748..f4fa4fe 100755
--- a/src/jalview/schemabinding/version2/Pdbentry.java
+++ b/src/jalview/schemabinding/version2/Pdbentry.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,346 +7,358 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
 //---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import java.util.*;
 
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import java.util.Enumeration;
-import java.util.Vector;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
+import org.exolab.castor.xml.*;
 
 /**
  * Class Pdbentry.
- * 
+ *
  * @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();
-        _items = new Vector();
-    } //-- jalview.schemabinding.version2.Pdbentry()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method addPdbentryItem
-     * 
-     * 
-     * 
-     * @param vPdbentryItem
-     */
-    public void addPdbentryItem(jalview.schemabinding.version2.PdbentryItem vPdbentryItem)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _items.addElement(vPdbentryItem);
-    } //-- void addPdbentryItem(jalview.schemabinding.version2.PdbentryItem) 
-
-    /**
-     * Method addPdbentryItem
-     * 
-     * 
-     * 
-     * @param index
-     * @param vPdbentryItem
-     */
-    public void addPdbentryItem(int index, jalview.schemabinding.version2.PdbentryItem vPdbentryItem)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _items.insertElementAt(vPdbentryItem, index);
-    } //-- void addPdbentryItem(int, jalview.schemabinding.version2.PdbentryItem) 
-
-    /**
-     * Method enumeratePdbentryItem
-     * 
-     * 
-     * 
-     * @return Enumeration
-     */
-    public java.util.Enumeration enumeratePdbentryItem()
-    {
-        return _items.elements();
-    } //-- java.util.Enumeration enumeratePdbentryItem() 
-
-    /**
-     * Returns the value of field 'file'.
-     * 
-     * @return String
-     * @return the value of field 'file'.
-     */
-    public java.lang.String getFile()
-    {
-        return this._file;
-    } //-- java.lang.String getFile() 
-
-    /**
-     * Returns the value of field 'id'.
-     * 
-     * @return String
-     * @return the value of field 'id'.
-     */
-    public java.lang.String getId()
-    {
-        return this._id;
-    } //-- java.lang.String getId() 
-
-    /**
-     * Method getPdbentryItem
-     * 
-     * 
-     * 
-     * @param index
-     * @return PdbentryItem
-     */
-    public jalview.schemabinding.version2.PdbentryItem getPdbentryItem(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _items.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        
-        return (jalview.schemabinding.version2.PdbentryItem) _items.elementAt(index);
-    } //-- jalview.schemabinding.version2.PdbentryItem getPdbentryItem(int) 
-
-    /**
-     * Method getPdbentryItem
-     * 
-     * 
-     * 
-     * @return PdbentryItem
-     */
-    public jalview.schemabinding.version2.PdbentryItem[] getPdbentryItem()
-    {
-        int size = _items.size();
-        jalview.schemabinding.version2.PdbentryItem[] mArray = new jalview.schemabinding.version2.PdbentryItem[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = (jalview.schemabinding.version2.PdbentryItem) _items.elementAt(index);
-        }
-        return mArray;
-    } //-- jalview.schemabinding.version2.PdbentryItem[] getPdbentryItem() 
-
-    /**
-     * Method getPdbentryItemCount
-     * 
-     * 
-     * 
-     * @return int
-     */
-    public int getPdbentryItemCount()
-    {
-        return _items.size();
-    } //-- int getPdbentryItemCount() 
-
-    /**
-     * Returns the value of field 'type'.
-     * 
-     * @return String
-     * @return the value of field 'type'.
-     */
-    public java.lang.String getType()
-    {
-        return this._type;
-    } //-- java.lang.String getType() 
-
-    /**
-     * Method isValid
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean isValid()
-    {
-        try {
-            validate();
-        }
-        catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    } //-- boolean isValid() 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param out
-     */
-    public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, out);
-    } //-- void marshal(java.io.Writer) 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param handler
-     */
-    public void marshal(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, handler);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
-
-    /**
-     * Method removeAllPdbentryItem
-     * 
-     */
-    public void removeAllPdbentryItem()
-    {
-        _items.removeAllElements();
-    } //-- void removeAllPdbentryItem() 
-
-    /**
-     * Method removePdbentryItem
-     * 
-     * 
-     * 
-     * @param index
-     * @return PdbentryItem
-     */
-    public jalview.schemabinding.version2.PdbentryItem removePdbentryItem(int index)
-    {
-        java.lang.Object obj = _items.elementAt(index);
-        _items.removeElementAt(index);
-        return (jalview.schemabinding.version2.PdbentryItem) obj;
-    } //-- jalview.schemabinding.version2.PdbentryItem removePdbentryItem(int) 
-
-    /**
-     * Sets the value of field 'file'.
-     * 
-     * @param file the value of field 'file'.
-     */
-    public void setFile(java.lang.String file)
-    {
-        this._file = file;
-    } //-- void setFile(java.lang.String) 
-
-    /**
-     * Sets the value of field 'id'.
-     * 
-     * @param id the value of field 'id'.
-     */
-    public void setId(java.lang.String id)
+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();
+    _items = new Vector();
+  } //-- jalview.schemabinding.version2.Pdbentry()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Method addPdbentryItem
+   *
+   *
+   *
+   * @param vPdbentryItem
+   */
+  public void addPdbentryItem(jalview.schemabinding.version2.PdbentryItem
+                              vPdbentryItem)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _items.addElement(vPdbentryItem);
+  } //-- void addPdbentryItem(jalview.schemabinding.version2.PdbentryItem)
+
+  /**
+   * Method addPdbentryItem
+   *
+   *
+   *
+   * @param index
+   * @param vPdbentryItem
+   */
+  public void addPdbentryItem(int index,
+                              jalview.schemabinding.version2.PdbentryItem
+                              vPdbentryItem)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _items.insertElementAt(vPdbentryItem, index);
+  } //-- void addPdbentryItem(int, jalview.schemabinding.version2.PdbentryItem)
+
+  /**
+   * Method enumeratePdbentryItem
+   *
+   *
+   *
+   * @return Enumeration
+   */
+  public java.util.Enumeration enumeratePdbentryItem()
+  {
+    return _items.elements();
+  } //-- java.util.Enumeration enumeratePdbentryItem()
+
+  /**
+   * Returns the value of field 'file'.
+   *
+   * @return String
+   * @return the value of field 'file'.
+   */
+  public java.lang.String getFile()
+  {
+    return this._file;
+  } //-- java.lang.String getFile()
+
+  /**
+   * Returns the value of field 'id'.
+   *
+   * @return String
+   * @return the value of field 'id'.
+   */
+  public java.lang.String getId()
+  {
+    return this._id;
+  } //-- java.lang.String getId()
+
+  /**
+   * Method getPdbentryItem
+   *
+   *
+   *
+   * @param index
+   * @return PdbentryItem
+   */
+  public jalview.schemabinding.version2.PdbentryItem getPdbentryItem(int index)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _items.size()))
     {
-        this._id = id;
-    } //-- void setId(java.lang.String) 
-
-    /**
-     * Method setPdbentryItem
-     * 
-     * 
-     * 
-     * @param index
-     * @param vPdbentryItem
-     */
-    public void setPdbentryItem(int index, jalview.schemabinding.version2.PdbentryItem vPdbentryItem)
-        throws java.lang.IndexOutOfBoundsException
+      throw new IndexOutOfBoundsException();
+    }
+
+    return (jalview.schemabinding.version2.PdbentryItem) _items.elementAt(index);
+  } //-- jalview.schemabinding.version2.PdbentryItem getPdbentryItem(int)
+
+  /**
+   * Method getPdbentryItem
+   *
+   *
+   *
+   * @return PdbentryItem
+   */
+  public jalview.schemabinding.version2.PdbentryItem[] getPdbentryItem()
+  {
+    int size = _items.size();
+    jalview.schemabinding.version2.PdbentryItem[] mArray = new jalview.
+        schemabinding.version2.PdbentryItem[size];
+    for (int index = 0; index < size; index++)
     {
-        //-- check bounds for index
-        if ((index < 0) || (index > _items.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        _items.setElementAt(vPdbentryItem, index);
-    } //-- void setPdbentryItem(int, jalview.schemabinding.version2.PdbentryItem) 
-
-    /**
-     * Method setPdbentryItem
-     * 
-     * 
-     * 
-     * @param pdbentryItemArray
-     */
-    public void setPdbentryItem(jalview.schemabinding.version2.PdbentryItem[] pdbentryItemArray)
+      mArray[index] = (jalview.schemabinding.version2.PdbentryItem) _items.
+          elementAt(index);
+    }
+    return mArray;
+  } //-- jalview.schemabinding.version2.PdbentryItem[] getPdbentryItem()
+
+  /**
+   * Method getPdbentryItemCount
+   *
+   *
+   *
+   * @return int
+   */
+  public int getPdbentryItemCount()
+  {
+    return _items.size();
+  } //-- int getPdbentryItemCount()
+
+  /**
+   * Returns the value of field 'type'.
+   *
+   * @return String
+   * @return the value of field 'type'.
+   */
+  public java.lang.String getType()
+  {
+    return this._type;
+  } //-- java.lang.String getType()
+
+  /**
+   * Method isValid
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean isValid()
+  {
+    try
     {
-        //-- copy array
-        _items.removeAllElements();
-        for (int i = 0; i < pdbentryItemArray.length; i++) {
-            _items.addElement(pdbentryItemArray[i]);
-        }
-    } //-- void setPdbentryItem(jalview.schemabinding.version2.PdbentryItem) 
-
-    /**
-     * Sets the value of field 'type'.
-     * 
-     * @param type the value of field 'type'.
-     */
-    public void setType(java.lang.String type)
+      validate();
+    }
+    catch (org.exolab.castor.xml.ValidationException vex)
     {
-        this._type = type;
-    } //-- void setType(java.lang.String) 
-
-    /**
-     * Method unmarshal
-     * 
-     * 
-     * 
-     * @param reader
-     * @return Object
-     */
-    public static java.lang.Object unmarshal(java.io.Reader reader)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+      return false;
+    }
+    return true;
+  } //-- boolean isValid()
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param out
+   */
+  public void marshal(java.io.Writer out)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, out);
+  } //-- void marshal(java.io.Writer)
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param handler
+   */
+  public void marshal(org.xml.sax.ContentHandler handler)
+      throws java.io.IOException, org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, handler);
+  } //-- void marshal(org.xml.sax.ContentHandler)
+
+  /**
+   * Method removeAllPdbentryItem
+   *
+   */
+  public void removeAllPdbentryItem()
+  {
+    _items.removeAllElements();
+  } //-- void removeAllPdbentryItem()
+
+  /**
+   * Method removePdbentryItem
+   *
+   *
+   *
+   * @param index
+   * @return PdbentryItem
+   */
+  public jalview.schemabinding.version2.PdbentryItem removePdbentryItem(int
+      index)
+  {
+    java.lang.Object obj = _items.elementAt(index);
+    _items.removeElementAt(index);
+    return (jalview.schemabinding.version2.PdbentryItem) obj;
+  } //-- jalview.schemabinding.version2.PdbentryItem removePdbentryItem(int)
+
+  /**
+   * Sets the value of field 'file'.
+   *
+   * @param file the value of field 'file'.
+   */
+  public void setFile(java.lang.String file)
+  {
+    this._file = file;
+  } //-- void setFile(java.lang.String)
+
+  /**
+   * Sets the value of field 'id'.
+   *
+   * @param id the value of field 'id'.
+   */
+  public void setId(java.lang.String id)
+  {
+    this._id = id;
+  } //-- void setId(java.lang.String)
+
+  /**
+   * Method setPdbentryItem
+   *
+   *
+   *
+   * @param index
+   * @param vPdbentryItem
+   */
+  public void setPdbentryItem(int index,
+                              jalview.schemabinding.version2.PdbentryItem
+                              vPdbentryItem)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _items.size()))
     {
-        return (jalview.schemabinding.version2.Pdbentry) Unmarshaller.unmarshal(jalview.schemabinding.version2.Pdbentry.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
-
-    /**
-     * Method validate
-     * 
-     */
-    public void validate()
-        throws org.exolab.castor.xml.ValidationException
+      throw new IndexOutOfBoundsException();
+    }
+    _items.setElementAt(vPdbentryItem, index);
+  } //-- void setPdbentryItem(int, jalview.schemabinding.version2.PdbentryItem)
+
+  /**
+   * Method setPdbentryItem
+   *
+   *
+   *
+   * @param pdbentryItemArray
+   */
+  public void setPdbentryItem(jalview.schemabinding.version2.PdbentryItem[]
+                              pdbentryItemArray)
+  {
+    //-- copy array
+    _items.removeAllElements();
+    for (int i = 0; i < pdbentryItemArray.length; i++)
     {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    } //-- void validate() 
+      _items.addElement(pdbentryItemArray[i]);
+    }
+  } //-- void setPdbentryItem(jalview.schemabinding.version2.PdbentryItem)
+
+  /**
+   * Sets the value of field 'type'.
+   *
+   * @param type the value of field 'type'.
+   */
+  public void setType(java.lang.String type)
+  {
+    this._type = type;
+  } //-- void setType(java.lang.String)
+
+  /**
+   * Method unmarshal
+   *
+   *
+   *
+   * @param reader
+   * @return Object
+   */
+  public static java.lang.Object unmarshal(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);
+  } //-- java.lang.Object unmarshal(java.io.Reader)
+
+  /**
+   * Method validate
+   *
+   */
+  public void validate()
+      throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.
+        Validator();
+    validator.validate(this);
+  } //-- void validate()
 
 }
diff --git a/src/jalview/schemabinding/version2/PdbentryDescriptor.java b/src/jalview/schemabinding/version2/PdbentryDescriptor.java
index 61a9eda..e6fa0e1 100755
--- a/src/jalview/schemabinding/version2/PdbentryDescriptor.java
+++ b/src/jalview/schemabinding/version2/PdbentryDescriptor.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,309 +7,337 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
-import org.exolab.castor.mapping.AccessMode;
-import org.exolab.castor.xml.TypeValidator;
-import org.exolab.castor.xml.XMLFieldDescriptor;
 import org.exolab.castor.xml.validators.*;
 
 /**
  * Class PdbentryDescriptor.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class PdbentryDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field nsPrefix
-     */
-    private java.lang.String nsPrefix;
-
-    /**
-     * Field nsURI
-     */
-    private java.lang.String nsURI;
-
-    /**
-     * Field xmlName
-     */
-    private java.lang.String xmlName;
-
-    /**
-     * Field identity
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor identity;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public PdbentryDescriptor() {
-        super();
-        xmlName = "pdbentry";
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.xml.XMLFieldHandler              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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _id
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            StringValidator typeValidator = new StringValidator();
-            typeValidator.setWhiteSpace("preserve");
-            fieldValidator.setValidator(typeValidator);
+public class PdbentryDescriptor
+    extends org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  //--------------------------/
+  //- Class/Member Variables -/
+  //--------------------------/
+
+  /**
+   * Field nsPrefix
+   */
+  private java.lang.String nsPrefix;
+
+  /**
+   * Field nsURI
+   */
+  private java.lang.String nsURI;
+
+  /**
+   * Field xmlName
+   */
+  private java.lang.String xmlName;
+
+  /**
+   * Field identity
+   */
+  private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+  //----------------/
+  //- Constructors -/
+  //----------------/
+
+  public PdbentryDescriptor()
+  {
+    super();
+    xmlName = "pdbentry";
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.xml.XMLFieldHandler 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);
         }
-        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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _type
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            StringValidator typeValidator = new StringValidator();
-            typeValidator.setWhiteSpace("preserve");
-            fieldValidator.setValidator(typeValidator);
+        catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _file
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            StringValidator typeValidator = new StringValidator();
-            typeValidator.setWhiteSpace("preserve");
-            fieldValidator.setValidator(typeValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    });
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _id
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { //-- local scope
+      StringValidator typeValidator = new StringValidator();
+      typeValidator.setWhiteSpace("preserve");
+      fieldValidator.setValidator(typeValidator);
+    }
+    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);
         }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-        //-- _items
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.PdbentryItem.class, "_items", (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 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.PdbentryItemDescriptor());
-        desc.setMultivalued(true);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _items
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(0);
-        { //-- local scope
+        catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-    } //-- jalview.schemabinding.version2.PdbentryDescriptor()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method getAccessMode
-     * 
-     * 
-     * 
-     * @return AccessMode
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode()
-    {
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
-
-    /**
-     * Method getExtends
-     * 
-     * 
-     * 
-     * @return ClassDescriptor
-     */
-    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+      }
+    });
+    desc.setHandler(handler);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _type
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      StringValidator typeValidator = new StringValidator();
+      typeValidator.setWhiteSpace("preserve");
+      fieldValidator.setValidator(typeValidator);
+    }
+    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;
-    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
-
-    /**
-     * Method getIdentity
-     * 
-     * 
-     * 
-     * @return FieldDescriptor
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
-    {
-        return identity;
-    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
-
-    /**
-     * Method getJavaClass
-     * 
-     * 
-     * 
-     * @return Class
-     */
-    public java.lang.Class getJavaClass()
-    {
-        return jalview.schemabinding.version2.Pdbentry.class;
-    } //-- java.lang.Class getJavaClass() 
-
-    /**
-     * Method getNameSpacePrefix
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpacePrefix()
-    {
-        return nsPrefix;
-    } //-- java.lang.String getNameSpacePrefix() 
-
-    /**
-     * Method getNameSpaceURI
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpaceURI()
-    {
-        return nsURI;
-    } //-- java.lang.String getNameSpaceURI() 
-
-    /**
-     * Method getValidator
-     * 
-     * 
-     * 
-     * @return TypeValidator
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator()
-    {
-        return this;
-    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
-
-    /**
-     * Method getXMLName
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getXMLName()
+      }
+    });
+    desc.setHandler(handler);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _file
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      StringValidator typeValidator = new StringValidator();
+      typeValidator.setWhiteSpace("preserve");
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    //-- initialize element descriptors
+
+    //-- _items
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.
+        schemabinding.version2.PdbentryItem.class, "_items", (String)null,
+        org.exolab.castor.xml.NodeType.Element);
+    handler = (new org.exolab.castor.xml.XMLFieldHandler()
     {
-        return xmlName;
-    } //-- java.lang.String getXMLName() 
+      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 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.
+                            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);
+  } //-- jalview.schemabinding.version2.PdbentryDescriptor()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Method getAccessMode
+   *
+   *
+   *
+   * @return AccessMode
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
+
+  /**
+   * Method getExtends
+   *
+   *
+   *
+   * @return ClassDescriptor
+   */
+  public org.exolab.castor.mapping.ClassDescriptor getExtends()
+  {
+    return null;
+  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
+
+  /**
+   * Method getIdentity
+   *
+   *
+   *
+   * @return FieldDescriptor
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return identity;
+  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
+
+  /**
+   * Method getJavaClass
+   *
+   *
+   *
+   * @return Class
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.Pdbentry.class;
+  } //-- java.lang.Class getJavaClass()
+
+  /**
+   * Method getNameSpacePrefix
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return nsPrefix;
+  } //-- java.lang.String getNameSpacePrefix()
+
+  /**
+   * Method getNameSpaceURI
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return nsURI;
+  } //-- java.lang.String getNameSpaceURI()
+
+  /**
+   * Method getValidator
+   *
+   *
+   *
+   * @return TypeValidator
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  } //-- org.exolab.castor.xml.TypeValidator getValidator()
+
+  /**
+   * Method getXMLName
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getXMLName()
+  {
+    return xmlName;
+  } //-- java.lang.String getXMLName()
 
 }
diff --git a/src/jalview/schemabinding/version2/PdbentryItem.java b/src/jalview/schemabinding/version2/PdbentryItem.java
index 6f64036..527f5ab 100755
--- a/src/jalview/schemabinding/version2/PdbentryItem.java
+++ b/src/jalview/schemabinding/version2/PdbentryItem.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,191 +7,197 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
-import java.io.Serializable;
-import java.util.Enumeration;
-import java.util.Vector;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
+import java.util.*;
 
 /**
  * Class PdbentryItem.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class PdbentryItem implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _propertyList
-     */
-    private java.util.Vector _propertyList;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public PdbentryItem() {
-        super();
-        _propertyList = new Vector();
-    } //-- jalview.schemabinding.version2.PdbentryItem()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method addProperty
-     * 
-     * 
-     * 
-     * @param vProperty
-     */
-    public void addProperty(jalview.schemabinding.version2.Property vProperty)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _propertyList.addElement(vProperty);
-    } //-- void addProperty(jalview.schemabinding.version2.Property) 
-
-    /**
-     * Method addProperty
-     * 
-     * 
-     * 
-     * @param index
-     * @param vProperty
-     */
-    public void addProperty(int index, jalview.schemabinding.version2.Property vProperty)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _propertyList.insertElementAt(vProperty, index);
-    } //-- void addProperty(int, jalview.schemabinding.version2.Property) 
-
-    /**
-     * Method enumerateProperty
-     * 
-     * 
-     * 
-     * @return Enumeration
-     */
-    public java.util.Enumeration enumerateProperty()
-    {
-        return _propertyList.elements();
-    } //-- java.util.Enumeration enumerateProperty() 
-
-    /**
-     * Method getProperty
-     * 
-     * 
-     * 
-     * @param index
-     * @return Property
-     */
-    public jalview.schemabinding.version2.Property getProperty(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _propertyList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        
-        return (jalview.schemabinding.version2.Property) _propertyList.elementAt(index);
-    } //-- jalview.schemabinding.version2.Property getProperty(int) 
-
-    /**
-     * Method getProperty
-     * 
-     * 
-     * 
-     * @return Property
-     */
-    public jalview.schemabinding.version2.Property[] getProperty()
-    {
-        int size = _propertyList.size();
-        jalview.schemabinding.version2.Property[] mArray = new jalview.schemabinding.version2.Property[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = (jalview.schemabinding.version2.Property) _propertyList.elementAt(index);
-        }
-        return mArray;
-    } //-- jalview.schemabinding.version2.Property[] getProperty() 
-
-    /**
-     * Method getPropertyCount
-     * 
-     * 
-     * 
-     * @return int
-     */
-    public int getPropertyCount()
-    {
-        return _propertyList.size();
-    } //-- int getPropertyCount() 
-
-    /**
-     * Method removeAllProperty
-     * 
-     */
-    public void removeAllProperty()
+public class PdbentryItem
+    implements java.io.Serializable
+{
+
+  //--------------------------/
+  //- Class/Member Variables -/
+  //--------------------------/
+
+  /**
+   * Field _propertyList
+   */
+  private java.util.Vector _propertyList;
+
+  //----------------/
+  //- Constructors -/
+  //----------------/
+
+  public PdbentryItem()
+  {
+    super();
+    _propertyList = new Vector();
+  } //-- jalview.schemabinding.version2.PdbentryItem()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Method addProperty
+   *
+   *
+   *
+   * @param vProperty
+   */
+  public void addProperty(jalview.schemabinding.version2.Property vProperty)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _propertyList.addElement(vProperty);
+  } //-- void addProperty(jalview.schemabinding.version2.Property)
+
+  /**
+   * Method addProperty
+   *
+   *
+   *
+   * @param index
+   * @param vProperty
+   */
+  public void addProperty(int index,
+                          jalview.schemabinding.version2.Property vProperty)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _propertyList.insertElementAt(vProperty, index);
+  } //-- void addProperty(int, jalview.schemabinding.version2.Property)
+
+  /**
+   * Method enumerateProperty
+   *
+   *
+   *
+   * @return Enumeration
+   */
+  public java.util.Enumeration enumerateProperty()
+  {
+    return _propertyList.elements();
+  } //-- java.util.Enumeration enumerateProperty()
+
+  /**
+   * Method getProperty
+   *
+   *
+   *
+   * @param index
+   * @return Property
+   */
+  public jalview.schemabinding.version2.Property getProperty(int index)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _propertyList.size()))
     {
-        _propertyList.removeAllElements();
-    } //-- void removeAllProperty() 
-
-    /**
-     * Method removeProperty
-     * 
-     * 
-     * 
-     * @param index
-     * @return Property
-     */
-    public jalview.schemabinding.version2.Property removeProperty(int index)
+      throw new IndexOutOfBoundsException();
+    }
+
+    return (jalview.schemabinding.version2.Property) _propertyList.elementAt(
+        index);
+  } //-- jalview.schemabinding.version2.Property getProperty(int)
+
+  /**
+   * Method getProperty
+   *
+   *
+   *
+   * @return Property
+   */
+  public jalview.schemabinding.version2.Property[] getProperty()
+  {
+    int size = _propertyList.size();
+    jalview.schemabinding.version2.Property[] mArray = new jalview.
+        schemabinding.version2.Property[size];
+    for (int index = 0; index < size; index++)
     {
-        java.lang.Object obj = _propertyList.elementAt(index);
-        _propertyList.removeElementAt(index);
-        return (jalview.schemabinding.version2.Property) obj;
-    } //-- jalview.schemabinding.version2.Property removeProperty(int) 
-
-    /**
-     * Method setProperty
-     * 
-     * 
-     * 
-     * @param index
-     * @param vProperty
-     */
-    public void setProperty(int index, jalview.schemabinding.version2.Property vProperty)
-        throws java.lang.IndexOutOfBoundsException
+      mArray[index] = (jalview.schemabinding.version2.Property) _propertyList.
+          elementAt(index);
+    }
+    return mArray;
+  } //-- jalview.schemabinding.version2.Property[] getProperty()
+
+  /**
+   * Method getPropertyCount
+   *
+   *
+   *
+   * @return int
+   */
+  public int getPropertyCount()
+  {
+    return _propertyList.size();
+  } //-- int getPropertyCount()
+
+  /**
+   * Method removeAllProperty
+   *
+   */
+  public void removeAllProperty()
+  {
+    _propertyList.removeAllElements();
+  } //-- void removeAllProperty()
+
+  /**
+   * Method removeProperty
+   *
+   *
+   *
+   * @param index
+   * @return Property
+   */
+  public jalview.schemabinding.version2.Property removeProperty(int index)
+  {
+    java.lang.Object obj = _propertyList.elementAt(index);
+    _propertyList.removeElementAt(index);
+    return (jalview.schemabinding.version2.Property) obj;
+  } //-- jalview.schemabinding.version2.Property removeProperty(int)
+
+  /**
+   * Method setProperty
+   *
+   *
+   *
+   * @param index
+   * @param vProperty
+   */
+  public void setProperty(int index,
+                          jalview.schemabinding.version2.Property vProperty)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _propertyList.size()))
     {
-        //-- check bounds for index
-        if ((index < 0) || (index > _propertyList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        _propertyList.setElementAt(vProperty, index);
-    } //-- void setProperty(int, jalview.schemabinding.version2.Property) 
-
-    /**
-     * Method setProperty
-     * 
-     * 
-     * 
-     * @param propertyArray
-     */
-    public void setProperty(jalview.schemabinding.version2.Property[] propertyArray)
+      throw new IndexOutOfBoundsException();
+    }
+    _propertyList.setElementAt(vProperty, index);
+  } //-- void setProperty(int, jalview.schemabinding.version2.Property)
+
+  /**
+   * Method setProperty
+   *
+   *
+   *
+   * @param propertyArray
+   */
+  public void setProperty(jalview.schemabinding.version2.Property[]
+                          propertyArray)
+  {
+    //-- copy array
+    _propertyList.removeAllElements();
+    for (int i = 0; i < propertyArray.length; i++)
     {
-        //-- copy array
-        _propertyList.removeAllElements();
-        for (int i = 0; i < propertyArray.length; i++) {
-            _propertyList.addElement(propertyArray[i]);
-        }
-    } //-- void setProperty(jalview.schemabinding.version2.Property) 
+      _propertyList.addElement(propertyArray[i]);
+    }
+  } //-- void setProperty(jalview.schemabinding.version2.Property)
 
 }
diff --git a/src/jalview/schemabinding/version2/PdbentryItemDescriptor.java b/src/jalview/schemabinding/version2/PdbentryItemDescriptor.java
index d9d36c0..7c1b0d4 100755
--- a/src/jalview/schemabinding/version2/PdbentryItemDescriptor.java
+++ b/src/jalview/schemabinding/version2/PdbentryItemDescriptor.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,202 +7,207 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
 //---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
 
-import org.exolab.castor.mapping.AccessMode;
-import org.exolab.castor.xml.TypeValidator;
-import org.exolab.castor.xml.XMLFieldDescriptor;
-import org.exolab.castor.xml.validators.*;
 
 /**
  * Class PdbentryItemDescriptor.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class PdbentryItemDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field nsPrefix
-     */
-    private java.lang.String nsPrefix;
-
-    /**
-     * Field nsURI
-     */
-    private java.lang.String nsURI;
-
-    /**
-     * Field xmlName
-     */
-    private java.lang.String xmlName;
-
-    /**
-     * Field identity
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor identity;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public PdbentryItemDescriptor() {
-        super();
-        nsURI = "www.jalview.org";
-        xmlName = "pdbentry";
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.xml.XMLFieldHandler              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 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);
-    } //-- jalview.schemabinding.version2.PdbentryItemDescriptor()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method getAccessMode
-     * 
-     * 
-     * 
-     * @return AccessMode
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode()
-    {
-        return null;
-    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
-
-    /**
-     * Method getExtends
-     * 
-     * 
-     * 
-     * @return ClassDescriptor
-     */
-    public org.exolab.castor.mapping.ClassDescriptor getExtends()
-    {
-        return null;
-    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
-
-    /**
-     * Method getIdentity
-     * 
-     * 
-     * 
-     * @return FieldDescriptor
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
-    {
-        return identity;
-    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
-
-    /**
-     * Method getJavaClass
-     * 
-     * 
-     * 
-     * @return Class
-     */
-    public java.lang.Class getJavaClass()
+public class PdbentryItemDescriptor
+    extends org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  //--------------------------/
+  //- Class/Member Variables -/
+  //--------------------------/
+
+  /**
+   * Field nsPrefix
+   */
+  private java.lang.String nsPrefix;
+
+  /**
+   * Field nsURI
+   */
+  private java.lang.String nsURI;
+
+  /**
+   * Field xmlName
+   */
+  private java.lang.String xmlName;
+
+  /**
+   * Field identity
+   */
+  private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+  //----------------/
+  //- Constructors -/
+  //----------------/
+
+  public PdbentryItemDescriptor()
+  {
+    super();
+    nsURI = "www.jalview.org";
+    xmlName = "pdbentry";
+
+    //-- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.xml.XMLFieldHandler 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()
     {
-        return jalview.schemabinding.version2.PdbentryItem.class;
-    } //-- java.lang.Class getJavaClass() 
-
-    /**
-     * Method getNameSpacePrefix
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpacePrefix()
-    {
-        return nsPrefix;
-    } //-- java.lang.String getNameSpacePrefix() 
-
-    /**
-     * Method getNameSpaceURI
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpaceURI()
-    {
-        return nsURI;
-    } //-- java.lang.String getNameSpaceURI() 
-
-    /**
-     * Method getValidator
-     * 
-     * 
-     * 
-     * @return TypeValidator
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator()
-    {
-        return this;
-    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
-
-    /**
-     * Method getXMLName
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getXMLName()
-    {
-        return xmlName;
-    } //-- java.lang.String getXMLName() 
+      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 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);
+  } //-- jalview.schemabinding.version2.PdbentryItemDescriptor()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Method getAccessMode
+   *
+   *
+   *
+   * @return AccessMode
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
+
+  /**
+   * Method getExtends
+   *
+   *
+   *
+   * @return ClassDescriptor
+   */
+  public org.exolab.castor.mapping.ClassDescriptor getExtends()
+  {
+    return null;
+  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
+
+  /**
+   * Method getIdentity
+   *
+   *
+   *
+   * @return FieldDescriptor
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return identity;
+  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
+
+  /**
+   * Method getJavaClass
+   *
+   *
+   *
+   * @return Class
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.PdbentryItem.class;
+  } //-- java.lang.Class getJavaClass()
+
+  /**
+   * Method getNameSpacePrefix
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return nsPrefix;
+  } //-- java.lang.String getNameSpacePrefix()
+
+  /**
+   * Method getNameSpaceURI
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return nsURI;
+  } //-- java.lang.String getNameSpaceURI()
+
+  /**
+   * Method getValidator
+   *
+   *
+   *
+   * @return TypeValidator
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  } //-- org.exolab.castor.xml.TypeValidator getValidator()
+
+  /**
+   * Method getXMLName
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getXMLName()
+  {
+    return xmlName;
+  } //-- java.lang.String getXMLName()
 
 }
diff --git a/src/jalview/schemabinding/version2/Pdbids.java b/src/jalview/schemabinding/version2/Pdbids.java
index 53b2e91..8625b88 100755
--- a/src/jalview/schemabinding/version2/Pdbids.java
+++ b/src/jalview/schemabinding/version2/Pdbids.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,112 +7,110 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
+import org.exolab.castor.xml.*;
 
 /**
  * Class Pdbids.
- * 
+ *
  * @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();
+  } //-- jalview.schemabinding.version2.Pdbids()
 
-    public Pdbids() {
-        super();
-    } //-- jalview.schemabinding.version2.Pdbids()
+  //-----------/
+  //- Methods -/
+  //-----------/
 
+  /**
+   * Method isValid
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    }
+    catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  } //-- boolean isValid()
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param out
+   */
+  public void marshal(java.io.Writer out)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
 
-    /**
-     * Method isValid
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean isValid()
-    {
-        try {
-            validate();
-        }
-        catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    } //-- boolean isValid() 
+    Marshaller.marshal(this, out);
+  } //-- void marshal(java.io.Writer)
 
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param out
-     */
-    public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, out);
-    } //-- void marshal(java.io.Writer) 
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param handler
+   */
+  public void marshal(org.xml.sax.ContentHandler handler)
+      throws java.io.IOException, org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
 
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param handler
-     */
-    public void marshal(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, handler);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
+    Marshaller.marshal(this, handler);
+  } //-- void marshal(org.xml.sax.ContentHandler)
 
-    /**
-     * Method unmarshal
-     * 
-     * 
-     * 
-     * @param reader
-     * @return Object
-     */
-    public static java.lang.Object unmarshal(java.io.Reader reader)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        return (jalview.schemabinding.version2.Pdbids) Unmarshaller.unmarshal(jalview.schemabinding.version2.Pdbids.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
+  /**
+   * Method unmarshal
+   *
+   *
+   *
+   * @param reader
+   * @return Object
+   */
+  public static java.lang.Object unmarshal(java.io.Reader reader)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.Pdbids) Unmarshaller.unmarshal(
+        jalview.schemabinding.version2.Pdbids.class, reader);
+  } //-- java.lang.Object unmarshal(java.io.Reader)
 
-    /**
-     * Method validate
-     * 
-     */
-    public void validate()
-        throws org.exolab.castor.xml.ValidationException
-    {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    } //-- void validate() 
+  /**
+   * Method validate
+   *
+   */
+  public void validate()
+      throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.
+        Validator();
+    validator.validate(this);
+  } //-- void validate()
 
 }
diff --git a/src/jalview/schemabinding/version2/PdbidsDescriptor.java b/src/jalview/schemabinding/version2/PdbidsDescriptor.java
index 607f122..2d539c9 100755
--- a/src/jalview/schemabinding/version2/PdbidsDescriptor.java
+++ b/src/jalview/schemabinding/version2/PdbidsDescriptor.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,160 +7,159 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
 //---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
 
-import org.exolab.castor.mapping.AccessMode;
-import org.exolab.castor.xml.TypeValidator;
-import org.exolab.castor.xml.XMLFieldDescriptor;
-import org.exolab.castor.xml.validators.*;
 
 /**
  * Class PdbidsDescriptor.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class PdbidsDescriptor extends PdbentryDescriptor {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field nsPrefix
-     */
-    private java.lang.String nsPrefix;
-
-    /**
-     * Field nsURI
-     */
-    private java.lang.String nsURI;
-
-    /**
-     * Field xmlName
-     */
-    private java.lang.String xmlName;
-
-    /**
-     * Field identity
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor identity;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public PdbidsDescriptor() {
-        super();
-        setExtendsWithoutFlatten(new PdbentryDescriptor());
-        nsURI = "www.jalview.org";
-        xmlName = "pdbids";
-    } //-- jalview.schemabinding.version2.PdbidsDescriptor()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method getAccessMode
-     * 
-     * 
-     * 
-     * @return AccessMode
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode()
-    {
-        return null;
-    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
-
-    /**
-     * Method getExtends
-     * 
-     * 
-     * 
-     * @return ClassDescriptor
-     */
-    public org.exolab.castor.mapping.ClassDescriptor getExtends()
-    {
-        return super.getExtends();
-    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
-
-    /**
-     * Method getIdentity
-     * 
-     * 
-     * 
-     * @return FieldDescriptor
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
-    {
-        if (identity == null)
-            return super.getIdentity();
-        return identity;
-    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
-
-    /**
-     * Method getJavaClass
-     * 
-     * 
-     * 
-     * @return Class
-     */
-    public java.lang.Class getJavaClass()
-    {
-        return jalview.schemabinding.version2.Pdbids.class;
-    } //-- java.lang.Class getJavaClass() 
-
-    /**
-     * Method getNameSpacePrefix
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpacePrefix()
-    {
-        return nsPrefix;
-    } //-- java.lang.String getNameSpacePrefix() 
-
-    /**
-     * Method getNameSpaceURI
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpaceURI()
-    {
-        return nsURI;
-    } //-- java.lang.String getNameSpaceURI() 
-
-    /**
-     * Method getValidator
-     * 
-     * 
-     * 
-     * @return TypeValidator
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator()
-    {
-        return this;
-    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
-
-    /**
-     * Method getXMLName
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getXMLName()
+public class PdbidsDescriptor
+    extends PdbentryDescriptor
+{
+
+  //--------------------------/
+  //- Class/Member Variables -/
+  //--------------------------/
+
+  /**
+   * Field nsPrefix
+   */
+  private java.lang.String nsPrefix;
+
+  /**
+   * Field nsURI
+   */
+  private java.lang.String nsURI;
+
+  /**
+   * Field xmlName
+   */
+  private java.lang.String xmlName;
+
+  /**
+   * Field identity
+   */
+  private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+  //----------------/
+  //- Constructors -/
+  //----------------/
+
+  public PdbidsDescriptor()
+  {
+    super();
+    setExtendsWithoutFlatten(new PdbentryDescriptor());
+    nsURI = "www.jalview.org";
+    xmlName = "pdbids";
+  } //-- jalview.schemabinding.version2.PdbidsDescriptor()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Method getAccessMode
+   *
+   *
+   *
+   * @return AccessMode
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
+
+  /**
+   * Method getExtends
+   *
+   *
+   *
+   * @return ClassDescriptor
+   */
+  public org.exolab.castor.mapping.ClassDescriptor getExtends()
+  {
+    return super.getExtends();
+  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
+
+  /**
+   * Method getIdentity
+   *
+   *
+   *
+   * @return FieldDescriptor
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    if (identity == null)
     {
-        return xmlName;
-    } //-- java.lang.String getXMLName() 
+      return super.getIdentity();
+    }
+    return identity;
+  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
+
+  /**
+   * Method getJavaClass
+   *
+   *
+   *
+   * @return Class
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.Pdbids.class;
+  } //-- java.lang.Class getJavaClass()
+
+  /**
+   * Method getNameSpacePrefix
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return nsPrefix;
+  } //-- java.lang.String getNameSpacePrefix()
+
+  /**
+   * Method getNameSpaceURI
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return nsURI;
+  } //-- java.lang.String getNameSpaceURI()
+
+  /**
+   * Method getValidator
+   *
+   *
+   *
+   * @return TypeValidator
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  } //-- org.exolab.castor.xml.TypeValidator getValidator()
+
+  /**
+   * Method getXMLName
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getXMLName()
+  {
+    return xmlName;
+  } //-- java.lang.String getXMLName()
 
 }
diff --git a/src/jalview/schemabinding/version2/Property.java b/src/jalview/schemabinding/version2/Property.java
index 338dd90..4059340 100755
--- a/src/jalview/schemabinding/version2/Property.java
+++ b/src/jalview/schemabinding/version2/Property.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,167 +7,166 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
+import org.exolab.castor.xml.*;
 
 /**
  * Class Property.
- * 
+ *
  * @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();
-    } //-- jalview.schemabinding.version2.Property()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Returns the value of field 'name'.
-     * 
-     * @return String
-     * @return the value of field 'name'.
-     */
-    public java.lang.String getName()
-    {
-        return this._name;
-    } //-- java.lang.String getName() 
-
-    /**
-     * Returns the value of field 'value'.
-     * 
-     * @return String
-     * @return the value of field 'value'.
-     */
-    public java.lang.String getValue()
-    {
-        return this._value;
-    } //-- java.lang.String getValue() 
-
-    /**
-     * Method isValid
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean isValid()
-    {
-        try {
-            validate();
-        }
-        catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    } //-- boolean isValid() 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param out
-     */
-    public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, out);
-    } //-- void marshal(java.io.Writer) 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param handler
-     */
-    public void marshal(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, handler);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
-
-    /**
-     * Sets the value of field 'name'.
-     * 
-     * @param name the value of field 'name'.
-     */
-    public void setName(java.lang.String name)
-    {
-        this._name = name;
-    } //-- void setName(java.lang.String) 
-
-    /**
-     * Sets the value of field 'value'.
-     * 
-     * @param value the value of field 'value'.
-     */
-    public void setValue(java.lang.String value)
-    {
-        this._value = value;
-    } //-- void setValue(java.lang.String) 
-
-    /**
-     * Method unmarshal
-     * 
-     * 
-     * 
-     * @param reader
-     * @return Object
-     */
-    public static java.lang.Object unmarshal(java.io.Reader reader)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+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();
+  } //-- jalview.schemabinding.version2.Property()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Returns the value of field 'name'.
+   *
+   * @return String
+   * @return the value of field 'name'.
+   */
+  public java.lang.String getName()
+  {
+    return this._name;
+  } //-- java.lang.String getName()
+
+  /**
+   * Returns the value of field 'value'.
+   *
+   * @return String
+   * @return the value of field 'value'.
+   */
+  public java.lang.String getValue()
+  {
+    return this._value;
+  } //-- java.lang.String getValue()
+
+  /**
+   * Method isValid
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean isValid()
+  {
+    try
     {
-        return (jalview.schemabinding.version2.Property) Unmarshaller.unmarshal(jalview.schemabinding.version2.Property.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
-
-    /**
-     * Method validate
-     * 
-     */
-    public void validate()
-        throws org.exolab.castor.xml.ValidationException
+      validate();
+    }
+    catch (org.exolab.castor.xml.ValidationException vex)
     {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    } //-- void validate() 
+      return false;
+    }
+    return true;
+  } //-- boolean isValid()
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param out
+   */
+  public void marshal(java.io.Writer out)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, out);
+  } //-- void marshal(java.io.Writer)
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param handler
+   */
+  public void marshal(org.xml.sax.ContentHandler handler)
+      throws java.io.IOException, org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, handler);
+  } //-- void marshal(org.xml.sax.ContentHandler)
+
+  /**
+   * Sets the value of field 'name'.
+   *
+   * @param name the value of field 'name'.
+   */
+  public void setName(java.lang.String name)
+  {
+    this._name = name;
+  } //-- void setName(java.lang.String)
+
+  /**
+   * Sets the value of field 'value'.
+   *
+   * @param value the value of field 'value'.
+   */
+  public void setValue(java.lang.String value)
+  {
+    this._value = value;
+  } //-- void setValue(java.lang.String)
+
+  /**
+   * Method unmarshal
+   *
+   *
+   *
+   * @param reader
+   * @return Object
+   */
+  public static java.lang.Object unmarshal(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);
+  } //-- java.lang.Object unmarshal(java.io.Reader)
+
+  /**
+   * Method validate
+   *
+   */
+  public void validate()
+      throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.
+        Validator();
+    validator.validate(this);
+  } //-- void validate()
 
 }
diff --git a/src/jalview/schemabinding/version2/PropertyDescriptor.java b/src/jalview/schemabinding/version2/PropertyDescriptor.java
index e22704c..9d0eafa 100755
--- a/src/jalview/schemabinding/version2/PropertyDescriptor.java
+++ b/src/jalview/schemabinding/version2/PropertyDescriptor.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,240 +7,252 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
-import org.exolab.castor.mapping.AccessMode;
-import org.exolab.castor.xml.TypeValidator;
-import org.exolab.castor.xml.XMLFieldDescriptor;
 import org.exolab.castor.xml.validators.*;
 
 /**
  * Class PropertyDescriptor.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class PropertyDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field nsPrefix
-     */
-    private java.lang.String nsPrefix;
-
-    /**
-     * Field nsURI
-     */
-    private java.lang.String nsURI;
-
-    /**
-     * Field xmlName
-     */
-    private java.lang.String xmlName;
-
-    /**
-     * Field identity
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor identity;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public PropertyDescriptor() {
-        super();
-        nsURI = "www.jalview.org";
-        xmlName = "property";
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.xml.XMLFieldHandler              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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _name
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            StringValidator typeValidator = new StringValidator();
-            typeValidator.setWhiteSpace("preserve");
-            fieldValidator.setValidator(typeValidator);
+public class PropertyDescriptor
+    extends org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  //--------------------------/
+  //- Class/Member Variables -/
+  //--------------------------/
+
+  /**
+   * Field nsPrefix
+   */
+  private java.lang.String nsPrefix;
+
+  /**
+   * Field nsURI
+   */
+  private java.lang.String nsURI;
+
+  /**
+   * Field xmlName
+   */
+  private java.lang.String xmlName;
+
+  /**
+   * Field identity
+   */
+  private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+  //----------------/
+  //- Constructors -/
+  //----------------/
+
+  public PropertyDescriptor()
+  {
+    super();
+    nsURI = "www.jalview.org";
+    xmlName = "property";
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.xml.XMLFieldHandler 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);
         }
-        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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _value
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            StringValidator typeValidator = new StringValidator();
-            typeValidator.setWhiteSpace("preserve");
-            fieldValidator.setValidator(typeValidator);
+        catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-    } //-- jalview.schemabinding.version2.PropertyDescriptor()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method getAccessMode
-     * 
-     * 
-     * 
-     * @return AccessMode
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode()
-    {
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
-
-    /**
-     * Method getExtends
-     * 
-     * 
-     * 
-     * @return ClassDescriptor
-     */
-    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+      }
+    });
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _name
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { //-- local scope
+      StringValidator typeValidator = new StringValidator();
+      typeValidator.setWhiteSpace("preserve");
+      fieldValidator.setValidator(typeValidator);
+    }
+    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;
-    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
-
-    /**
-     * Method getIdentity
-     * 
-     * 
-     * 
-     * @return FieldDescriptor
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
-    {
-        return identity;
-    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
-
-    /**
-     * Method getJavaClass
-     * 
-     * 
-     * 
-     * @return Class
-     */
-    public java.lang.Class getJavaClass()
-    {
-        return jalview.schemabinding.version2.Property.class;
-    } //-- java.lang.Class getJavaClass() 
-
-    /**
-     * Method getNameSpacePrefix
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpacePrefix()
-    {
-        return nsPrefix;
-    } //-- java.lang.String getNameSpacePrefix() 
-
-    /**
-     * Method getNameSpaceURI
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpaceURI()
-    {
-        return nsURI;
-    } //-- java.lang.String getNameSpaceURI() 
-
-    /**
-     * Method getValidator
-     * 
-     * 
-     * 
-     * @return TypeValidator
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator()
-    {
-        return this;
-    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
-
-    /**
-     * Method getXMLName
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getXMLName()
-    {
-        return xmlName;
-    } //-- java.lang.String getXMLName() 
+      }
+    });
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _value
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { //-- local scope
+      StringValidator typeValidator = new StringValidator();
+      typeValidator.setWhiteSpace("preserve");
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    //-- initialize element descriptors
+
+  } //-- jalview.schemabinding.version2.PropertyDescriptor()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Method getAccessMode
+   *
+   *
+   *
+   * @return AccessMode
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
+
+  /**
+   * Method getExtends
+   *
+   *
+   *
+   * @return ClassDescriptor
+   */
+  public org.exolab.castor.mapping.ClassDescriptor getExtends()
+  {
+    return null;
+  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
+
+  /**
+   * Method getIdentity
+   *
+   *
+   *
+   * @return FieldDescriptor
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return identity;
+  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
+
+  /**
+   * Method getJavaClass
+   *
+   *
+   *
+   * @return Class
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.Property.class;
+  } //-- java.lang.Class getJavaClass()
+
+  /**
+   * Method getNameSpacePrefix
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return nsPrefix;
+  } //-- java.lang.String getNameSpacePrefix()
+
+  /**
+   * Method getNameSpaceURI
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return nsURI;
+  } //-- java.lang.String getNameSpaceURI()
+
+  /**
+   * Method getValidator
+   *
+   *
+   *
+   * @return TypeValidator
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  } //-- org.exolab.castor.xml.TypeValidator getValidator()
+
+  /**
+   * Method getXMLName
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getXMLName()
+  {
+    return xmlName;
+  } //-- java.lang.String getXMLName()
 
 }
diff --git a/src/jalview/schemabinding/version2/Sequence.java b/src/jalview/schemabinding/version2/Sequence.java
index 993ad23..372a2c5 100755
--- a/src/jalview/schemabinding/version2/Sequence.java
+++ b/src/jalview/schemabinding/version2/Sequence.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,270 +7,274 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
 //---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import java.util.*;
 
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import java.util.Enumeration;
-import java.util.Vector;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
+import org.exolab.castor.xml.*;
 
 /**
  * Class Sequence.
- * 
+ *
  * @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 -/
+  //--------------------------/
 
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
+  /**
+   * Field _DBRefList
+   */
+  private java.util.Vector _DBRefList;
 
-    /**
-     * Field _DBRefList
-     */
-    private java.util.Vector _DBRefList;
+  //----------------/
+  //- Constructors -/
+  //----------------/
 
+  public Sequence()
+  {
+    super();
+    _DBRefList = new Vector();
+  } //-- jalview.schemabinding.version2.Sequence()
 
-      //----------------/
-     //- Constructors -/
-    //----------------/
+  //-----------/
+  //- Methods -/
+  //-----------/
 
-    public Sequence() {
-        super();
-        _DBRefList = new Vector();
-    } //-- jalview.schemabinding.version2.Sequence()
+  /**
+   * Method addDBRef
+   *
+   *
+   *
+   * @param vDBRef
+   */
+  public void addDBRef(jalview.schemabinding.version2.DBRef vDBRef)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _DBRefList.addElement(vDBRef);
+  } //-- void addDBRef(jalview.schemabinding.version2.DBRef)
 
+  /**
+   * Method addDBRef
+   *
+   *
+   *
+   * @param index
+   * @param vDBRef
+   */
+  public void addDBRef(int index, jalview.schemabinding.version2.DBRef vDBRef)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _DBRefList.insertElementAt(vDBRef, index);
+  } //-- void addDBRef(int, jalview.schemabinding.version2.DBRef)
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+  /**
+   * Method enumerateDBRef
+   *
+   *
+   *
+   * @return Enumeration
+   */
+  public java.util.Enumeration enumerateDBRef()
+  {
+    return _DBRefList.elements();
+  } //-- java.util.Enumeration enumerateDBRef()
 
-    /**
-     * Method addDBRef
-     * 
-     * 
-     * 
-     * @param vDBRef
-     */
-    public void addDBRef(jalview.schemabinding.version2.DBRef vDBRef)
-        throws java.lang.IndexOutOfBoundsException
+  /**
+   * Method getDBRef
+   *
+   *
+   *
+   * @param index
+   * @return DBRef
+   */
+  public jalview.schemabinding.version2.DBRef getDBRef(int index)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _DBRefList.size()))
     {
-        _DBRefList.addElement(vDBRef);
-    } //-- void addDBRef(jalview.schemabinding.version2.DBRef) 
+      throw new IndexOutOfBoundsException();
+    }
 
-    /**
-     * Method addDBRef
-     * 
-     * 
-     * 
-     * @param index
-     * @param vDBRef
-     */
-    public void addDBRef(int index, jalview.schemabinding.version2.DBRef vDBRef)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _DBRefList.insertElementAt(vDBRef, index);
-    } //-- void addDBRef(int, jalview.schemabinding.version2.DBRef) 
+    return (jalview.schemabinding.version2.DBRef) _DBRefList.elementAt(index);
+  } //-- jalview.schemabinding.version2.DBRef getDBRef(int)
 
-    /**
-     * Method enumerateDBRef
-     * 
-     * 
-     * 
-     * @return Enumeration
-     */
-    public java.util.Enumeration enumerateDBRef()
+  /**
+   * Method getDBRef
+   *
+   *
+   *
+   * @return DBRef
+   */
+  public jalview.schemabinding.version2.DBRef[] getDBRef()
+  {
+    int size = _DBRefList.size();
+    jalview.schemabinding.version2.DBRef[] mArray = new jalview.schemabinding.
+        version2.DBRef[size];
+    for (int index = 0; index < size; index++)
     {
-        return _DBRefList.elements();
-    } //-- java.util.Enumeration enumerateDBRef() 
+      mArray[index] = (jalview.schemabinding.version2.DBRef) _DBRefList.
+          elementAt(index);
+    }
+    return mArray;
+  } //-- jalview.schemabinding.version2.DBRef[] getDBRef()
 
-    /**
-     * Method getDBRef
-     * 
-     * 
-     * 
-     * @param index
-     * @return DBRef
-     */
-    public jalview.schemabinding.version2.DBRef getDBRef(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _DBRefList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        
-        return (jalview.schemabinding.version2.DBRef) _DBRefList.elementAt(index);
-    } //-- jalview.schemabinding.version2.DBRef getDBRef(int) 
+  /**
+   * Method getDBRefCount
+   *
+   *
+   *
+   * @return int
+   */
+  public int getDBRefCount()
+  {
+    return _DBRefList.size();
+  } //-- int getDBRefCount()
 
-    /**
-     * Method getDBRef
-     * 
-     * 
-     * 
-     * @return DBRef
-     */
-    public jalview.schemabinding.version2.DBRef[] getDBRef()
+  /**
+   * Method isValid
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean isValid()
+  {
+    try
     {
-        int size = _DBRefList.size();
-        jalview.schemabinding.version2.DBRef[] mArray = new jalview.schemabinding.version2.DBRef[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = (jalview.schemabinding.version2.DBRef) _DBRefList.elementAt(index);
-        }
-        return mArray;
-    } //-- jalview.schemabinding.version2.DBRef[] getDBRef() 
-
-    /**
-     * Method getDBRefCount
-     * 
-     * 
-     * 
-     * @return int
-     */
-    public int getDBRefCount()
+      validate();
+    }
+    catch (org.exolab.castor.xml.ValidationException vex)
     {
-        return _DBRefList.size();
-    } //-- int getDBRefCount() 
+      return false;
+    }
+    return true;
+  } //-- boolean isValid()
 
-    /**
-     * Method isValid
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean isValid()
-    {
-        try {
-            validate();
-        }
-        catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    } //-- boolean isValid() 
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param out
+   */
+  public void marshal(java.io.Writer out)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
 
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param out
-     */
-    public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, out);
-    } //-- void marshal(java.io.Writer) 
+    Marshaller.marshal(this, out);
+  } //-- void marshal(java.io.Writer)
 
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param handler
-     */
-    public void marshal(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, handler);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param handler
+   */
+  public void marshal(org.xml.sax.ContentHandler handler)
+      throws java.io.IOException, org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
 
-    /**
-     * Method removeAllDBRef
-     * 
-     */
-    public void removeAllDBRef()
-    {
-        _DBRefList.removeAllElements();
-    } //-- void removeAllDBRef() 
+    Marshaller.marshal(this, handler);
+  } //-- void marshal(org.xml.sax.ContentHandler)
 
-    /**
-     * Method removeDBRef
-     * 
-     * 
-     * 
-     * @param index
-     * @return DBRef
-     */
-    public jalview.schemabinding.version2.DBRef removeDBRef(int index)
-    {
-        java.lang.Object obj = _DBRefList.elementAt(index);
-        _DBRefList.removeElementAt(index);
-        return (jalview.schemabinding.version2.DBRef) obj;
-    } //-- jalview.schemabinding.version2.DBRef removeDBRef(int) 
+  /**
+   * Method removeAllDBRef
+   *
+   */
+  public void removeAllDBRef()
+  {
+    _DBRefList.removeAllElements();
+  } //-- void removeAllDBRef()
 
-    /**
-     * Method setDBRef
-     * 
-     * 
-     * 
-     * @param index
-     * @param vDBRef
-     */
-    public void setDBRef(int index, jalview.schemabinding.version2.DBRef vDBRef)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _DBRefList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        _DBRefList.setElementAt(vDBRef, index);
-    } //-- void setDBRef(int, jalview.schemabinding.version2.DBRef) 
+  /**
+   * Method removeDBRef
+   *
+   *
+   *
+   * @param index
+   * @return DBRef
+   */
+  public jalview.schemabinding.version2.DBRef removeDBRef(int index)
+  {
+    java.lang.Object obj = _DBRefList.elementAt(index);
+    _DBRefList.removeElementAt(index);
+    return (jalview.schemabinding.version2.DBRef) obj;
+  } //-- jalview.schemabinding.version2.DBRef removeDBRef(int)
 
-    /**
-     * Method setDBRef
-     * 
-     * 
-     * 
-     * @param DBRefArray
-     */
-    public void setDBRef(jalview.schemabinding.version2.DBRef[] DBRefArray)
+  /**
+   * Method setDBRef
+   *
+   *
+   *
+   * @param index
+   * @param vDBRef
+   */
+  public void setDBRef(int index, jalview.schemabinding.version2.DBRef vDBRef)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _DBRefList.size()))
     {
-        //-- copy array
-        _DBRefList.removeAllElements();
-        for (int i = 0; i < DBRefArray.length; i++) {
-            _DBRefList.addElement(DBRefArray[i]);
-        }
-    } //-- void setDBRef(jalview.schemabinding.version2.DBRef) 
+      throw new IndexOutOfBoundsException();
+    }
+    _DBRefList.setElementAt(vDBRef, index);
+  } //-- void setDBRef(int, jalview.schemabinding.version2.DBRef)
 
-    /**
-     * Method unmarshal
-     * 
-     * 
-     * 
-     * @param reader
-     * @return Object
-     */
-    public static java.lang.Object unmarshal(java.io.Reader reader)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+  /**
+   * Method setDBRef
+   *
+   *
+   *
+   * @param DBRefArray
+   */
+  public void setDBRef(jalview.schemabinding.version2.DBRef[] DBRefArray)
+  {
+    //-- copy array
+    _DBRefList.removeAllElements();
+    for (int i = 0; i < DBRefArray.length; i++)
     {
-        return (jalview.schemabinding.version2.Sequence) Unmarshaller.unmarshal(jalview.schemabinding.version2.Sequence.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
+      _DBRefList.addElement(DBRefArray[i]);
+    }
+  } //-- void setDBRef(jalview.schemabinding.version2.DBRef)
 
-    /**
-     * Method validate
-     * 
-     */
-    public void validate()
-        throws org.exolab.castor.xml.ValidationException
-    {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    } //-- void validate() 
+  /**
+   * Method unmarshal
+   *
+   *
+   *
+   * @param reader
+   * @return Object
+   */
+  public static java.lang.Object unmarshal(java.io.Reader reader)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.Sequence) Unmarshaller.unmarshal(
+        jalview.schemabinding.version2.Sequence.class, reader);
+  } //-- java.lang.Object unmarshal(java.io.Reader)
+
+  /**
+   * Method validate
+   *
+   */
+  public void validate()
+      throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.
+        Validator();
+    validator.validate(this);
+  } //-- void validate()
 
 }
diff --git a/src/jalview/schemabinding/version2/SequenceDescriptor.java b/src/jalview/schemabinding/version2/SequenceDescriptor.java
index 555284a..8c621ca 100755
--- a/src/jalview/schemabinding/version2/SequenceDescriptor.java
+++ b/src/jalview/schemabinding/version2/SequenceDescriptor.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,205 +7,213 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
 //---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
 
-import org.exolab.castor.mapping.AccessMode;
-import org.exolab.castor.xml.TypeValidator;
-import org.exolab.castor.xml.XMLFieldDescriptor;
-import org.exolab.castor.xml.validators.*;
 
 /**
  * Class SequenceDescriptor.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class SequenceDescriptor extends jalview.schemabinding.version2.SequenceTypeDescriptor {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field nsPrefix
-     */
-    private java.lang.String nsPrefix;
-
-    /**
-     * Field nsURI
-     */
-    private java.lang.String nsURI;
-
-    /**
-     * Field xmlName
-     */
-    private java.lang.String xmlName;
-
-    /**
-     * Field identity
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor identity;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public SequenceDescriptor() {
-        super();
-        setExtendsWithoutFlatten(new jalview.schemabinding.version2.SequenceTypeDescriptor());
-        nsURI = "www.vamsas.ac.uk/jalview/version2";
-        xmlName = "Sequence";
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.xml.XMLFieldHandler              handler        = null;
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
-        //-- initialize attribute descriptors
-        
-        //-- 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 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);
-    } //-- jalview.schemabinding.version2.SequenceDescriptor()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method getAccessMode
-     * 
-     * 
-     * 
-     * @return AccessMode
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode()
-    {
-        return null;
-    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
-
-    /**
-     * Method getExtends
-     * 
-     * 
-     * 
-     * @return ClassDescriptor
-     */
-    public org.exolab.castor.mapping.ClassDescriptor getExtends()
-    {
-        return super.getExtends();
-    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
-
-    /**
-     * Method getIdentity
-     * 
-     * 
-     * 
-     * @return FieldDescriptor
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
-    {
-        if (identity == null)
-            return super.getIdentity();
-        return identity;
-    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
-
-    /**
-     * Method getJavaClass
-     * 
-     * 
-     * 
-     * @return Class
-     */
-    public java.lang.Class getJavaClass()
+public class SequenceDescriptor
+    extends jalview.schemabinding.version2.SequenceTypeDescriptor
+{
+
+  //--------------------------/
+  //- Class/Member Variables -/
+  //--------------------------/
+
+  /**
+   * Field nsPrefix
+   */
+  private java.lang.String nsPrefix;
+
+  /**
+   * Field nsURI
+   */
+  private java.lang.String nsURI;
+
+  /**
+   * Field xmlName
+   */
+  private java.lang.String xmlName;
+
+  /**
+   * Field identity
+   */
+  private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+  //----------------/
+  //- Constructors -/
+  //----------------/
+
+  public SequenceDescriptor()
+  {
+    super();
+    setExtendsWithoutFlatten(new jalview.schemabinding.version2.
+                             SequenceTypeDescriptor());
+    nsURI = "www.vamsas.ac.uk/jalview/version2";
+    xmlName = "Sequence";
+
+    //-- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.xml.XMLFieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    //-- initialize attribute descriptors
+
+    //-- 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()
     {
-        return jalview.schemabinding.version2.Sequence.class;
-    } //-- java.lang.Class getJavaClass() 
-
-    /**
-     * Method getNameSpacePrefix
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpacePrefix()
-    {
-        return nsPrefix;
-    } //-- java.lang.String getNameSpacePrefix() 
-
-    /**
-     * Method getNameSpaceURI
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpaceURI()
-    {
-        return nsURI;
-    } //-- java.lang.String getNameSpaceURI() 
-
-    /**
-     * Method getValidator
-     * 
-     * 
-     * 
-     * @return TypeValidator
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator()
-    {
-        return this;
-    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
-
-    /**
-     * Method getXMLName
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getXMLName()
+      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 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);
+  } //-- jalview.schemabinding.version2.SequenceDescriptor()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Method getAccessMode
+   *
+   *
+   *
+   * @return AccessMode
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
+
+  /**
+   * Method getExtends
+   *
+   *
+   *
+   * @return ClassDescriptor
+   */
+  public org.exolab.castor.mapping.ClassDescriptor getExtends()
+  {
+    return super.getExtends();
+  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
+
+  /**
+   * Method getIdentity
+   *
+   *
+   *
+   * @return FieldDescriptor
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    if (identity == null)
     {
-        return xmlName;
-    } //-- java.lang.String getXMLName() 
+      return super.getIdentity();
+    }
+    return identity;
+  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
+
+  /**
+   * Method getJavaClass
+   *
+   *
+   *
+   * @return Class
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.Sequence.class;
+  } //-- java.lang.Class getJavaClass()
+
+  /**
+   * Method getNameSpacePrefix
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return nsPrefix;
+  } //-- java.lang.String getNameSpacePrefix()
+
+  /**
+   * Method getNameSpaceURI
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return nsURI;
+  } //-- java.lang.String getNameSpaceURI()
+
+  /**
+   * Method getValidator
+   *
+   *
+   *
+   * @return TypeValidator
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  } //-- org.exolab.castor.xml.TypeValidator getValidator()
+
+  /**
+   * Method getXMLName
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getXMLName()
+  {
+    return xmlName;
+  } //-- java.lang.String getXMLName()
 
 }
diff --git a/src/jalview/schemabinding/version2/SequenceSet.java b/src/jalview/schemabinding/version2/SequenceSet.java
index 6f0342b..020cbb9 100755
--- a/src/jalview/schemabinding/version2/SequenceSet.java
+++ b/src/jalview/schemabinding/version2/SequenceSet.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,445 +7,467 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
 //---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import java.util.*;
 
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import java.util.Enumeration;
-import java.util.Vector;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
+import org.exolab.castor.xml.*;
 
 /**
  * Class SequenceSet.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class SequenceSet implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _gapChar
-     */
-    private java.lang.String _gapChar;
-
-    /**
-     * Field _sequenceList
-     */
-    private java.util.Vector _sequenceList;
-
-    /**
-     * Field _annotationList
-     */
-    private java.util.Vector _annotationList;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public SequenceSet() {
-        super();
-        _sequenceList = new Vector();
-        _annotationList = new Vector();
-    } //-- jalview.schemabinding.version2.SequenceSet()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method addAnnotation
-     * 
-     * 
-     * 
-     * @param vAnnotation
-     */
-    public void addAnnotation(jalview.schemabinding.version2.Annotation vAnnotation)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _annotationList.addElement(vAnnotation);
-    } //-- void addAnnotation(jalview.schemabinding.version2.Annotation) 
-
-    /**
-     * Method addAnnotation
-     * 
-     * 
-     * 
-     * @param index
-     * @param vAnnotation
-     */
-    public void addAnnotation(int index, jalview.schemabinding.version2.Annotation vAnnotation)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _annotationList.insertElementAt(vAnnotation, index);
-    } //-- void addAnnotation(int, jalview.schemabinding.version2.Annotation) 
-
-    /**
-     * Method addSequence
-     * 
-     * 
-     * 
-     * @param vSequence
-     */
-    public void addSequence(jalview.schemabinding.version2.Sequence vSequence)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _sequenceList.addElement(vSequence);
-    } //-- void addSequence(jalview.schemabinding.version2.Sequence) 
-
-    /**
-     * Method addSequence
-     * 
-     * 
-     * 
-     * @param index
-     * @param vSequence
-     */
-    public void addSequence(int index, jalview.schemabinding.version2.Sequence vSequence)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _sequenceList.insertElementAt(vSequence, index);
-    } //-- void addSequence(int, jalview.schemabinding.version2.Sequence) 
-
-    /**
-     * Method enumerateAnnotation
-     * 
-     * 
-     * 
-     * @return Enumeration
-     */
-    public java.util.Enumeration enumerateAnnotation()
-    {
-        return _annotationList.elements();
-    } //-- java.util.Enumeration enumerateAnnotation() 
-
-    /**
-     * Method enumerateSequence
-     * 
-     * 
-     * 
-     * @return Enumeration
-     */
-    public java.util.Enumeration enumerateSequence()
-    {
-        return _sequenceList.elements();
-    } //-- java.util.Enumeration enumerateSequence() 
-
-    /**
-     * Method getAnnotation
-     * 
-     * 
-     * 
-     * @param index
-     * @return Annotation
-     */
-    public jalview.schemabinding.version2.Annotation getAnnotation(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _annotationList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        
-        return (jalview.schemabinding.version2.Annotation) _annotationList.elementAt(index);
-    } //-- jalview.schemabinding.version2.Annotation getAnnotation(int) 
-
-    /**
-     * Method getAnnotation
-     * 
-     * 
-     * 
-     * @return Annotation
-     */
-    public jalview.schemabinding.version2.Annotation[] getAnnotation()
-    {
-        int size = _annotationList.size();
-        jalview.schemabinding.version2.Annotation[] mArray = new jalview.schemabinding.version2.Annotation[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = (jalview.schemabinding.version2.Annotation) _annotationList.elementAt(index);
-        }
-        return mArray;
-    } //-- jalview.schemabinding.version2.Annotation[] getAnnotation() 
-
-    /**
-     * Method getAnnotationCount
-     * 
-     * 
-     * 
-     * @return int
-     */
-    public int getAnnotationCount()
-    {
-        return _annotationList.size();
-    } //-- int getAnnotationCount() 
-
-    /**
-     * Returns the value of field 'gapChar'.
-     * 
-     * @return String
-     * @return the value of field 'gapChar'.
-     */
-    public java.lang.String getGapChar()
-    {
-        return this._gapChar;
-    } //-- java.lang.String getGapChar() 
-
-    /**
-     * Method getSequence
-     * 
-     * 
-     * 
-     * @param index
-     * @return Sequence
-     */
-    public jalview.schemabinding.version2.Sequence getSequence(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _sequenceList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        
-        return (jalview.schemabinding.version2.Sequence) _sequenceList.elementAt(index);
-    } //-- jalview.schemabinding.version2.Sequence getSequence(int) 
-
-    /**
-     * Method getSequence
-     * 
-     * 
-     * 
-     * @return Sequence
-     */
-    public jalview.schemabinding.version2.Sequence[] getSequence()
-    {
-        int size = _sequenceList.size();
-        jalview.schemabinding.version2.Sequence[] mArray = new jalview.schemabinding.version2.Sequence[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = (jalview.schemabinding.version2.Sequence) _sequenceList.elementAt(index);
-        }
-        return mArray;
-    } //-- jalview.schemabinding.version2.Sequence[] getSequence() 
-
-    /**
-     * Method getSequenceCount
-     * 
-     * 
-     * 
-     * @return int
-     */
-    public int getSequenceCount()
-    {
-        return _sequenceList.size();
-    } //-- int getSequenceCount() 
-
-    /**
-     * Method isValid
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean isValid()
-    {
-        try {
-            validate();
-        }
-        catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    } //-- boolean isValid() 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param out
-     */
-    public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, out);
-    } //-- void marshal(java.io.Writer) 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param handler
-     */
-    public void marshal(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, handler);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
-
-    /**
-     * Method removeAllAnnotation
-     * 
-     */
-    public void removeAllAnnotation()
-    {
-        _annotationList.removeAllElements();
-    } //-- void removeAllAnnotation() 
-
-    /**
-     * Method removeAllSequence
-     * 
-     */
-    public void removeAllSequence()
+public class SequenceSet
+    implements java.io.Serializable
+{
+
+  //--------------------------/
+  //- Class/Member Variables -/
+  //--------------------------/
+
+  /**
+   * Field _gapChar
+   */
+  private java.lang.String _gapChar;
+
+  /**
+   * Field _sequenceList
+   */
+  private java.util.Vector _sequenceList;
+
+  /**
+   * Field _annotationList
+   */
+  private java.util.Vector _annotationList;
+
+  //----------------/
+  //- Constructors -/
+  //----------------/
+
+  public SequenceSet()
+  {
+    super();
+    _sequenceList = new Vector();
+    _annotationList = new Vector();
+  } //-- jalview.schemabinding.version2.SequenceSet()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Method addAnnotation
+   *
+   *
+   *
+   * @param vAnnotation
+   */
+  public void addAnnotation(jalview.schemabinding.version2.Annotation
+                            vAnnotation)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _annotationList.addElement(vAnnotation);
+  } //-- void addAnnotation(jalview.schemabinding.version2.Annotation)
+
+  /**
+   * Method addAnnotation
+   *
+   *
+   *
+   * @param index
+   * @param vAnnotation
+   */
+  public void addAnnotation(int index,
+                            jalview.schemabinding.version2.Annotation
+                            vAnnotation)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _annotationList.insertElementAt(vAnnotation, index);
+  } //-- void addAnnotation(int, jalview.schemabinding.version2.Annotation)
+
+  /**
+   * Method addSequence
+   *
+   *
+   *
+   * @param vSequence
+   */
+  public void addSequence(jalview.schemabinding.version2.Sequence vSequence)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _sequenceList.addElement(vSequence);
+  } //-- void addSequence(jalview.schemabinding.version2.Sequence)
+
+  /**
+   * Method addSequence
+   *
+   *
+   *
+   * @param index
+   * @param vSequence
+   */
+  public void addSequence(int index,
+                          jalview.schemabinding.version2.Sequence vSequence)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _sequenceList.insertElementAt(vSequence, index);
+  } //-- void addSequence(int, jalview.schemabinding.version2.Sequence)
+
+  /**
+   * Method enumerateAnnotation
+   *
+   *
+   *
+   * @return Enumeration
+   */
+  public java.util.Enumeration enumerateAnnotation()
+  {
+    return _annotationList.elements();
+  } //-- java.util.Enumeration enumerateAnnotation()
+
+  /**
+   * Method enumerateSequence
+   *
+   *
+   *
+   * @return Enumeration
+   */
+  public java.util.Enumeration enumerateSequence()
+  {
+    return _sequenceList.elements();
+  } //-- java.util.Enumeration enumerateSequence()
+
+  /**
+   * Method getAnnotation
+   *
+   *
+   *
+   * @param index
+   * @return Annotation
+   */
+  public jalview.schemabinding.version2.Annotation getAnnotation(int index)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _annotationList.size()))
     {
-        _sequenceList.removeAllElements();
-    } //-- void removeAllSequence() 
-
-    /**
-     * Method removeAnnotation
-     * 
-     * 
-     * 
-     * @param index
-     * @return Annotation
-     */
-    public jalview.schemabinding.version2.Annotation removeAnnotation(int index)
+      throw new IndexOutOfBoundsException();
+    }
+
+    return (jalview.schemabinding.version2.Annotation) _annotationList.
+        elementAt(index);
+  } //-- jalview.schemabinding.version2.Annotation getAnnotation(int)
+
+  /**
+   * Method getAnnotation
+   *
+   *
+   *
+   * @return Annotation
+   */
+  public jalview.schemabinding.version2.Annotation[] getAnnotation()
+  {
+    int size = _annotationList.size();
+    jalview.schemabinding.version2.Annotation[] mArray = new jalview.
+        schemabinding.version2.Annotation[size];
+    for (int index = 0; index < size; index++)
     {
-        java.lang.Object obj = _annotationList.elementAt(index);
-        _annotationList.removeElementAt(index);
-        return (jalview.schemabinding.version2.Annotation) obj;
-    } //-- jalview.schemabinding.version2.Annotation removeAnnotation(int) 
-
-    /**
-     * Method removeSequence
-     * 
-     * 
-     * 
-     * @param index
-     * @return Sequence
-     */
-    public jalview.schemabinding.version2.Sequence removeSequence(int index)
+      mArray[index] = (jalview.schemabinding.version2.Annotation)
+          _annotationList.elementAt(index);
+    }
+    return mArray;
+  } //-- jalview.schemabinding.version2.Annotation[] getAnnotation()
+
+  /**
+   * Method getAnnotationCount
+   *
+   *
+   *
+   * @return int
+   */
+  public int getAnnotationCount()
+  {
+    return _annotationList.size();
+  } //-- int getAnnotationCount()
+
+  /**
+   * Returns the value of field 'gapChar'.
+   *
+   * @return String
+   * @return the value of field 'gapChar'.
+   */
+  public java.lang.String getGapChar()
+  {
+    return this._gapChar;
+  } //-- java.lang.String getGapChar()
+
+  /**
+   * Method getSequence
+   *
+   *
+   *
+   * @param index
+   * @return Sequence
+   */
+  public jalview.schemabinding.version2.Sequence getSequence(int index)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _sequenceList.size()))
     {
-        java.lang.Object obj = _sequenceList.elementAt(index);
-        _sequenceList.removeElementAt(index);
-        return (jalview.schemabinding.version2.Sequence) obj;
-    } //-- jalview.schemabinding.version2.Sequence removeSequence(int) 
-
-    /**
-     * Method setAnnotation
-     * 
-     * 
-     * 
-     * @param index
-     * @param vAnnotation
-     */
-    public void setAnnotation(int index, jalview.schemabinding.version2.Annotation vAnnotation)
-        throws java.lang.IndexOutOfBoundsException
+      throw new IndexOutOfBoundsException();
+    }
+
+    return (jalview.schemabinding.version2.Sequence) _sequenceList.elementAt(
+        index);
+  } //-- jalview.schemabinding.version2.Sequence getSequence(int)
+
+  /**
+   * Method getSequence
+   *
+   *
+   *
+   * @return Sequence
+   */
+  public jalview.schemabinding.version2.Sequence[] getSequence()
+  {
+    int size = _sequenceList.size();
+    jalview.schemabinding.version2.Sequence[] mArray = new jalview.
+        schemabinding.version2.Sequence[size];
+    for (int index = 0; index < size; index++)
     {
-        //-- check bounds for index
-        if ((index < 0) || (index > _annotationList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        _annotationList.setElementAt(vAnnotation, index);
-    } //-- void setAnnotation(int, jalview.schemabinding.version2.Annotation) 
-
-    /**
-     * Method setAnnotation
-     * 
-     * 
-     * 
-     * @param annotationArray
-     */
-    public void setAnnotation(jalview.schemabinding.version2.Annotation[] annotationArray)
+      mArray[index] = (jalview.schemabinding.version2.Sequence) _sequenceList.
+          elementAt(index);
+    }
+    return mArray;
+  } //-- jalview.schemabinding.version2.Sequence[] getSequence()
+
+  /**
+   * Method getSequenceCount
+   *
+   *
+   *
+   * @return int
+   */
+  public int getSequenceCount()
+  {
+    return _sequenceList.size();
+  } //-- int getSequenceCount()
+
+  /**
+   * Method isValid
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean isValid()
+  {
+    try
     {
-        //-- copy array
-        _annotationList.removeAllElements();
-        for (int i = 0; i < annotationArray.length; i++) {
-            _annotationList.addElement(annotationArray[i]);
-        }
-    } //-- void setAnnotation(jalview.schemabinding.version2.Annotation) 
-
-    /**
-     * Sets the value of field 'gapChar'.
-     * 
-     * @param gapChar the value of field 'gapChar'.
-     */
-    public void setGapChar(java.lang.String gapChar)
+      validate();
+    }
+    catch (org.exolab.castor.xml.ValidationException vex)
     {
-        this._gapChar = gapChar;
-    } //-- void setGapChar(java.lang.String) 
-
-    /**
-     * Method setSequence
-     * 
-     * 
-     * 
-     * @param index
-     * @param vSequence
-     */
-    public void setSequence(int index, jalview.schemabinding.version2.Sequence vSequence)
-        throws java.lang.IndexOutOfBoundsException
+      return false;
+    }
+    return true;
+  } //-- boolean isValid()
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param out
+   */
+  public void marshal(java.io.Writer out)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, out);
+  } //-- void marshal(java.io.Writer)
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param handler
+   */
+  public void marshal(org.xml.sax.ContentHandler handler)
+      throws java.io.IOException, org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, handler);
+  } //-- void marshal(org.xml.sax.ContentHandler)
+
+  /**
+   * Method removeAllAnnotation
+   *
+   */
+  public void removeAllAnnotation()
+  {
+    _annotationList.removeAllElements();
+  } //-- void removeAllAnnotation()
+
+  /**
+   * Method removeAllSequence
+   *
+   */
+  public void removeAllSequence()
+  {
+    _sequenceList.removeAllElements();
+  } //-- void removeAllSequence()
+
+  /**
+   * Method removeAnnotation
+   *
+   *
+   *
+   * @param index
+   * @return Annotation
+   */
+  public jalview.schemabinding.version2.Annotation removeAnnotation(int index)
+  {
+    java.lang.Object obj = _annotationList.elementAt(index);
+    _annotationList.removeElementAt(index);
+    return (jalview.schemabinding.version2.Annotation) obj;
+  } //-- jalview.schemabinding.version2.Annotation removeAnnotation(int)
+
+  /**
+   * Method removeSequence
+   *
+   *
+   *
+   * @param index
+   * @return Sequence
+   */
+  public jalview.schemabinding.version2.Sequence removeSequence(int index)
+  {
+    java.lang.Object obj = _sequenceList.elementAt(index);
+    _sequenceList.removeElementAt(index);
+    return (jalview.schemabinding.version2.Sequence) obj;
+  } //-- jalview.schemabinding.version2.Sequence removeSequence(int)
+
+  /**
+   * Method setAnnotation
+   *
+   *
+   *
+   * @param index
+   * @param vAnnotation
+   */
+  public void setAnnotation(int index,
+                            jalview.schemabinding.version2.Annotation
+                            vAnnotation)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _annotationList.size()))
     {
-        //-- check bounds for index
-        if ((index < 0) || (index > _sequenceList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        _sequenceList.setElementAt(vSequence, index);
-    } //-- void setSequence(int, jalview.schemabinding.version2.Sequence) 
-
-    /**
-     * Method setSequence
-     * 
-     * 
-     * 
-     * @param sequenceArray
-     */
-    public void setSequence(jalview.schemabinding.version2.Sequence[] sequenceArray)
+      throw new IndexOutOfBoundsException();
+    }
+    _annotationList.setElementAt(vAnnotation, index);
+  } //-- void setAnnotation(int, jalview.schemabinding.version2.Annotation)
+
+  /**
+   * Method setAnnotation
+   *
+   *
+   *
+   * @param annotationArray
+   */
+  public void setAnnotation(jalview.schemabinding.version2.Annotation[]
+                            annotationArray)
+  {
+    //-- copy array
+    _annotationList.removeAllElements();
+    for (int i = 0; i < annotationArray.length; i++)
     {
-        //-- copy array
-        _sequenceList.removeAllElements();
-        for (int i = 0; i < sequenceArray.length; i++) {
-            _sequenceList.addElement(sequenceArray[i]);
-        }
-    } //-- void setSequence(jalview.schemabinding.version2.Sequence) 
-
-    /**
-     * Method unmarshal
-     * 
-     * 
-     * 
-     * @param reader
-     * @return Object
-     */
-    public static java.lang.Object unmarshal(java.io.Reader reader)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+      _annotationList.addElement(annotationArray[i]);
+    }
+  } //-- void setAnnotation(jalview.schemabinding.version2.Annotation)
+
+  /**
+   * Sets the value of field 'gapChar'.
+   *
+   * @param gapChar the value of field 'gapChar'.
+   */
+  public void setGapChar(java.lang.String gapChar)
+  {
+    this._gapChar = gapChar;
+  } //-- void setGapChar(java.lang.String)
+
+  /**
+   * Method setSequence
+   *
+   *
+   *
+   * @param index
+   * @param vSequence
+   */
+  public void setSequence(int index,
+                          jalview.schemabinding.version2.Sequence vSequence)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _sequenceList.size()))
     {
-        return (jalview.schemabinding.version2.SequenceSet) Unmarshaller.unmarshal(jalview.schemabinding.version2.SequenceSet.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
-
-    /**
-     * Method validate
-     * 
-     */
-    public void validate()
-        throws org.exolab.castor.xml.ValidationException
+      throw new IndexOutOfBoundsException();
+    }
+    _sequenceList.setElementAt(vSequence, index);
+  } //-- void setSequence(int, jalview.schemabinding.version2.Sequence)
+
+  /**
+   * Method setSequence
+   *
+   *
+   *
+   * @param sequenceArray
+   */
+  public void setSequence(jalview.schemabinding.version2.Sequence[]
+                          sequenceArray)
+  {
+    //-- copy array
+    _sequenceList.removeAllElements();
+    for (int i = 0; i < sequenceArray.length; i++)
     {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    } //-- void validate() 
+      _sequenceList.addElement(sequenceArray[i]);
+    }
+  } //-- void setSequence(jalview.schemabinding.version2.Sequence)
+
+  /**
+   * Method unmarshal
+   *
+   *
+   *
+   * @param reader
+   * @return Object
+   */
+  public static java.lang.Object unmarshal(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);
+  } //-- java.lang.Object unmarshal(java.io.Reader)
+
+  /**
+   * Method validate
+   *
+   */
+  public void validate()
+      throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.
+        Validator();
+    validator.validate(this);
+  } //-- void validate()
 
 }
diff --git a/src/jalview/schemabinding/version2/SequenceSetDescriptor.java b/src/jalview/schemabinding/version2/SequenceSetDescriptor.java
index 70ad2dc..938f1ed 100755
--- a/src/jalview/schemabinding/version2/SequenceSetDescriptor.java
+++ b/src/jalview/schemabinding/version2/SequenceSetDescriptor.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,275 +7,297 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
-import org.exolab.castor.mapping.AccessMode;
-import org.exolab.castor.xml.TypeValidator;
-import org.exolab.castor.xml.XMLFieldDescriptor;
 import org.exolab.castor.xml.validators.*;
 
 /**
  * Class SequenceSetDescriptor.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class SequenceSetDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field nsPrefix
-     */
-    private java.lang.String nsPrefix;
-
-    /**
-     * Field nsURI
-     */
-    private java.lang.String nsURI;
-
-    /**
-     * Field xmlName
-     */
-    private java.lang.String xmlName;
-
-    /**
-     * Field identity
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor identity;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public SequenceSetDescriptor() {
-        super();
-        nsURI = "www.vamsas.ac.uk/jalview/version2";
-        xmlName = "SequenceSet";
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.xml.XMLFieldHandler              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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _gapChar
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            StringValidator typeValidator = new StringValidator();
-            typeValidator.setWhiteSpace("preserve");
-            fieldValidator.setValidator(typeValidator);
-        }
-        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 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 class SequenceSetDescriptor
+    extends org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  //--------------------------/
+  //- Class/Member Variables -/
+  //--------------------------/
+
+  /**
+   * Field nsPrefix
+   */
+  private java.lang.String nsPrefix;
+
+  /**
+   * Field nsURI
+   */
+  private java.lang.String nsURI;
+
+  /**
+   * Field xmlName
+   */
+  private java.lang.String xmlName;
+
+  /**
+   * Field identity
+   */
+  private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+  //----------------/
+  //- Constructors -/
+  //----------------/
+
+  public SequenceSetDescriptor()
+  {
+    super();
+    nsURI = "www.vamsas.ac.uk/jalview/version2";
+    xmlName = "SequenceSet";
+
+    //-- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.xml.XMLFieldHandler 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);
         }
-        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 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
+        catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-    } //-- jalview.schemabinding.version2.SequenceSetDescriptor()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method getAccessMode
-     * 
-     * 
-     * 
-     * @return AccessMode
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode()
-    {
-        return null;
-    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
-
-    /**
-     * Method getExtends
-     * 
-     * 
-     * 
-     * @return ClassDescriptor
-     */
-    public org.exolab.castor.mapping.ClassDescriptor getExtends()
-    {
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
-
-    /**
-     * Method getIdentity
-     * 
-     * 
-     * 
-     * @return FieldDescriptor
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
-    {
-        return identity;
-    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
-
-    /**
-     * Method getJavaClass
-     * 
-     * 
-     * 
-     * @return Class
-     */
-    public java.lang.Class getJavaClass()
-    {
-        return jalview.schemabinding.version2.SequenceSet.class;
-    } //-- java.lang.Class getJavaClass() 
-
-    /**
-     * Method getNameSpacePrefix
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpacePrefix()
-    {
-        return nsPrefix;
-    } //-- java.lang.String getNameSpacePrefix() 
-
-    /**
-     * Method getNameSpaceURI
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpaceURI()
-    {
-        return nsURI;
-    } //-- java.lang.String getNameSpaceURI() 
-
-    /**
-     * Method getValidator
-     * 
-     * 
-     * 
-     * @return TypeValidator
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator()
+      }
+    });
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _gapChar
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { //-- local scope
+      StringValidator typeValidator = new StringValidator();
+      typeValidator.setWhiteSpace("preserve");
+      fieldValidator.setValidator(typeValidator);
+    }
+    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()
     {
-        return this;
-    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
-
-    /**
-     * Method getXMLName
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getXMLName()
+      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 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()
     {
-        return xmlName;
-    } //-- java.lang.String getXMLName() 
+      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 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);
+  } //-- jalview.schemabinding.version2.SequenceSetDescriptor()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Method getAccessMode
+   *
+   *
+   *
+   * @return AccessMode
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
+
+  /**
+   * Method getExtends
+   *
+   *
+   *
+   * @return ClassDescriptor
+   */
+  public org.exolab.castor.mapping.ClassDescriptor getExtends()
+  {
+    return null;
+  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
+
+  /**
+   * Method getIdentity
+   *
+   *
+   *
+   * @return FieldDescriptor
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return identity;
+  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
+
+  /**
+   * Method getJavaClass
+   *
+   *
+   *
+   * @return Class
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.SequenceSet.class;
+  } //-- java.lang.Class getJavaClass()
+
+  /**
+   * Method getNameSpacePrefix
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return nsPrefix;
+  } //-- java.lang.String getNameSpacePrefix()
+
+  /**
+   * Method getNameSpaceURI
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return nsURI;
+  } //-- java.lang.String getNameSpaceURI()
+
+  /**
+   * Method getValidator
+   *
+   *
+   *
+   * @return TypeValidator
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  } //-- org.exolab.castor.xml.TypeValidator getValidator()
+
+  /**
+   * Method getXMLName
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getXMLName()
+  {
+    return xmlName;
+  } //-- java.lang.String getXMLName()
 
 }
diff --git a/src/jalview/schemabinding/version2/SequenceType.java b/src/jalview/schemabinding/version2/SequenceType.java
index d413e2d..4c60f87 100755
--- a/src/jalview/schemabinding/version2/SequenceType.java
+++ b/src/jalview/schemabinding/version2/SequenceType.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,219 +7,218 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
+import org.exolab.castor.xml.*;
 
 /**
  * Class SequenceType.
- * 
+ *
  * @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();
-    } //-- jalview.schemabinding.version2.SequenceType()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Returns the value of field 'description'.
-     * 
-     * @return String
-     * @return the value of field 'description'.
-     */
-    public java.lang.String getDescription()
-    {
-        return this._description;
-    } //-- java.lang.String getDescription() 
-
-    /**
-     * Returns the value of field 'id'.
-     * 
-     * @return String
-     * @return the value of field 'id'.
-     */
-    public java.lang.String getId()
-    {
-        return this._id;
-    } //-- java.lang.String getId() 
-
-    /**
-     * Returns the value of field 'name'.
-     * 
-     * @return String
-     * @return the value of field 'name'.
-     */
-    public java.lang.String getName()
-    {
-        return this._name;
-    } //-- java.lang.String getName() 
-
-    /**
-     * Returns the value of field 'sequence'.
-     * 
-     * @return String
-     * @return the value of field 'sequence'.
-     */
-    public java.lang.String getSequence()
-    {
-        return this._sequence;
-    } //-- java.lang.String getSequence() 
-
-    /**
-     * Method isValid
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean isValid()
-    {
-        try {
-            validate();
-        }
-        catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    } //-- boolean isValid() 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param out
-     */
-    public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, out);
-    } //-- void marshal(java.io.Writer) 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param handler
-     */
-    public void marshal(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, handler);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
-
-    /**
-     * Sets the value of field 'description'.
-     * 
-     * @param description the value of field 'description'.
-     */
-    public void setDescription(java.lang.String description)
-    {
-        this._description = description;
-    } //-- void setDescription(java.lang.String) 
-
-    /**
-     * Sets the value of field 'id'.
-     * 
-     * @param id the value of field 'id'.
-     */
-    public void setId(java.lang.String id)
-    {
-        this._id = id;
-    } //-- void setId(java.lang.String) 
-
-    /**
-     * Sets the value of field 'name'.
-     * 
-     * @param name the value of field 'name'.
-     */
-    public void setName(java.lang.String name)
-    {
-        this._name = name;
-    } //-- void setName(java.lang.String) 
-
-    /**
-     * Sets the value of field 'sequence'.
-     * 
-     * @param sequence the value of field 'sequence'.
-     */
-    public void setSequence(java.lang.String sequence)
-    {
-        this._sequence = sequence;
-    } //-- void setSequence(java.lang.String) 
-
-    /**
-     * Method unmarshal
-     * 
-     * 
-     * 
-     * @param reader
-     * @return Object
-     */
-    public static java.lang.Object unmarshal(java.io.Reader reader)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+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();
+  } //-- jalview.schemabinding.version2.SequenceType()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Returns the value of field 'description'.
+   *
+   * @return String
+   * @return the value of field 'description'.
+   */
+  public java.lang.String getDescription()
+  {
+    return this._description;
+  } //-- java.lang.String getDescription()
+
+  /**
+   * Returns the value of field 'id'.
+   *
+   * @return String
+   * @return the value of field 'id'.
+   */
+  public java.lang.String getId()
+  {
+    return this._id;
+  } //-- java.lang.String getId()
+
+  /**
+   * Returns the value of field 'name'.
+   *
+   * @return String
+   * @return the value of field 'name'.
+   */
+  public java.lang.String getName()
+  {
+    return this._name;
+  } //-- java.lang.String getName()
+
+  /**
+   * Returns the value of field 'sequence'.
+   *
+   * @return String
+   * @return the value of field 'sequence'.
+   */
+  public java.lang.String getSequence()
+  {
+    return this._sequence;
+  } //-- java.lang.String getSequence()
+
+  /**
+   * Method isValid
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean isValid()
+  {
+    try
     {
-        return (jalview.schemabinding.version2.SequenceType) Unmarshaller.unmarshal(jalview.schemabinding.version2.SequenceType.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
-
-    /**
-     * Method validate
-     * 
-     */
-    public void validate()
-        throws org.exolab.castor.xml.ValidationException
+      validate();
+    }
+    catch (org.exolab.castor.xml.ValidationException vex)
     {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    } //-- void validate() 
+      return false;
+    }
+    return true;
+  } //-- boolean isValid()
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param out
+   */
+  public void marshal(java.io.Writer out)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, out);
+  } //-- void marshal(java.io.Writer)
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param handler
+   */
+  public void marshal(org.xml.sax.ContentHandler handler)
+      throws java.io.IOException, org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, handler);
+  } //-- void marshal(org.xml.sax.ContentHandler)
+
+  /**
+   * Sets the value of field 'description'.
+   *
+   * @param description the value of field 'description'.
+   */
+  public void setDescription(java.lang.String description)
+  {
+    this._description = description;
+  } //-- void setDescription(java.lang.String)
+
+  /**
+   * Sets the value of field 'id'.
+   *
+   * @param id the value of field 'id'.
+   */
+  public void setId(java.lang.String id)
+  {
+    this._id = id;
+  } //-- void setId(java.lang.String)
+
+  /**
+   * Sets the value of field 'name'.
+   *
+   * @param name the value of field 'name'.
+   */
+  public void setName(java.lang.String name)
+  {
+    this._name = name;
+  } //-- void setName(java.lang.String)
+
+  /**
+   * Sets the value of field 'sequence'.
+   *
+   * @param sequence the value of field 'sequence'.
+   */
+  public void setSequence(java.lang.String sequence)
+  {
+    this._sequence = sequence;
+  } //-- void setSequence(java.lang.String)
+
+  /**
+   * Method unmarshal
+   *
+   *
+   *
+   * @param reader
+   * @return Object
+   */
+  public static java.lang.Object unmarshal(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);
+  } //-- java.lang.Object unmarshal(java.io.Reader)
+
+  /**
+   * Method validate
+   *
+   */
+  public void validate()
+      throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.
+        Validator();
+    validator.validate(this);
+  } //-- void validate()
 
 }
diff --git a/src/jalview/schemabinding/version2/SequenceTypeDescriptor.java b/src/jalview/schemabinding/version2/SequenceTypeDescriptor.java
index ef6c636..2910786 100755
--- a/src/jalview/schemabinding/version2/SequenceTypeDescriptor.java
+++ b/src/jalview/schemabinding/version2/SequenceTypeDescriptor.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,315 +7,342 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
-import org.exolab.castor.mapping.AccessMode;
-import org.exolab.castor.xml.TypeValidator;
-import org.exolab.castor.xml.XMLFieldDescriptor;
 import org.exolab.castor.xml.validators.*;
 
 /**
  * Class SequenceTypeDescriptor.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class SequenceTypeDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field nsPrefix
-     */
-    private java.lang.String nsPrefix;
-
-    /**
-     * Field nsURI
-     */
-    private java.lang.String nsURI;
-
-    /**
-     * Field xmlName
-     */
-    private java.lang.String xmlName;
-
-    /**
-     * Field identity
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor identity;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public SequenceTypeDescriptor() {
-        super();
-        nsURI = "www.vamsas.ac.uk/jalview/version2";
-        xmlName = "SequenceType";
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.xml.XMLFieldHandler              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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _id
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            StringValidator typeValidator = new StringValidator();
-            typeValidator.setWhiteSpace("preserve");
-            fieldValidator.setValidator(typeValidator);
+public class SequenceTypeDescriptor
+    extends org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  //--------------------------/
+  //- Class/Member Variables -/
+  //--------------------------/
+
+  /**
+   * Field nsPrefix
+   */
+  private java.lang.String nsPrefix;
+
+  /**
+   * Field nsURI
+   */
+  private java.lang.String nsURI;
+
+  /**
+   * Field xmlName
+   */
+  private java.lang.String xmlName;
+
+  /**
+   * Field identity
+   */
+  private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+  //----------------/
+  //- Constructors -/
+  //----------------/
+
+  public SequenceTypeDescriptor()
+  {
+    super();
+    nsURI = "www.vamsas.ac.uk/jalview/version2";
+    xmlName = "SequenceType";
+
+    //-- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.xml.XMLFieldHandler 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);
         }
-        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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _description
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            StringValidator typeValidator = new StringValidator();
-            typeValidator.setWhiteSpace("preserve");
-            fieldValidator.setValidator(typeValidator);
+        catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        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
-            StringValidator typeValidator = new StringValidator();
-            typeValidator.setWhiteSpace("preserve");
-            fieldValidator.setValidator(typeValidator);
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    });
+    desc.setHandler(handler);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _id
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      StringValidator typeValidator = new StringValidator();
+      typeValidator.setWhiteSpace("preserve");
+      fieldValidator.setValidator(typeValidator);
+    }
+    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);
         }
-        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
-            StringValidator typeValidator = new StringValidator();
-            typeValidator.setWhiteSpace("preserve");
-            fieldValidator.setValidator(typeValidator);
+        catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-    } //-- jalview.schemabinding.version2.SequenceTypeDescriptor()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method getAccessMode
-     * 
-     * 
-     * 
-     * @return AccessMode
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode()
-    {
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
-
-    /**
-     * Method getExtends
-     * 
-     * 
-     * 
-     * @return ClassDescriptor
-     */
-    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+      }
+    });
+    desc.setHandler(handler);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _description
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      StringValidator typeValidator = new StringValidator();
+      typeValidator.setWhiteSpace("preserve");
+      fieldValidator.setValidator(typeValidator);
+    }
+    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;
-    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
-
-    /**
-     * Method getIdentity
-     * 
-     * 
-     * 
-     * @return FieldDescriptor
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
-    {
-        return identity;
-    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
-
-    /**
-     * Method getJavaClass
-     * 
-     * 
-     * 
-     * @return Class
-     */
-    public java.lang.Class getJavaClass()
-    {
-        return jalview.schemabinding.version2.SequenceType.class;
-    } //-- java.lang.Class getJavaClass() 
-
-    /**
-     * Method getNameSpacePrefix
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpacePrefix()
-    {
-        return nsPrefix;
-    } //-- java.lang.String getNameSpacePrefix() 
-
-    /**
-     * Method getNameSpaceURI
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpaceURI()
-    {
-        return nsURI;
-    } //-- java.lang.String getNameSpaceURI() 
-
-    /**
-     * Method getValidator
-     * 
-     * 
-     * 
-     * @return TypeValidator
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator()
-    {
-        return this;
-    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
-
-    /**
-     * Method getXMLName
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getXMLName()
+      }
+    });
+    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
+      StringValidator typeValidator = new StringValidator();
+      typeValidator.setWhiteSpace("preserve");
+      fieldValidator.setValidator(typeValidator);
+    }
+    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()
     {
-        return xmlName;
-    } //-- java.lang.String getXMLName() 
+      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
+      StringValidator typeValidator = new StringValidator();
+      typeValidator.setWhiteSpace("preserve");
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+  } //-- jalview.schemabinding.version2.SequenceTypeDescriptor()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Method getAccessMode
+   *
+   *
+   *
+   * @return AccessMode
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
+
+  /**
+   * Method getExtends
+   *
+   *
+   *
+   * @return ClassDescriptor
+   */
+  public org.exolab.castor.mapping.ClassDescriptor getExtends()
+  {
+    return null;
+  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
+
+  /**
+   * Method getIdentity
+   *
+   *
+   *
+   * @return FieldDescriptor
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return identity;
+  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
+
+  /**
+   * Method getJavaClass
+   *
+   *
+   *
+   * @return Class
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.SequenceType.class;
+  } //-- java.lang.Class getJavaClass()
+
+  /**
+   * Method getNameSpacePrefix
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return nsPrefix;
+  } //-- java.lang.String getNameSpacePrefix()
+
+  /**
+   * Method getNameSpaceURI
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return nsURI;
+  } //-- java.lang.String getNameSpaceURI()
+
+  /**
+   * Method getValidator
+   *
+   *
+   *
+   * @return TypeValidator
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  } //-- org.exolab.castor.xml.TypeValidator getValidator()
+
+  /**
+   * Method getXMLName
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getXMLName()
+  {
+    return xmlName;
+  } //-- java.lang.String getXMLName()
 
 }
diff --git a/src/jalview/schemabinding/version2/Setting.java b/src/jalview/schemabinding/version2/Setting.java
index 668ef9d..4f85d33 100755
--- a/src/jalview/schemabinding/version2/Setting.java
+++ b/src/jalview/schemabinding/version2/Setting.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,247 +7,246 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
+import org.exolab.castor.xml.*;
 
 /**
  * Class Setting.
- * 
+ *
  * @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();
-    } //-- jalview.schemabinding.version2.Setting()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method deleteColour
-     * 
-     */
-    public void deleteColour()
-    {
-        this._has_colour= false;
-    } //-- void deleteColour() 
-
-    /**
-     * Method deleteDisplay
-     * 
-     */
-    public void deleteDisplay()
-    {
-        this._has_display= false;
-    } //-- void deleteDisplay() 
-
-    /**
-     * Returns the value of field 'colour'.
-     * 
-     * @return int
-     * @return the value of field 'colour'.
-     */
-    public int getColour()
-    {
-        return this._colour;
-    } //-- int getColour() 
-
-    /**
-     * Returns the value of field 'display'.
-     * 
-     * @return boolean
-     * @return the value of field 'display'.
-     */
-    public boolean getDisplay()
-    {
-        return this._display;
-    } //-- boolean getDisplay() 
-
-    /**
-     * Returns the value of field 'type'.
-     * 
-     * @return String
-     * @return the value of field 'type'.
-     */
-    public java.lang.String getType()
-    {
-        return this._type;
-    } //-- java.lang.String getType() 
-
-    /**
-     * Method hasColour
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasColour()
-    {
-        return this._has_colour;
-    } //-- boolean hasColour() 
-
-    /**
-     * Method hasDisplay
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasDisplay()
-    {
-        return this._has_display;
-    } //-- boolean hasDisplay() 
-
-    /**
-     * Method isValid
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean isValid()
-    {
-        try {
-            validate();
-        }
-        catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    } //-- boolean isValid() 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param out
-     */
-    public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, out);
-    } //-- void marshal(java.io.Writer) 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param handler
-     */
-    public void marshal(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, handler);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
-
-    /**
-     * Sets the value of field 'colour'.
-     * 
-     * @param colour the value of field 'colour'.
-     */
-    public void setColour(int colour)
-    {
-        this._colour = colour;
-        this._has_colour = true;
-    } //-- void setColour(int) 
-
-    /**
-     * Sets the value of field 'display'.
-     * 
-     * @param display the value of field 'display'.
-     */
-    public void setDisplay(boolean display)
-    {
-        this._display = display;
-        this._has_display = true;
-    } //-- void setDisplay(boolean) 
-
-    /**
-     * Sets the value of field 'type'.
-     * 
-     * @param type the value of field 'type'.
-     */
-    public void setType(java.lang.String type)
-    {
-        this._type = type;
-    } //-- void setType(java.lang.String) 
-
-    /**
-     * Method unmarshal
-     * 
-     * 
-     * 
-     * @param reader
-     * @return Object
-     */
-    public static java.lang.Object unmarshal(java.io.Reader reader)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+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();
+  } //-- jalview.schemabinding.version2.Setting()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Method deleteColour
+   *
+   */
+  public void deleteColour()
+  {
+    this._has_colour = false;
+  } //-- void deleteColour()
+
+  /**
+   * Method deleteDisplay
+   *
+   */
+  public void deleteDisplay()
+  {
+    this._has_display = false;
+  } //-- void deleteDisplay()
+
+  /**
+   * Returns the value of field 'colour'.
+   *
+   * @return int
+   * @return the value of field 'colour'.
+   */
+  public int getColour()
+  {
+    return this._colour;
+  } //-- int getColour()
+
+  /**
+   * Returns the value of field 'display'.
+   *
+   * @return boolean
+   * @return the value of field 'display'.
+   */
+  public boolean getDisplay()
+  {
+    return this._display;
+  } //-- boolean getDisplay()
+
+  /**
+   * Returns the value of field 'type'.
+   *
+   * @return String
+   * @return the value of field 'type'.
+   */
+  public java.lang.String getType()
+  {
+    return this._type;
+  } //-- java.lang.String getType()
+
+  /**
+   * Method hasColour
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasColour()
+  {
+    return this._has_colour;
+  } //-- boolean hasColour()
+
+  /**
+   * Method hasDisplay
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasDisplay()
+  {
+    return this._has_display;
+  } //-- boolean hasDisplay()
+
+  /**
+   * Method isValid
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean isValid()
+  {
+    try
     {
-        return (jalview.schemabinding.version2.Setting) Unmarshaller.unmarshal(jalview.schemabinding.version2.Setting.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
-
-    /**
-     * Method validate
-     * 
-     */
-    public void validate()
-        throws org.exolab.castor.xml.ValidationException
+      validate();
+    }
+    catch (org.exolab.castor.xml.ValidationException vex)
     {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    } //-- void validate() 
+      return false;
+    }
+    return true;
+  } //-- boolean isValid()
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param out
+   */
+  public void marshal(java.io.Writer out)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, out);
+  } //-- void marshal(java.io.Writer)
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param handler
+   */
+  public void marshal(org.xml.sax.ContentHandler handler)
+      throws java.io.IOException, org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, handler);
+  } //-- void marshal(org.xml.sax.ContentHandler)
+
+  /**
+   * Sets the value of field 'colour'.
+   *
+   * @param colour the value of field 'colour'.
+   */
+  public void setColour(int colour)
+  {
+    this._colour = colour;
+    this._has_colour = true;
+  } //-- void setColour(int)
+
+  /**
+   * Sets the value of field 'display'.
+   *
+   * @param display the value of field 'display'.
+   */
+  public void setDisplay(boolean display)
+  {
+    this._display = display;
+    this._has_display = true;
+  } //-- void setDisplay(boolean)
+
+  /**
+   * Sets the value of field 'type'.
+   *
+   * @param type the value of field 'type'.
+   */
+  public void setType(java.lang.String type)
+  {
+    this._type = type;
+  } //-- void setType(java.lang.String)
+
+  /**
+   * Method unmarshal
+   *
+   *
+   *
+   * @param reader
+   * @return Object
+   */
+  public static java.lang.Object unmarshal(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);
+  } //-- java.lang.Object unmarshal(java.io.Reader)
+
+  /**
+   * Method validate
+   *
+   */
+  public void validate()
+      throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.
+        Validator();
+    validator.validate(this);
+  } //-- void validate()
 
 }
diff --git a/src/jalview/schemabinding/version2/SettingDescriptor.java b/src/jalview/schemabinding/version2/SettingDescriptor.java
index 6cadc16..9e19f65 100755
--- a/src/jalview/schemabinding/version2/SettingDescriptor.java
+++ b/src/jalview/schemabinding/version2/SettingDescriptor.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,284 +7,315 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
-import org.exolab.castor.mapping.AccessMode;
-import org.exolab.castor.xml.TypeValidator;
-import org.exolab.castor.xml.XMLFieldDescriptor;
 import org.exolab.castor.xml.validators.*;
 
 /**
  * Class SettingDescriptor.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class SettingDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field nsPrefix
-     */
-    private java.lang.String nsPrefix;
-
-    /**
-     * Field nsURI
-     */
-    private java.lang.String nsURI;
-
-    /**
-     * Field xmlName
-     */
-    private java.lang.String xmlName;
-
-    /**
-     * Field identity
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor identity;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public SettingDescriptor() {
-        super();
-        nsURI = "www.jalview.org";
-        xmlName = "setting";
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.xml.XMLFieldHandler              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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _type
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            StringValidator typeValidator = new StringValidator();
-            typeValidator.setWhiteSpace("preserve");
-            fieldValidator.setValidator(typeValidator);
-        }
-        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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _colour
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            IntegerValidator typeValidator= new IntegerValidator();
-            fieldValidator.setValidator(typeValidator);
+public class SettingDescriptor
+    extends org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  //--------------------------/
+  //- Class/Member Variables -/
+  //--------------------------/
+
+  /**
+   * Field nsPrefix
+   */
+  private java.lang.String nsPrefix;
+
+  /**
+   * Field nsURI
+   */
+  private java.lang.String nsURI;
+
+  /**
+   * Field xmlName
+   */
+  private java.lang.String xmlName;
+
+  /**
+   * Field identity
+   */
+  private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+  //----------------/
+  //- Constructors -/
+  //----------------/
+
+  public SettingDescriptor()
+  {
+    super();
+    nsURI = "www.jalview.org";
+    xmlName = "setting";
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.xml.XMLFieldHandler 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);
         }
-        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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _display
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            BooleanValidator typeValidator = new BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
+        catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-    } //-- jalview.schemabinding.version2.SettingDescriptor()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method getAccessMode
-     * 
-     * 
-     * 
-     * @return AccessMode
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode()
-    {
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
-
-    /**
-     * Method getExtends
-     * 
-     * 
-     * 
-     * @return ClassDescriptor
-     */
-    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+      }
+    });
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _type
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { //-- local scope
+      StringValidator typeValidator = new StringValidator();
+      typeValidator.setWhiteSpace("preserve");
+      fieldValidator.setValidator(typeValidator);
+    }
+    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;
-    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
-
-    /**
-     * Method getIdentity
-     * 
-     * 
-     * 
-     * @return FieldDescriptor
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
-    {
-        return identity;
-    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
-
-    /**
-     * Method getJavaClass
-     * 
-     * 
-     * 
-     * @return Class
-     */
-    public java.lang.Class getJavaClass()
-    {
-        return jalview.schemabinding.version2.Setting.class;
-    } //-- java.lang.Class getJavaClass() 
-
-    /**
-     * Method getNameSpacePrefix
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpacePrefix()
-    {
-        return nsPrefix;
-    } //-- java.lang.String getNameSpacePrefix() 
-
-    /**
-     * Method getNameSpaceURI
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpaceURI()
-    {
-        return nsURI;
-    } //-- java.lang.String getNameSpaceURI() 
-
-    /**
-     * Method getValidator
-     * 
-     * 
-     * 
-     * @return TypeValidator
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator()
-    {
-        return this;
-    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
-
-    /**
-     * Method getXMLName
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getXMLName()
+      }
+    });
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _colour
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { //-- local scope
+      IntegerValidator typeValidator = new IntegerValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    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()
     {
-        return xmlName;
-    } //-- java.lang.String getXMLName() 
+      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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _display
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { //-- local scope
+      BooleanValidator typeValidator = new BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    //-- initialize element descriptors
+
+  } //-- jalview.schemabinding.version2.SettingDescriptor()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Method getAccessMode
+   *
+   *
+   *
+   * @return AccessMode
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
+
+  /**
+   * Method getExtends
+   *
+   *
+   *
+   * @return ClassDescriptor
+   */
+  public org.exolab.castor.mapping.ClassDescriptor getExtends()
+  {
+    return null;
+  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
+
+  /**
+   * Method getIdentity
+   *
+   *
+   *
+   * @return FieldDescriptor
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return identity;
+  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
+
+  /**
+   * Method getJavaClass
+   *
+   *
+   *
+   * @return Class
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.Setting.class;
+  } //-- java.lang.Class getJavaClass()
+
+  /**
+   * Method getNameSpacePrefix
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return nsPrefix;
+  } //-- java.lang.String getNameSpacePrefix()
+
+  /**
+   * Method getNameSpaceURI
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return nsURI;
+  } //-- java.lang.String getNameSpaceURI()
+
+  /**
+   * Method getValidator
+   *
+   *
+   *
+   * @return TypeValidator
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  } //-- org.exolab.castor.xml.TypeValidator getValidator()
+
+  /**
+   * Method getXMLName
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getXMLName()
+  {
+    return xmlName;
+  } //-- java.lang.String getXMLName()
 
 }
diff --git a/src/jalview/schemabinding/version2/ThresholdLine.java b/src/jalview/schemabinding/version2/ThresholdLine.java
index 85854c1..ca6d5de 100755
--- a/src/jalview/schemabinding/version2/ThresholdLine.java
+++ b/src/jalview/schemabinding/version2/ThresholdLine.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,247 +7,246 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
+import org.exolab.castor.xml.*;
 
 /**
  * Class ThresholdLine.
- * 
+ *
  * @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();
-    } //-- jalview.schemabinding.version2.ThresholdLine()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method deleteColour
-     * 
-     */
-    public void deleteColour()
-    {
-        this._has_colour= false;
-    } //-- void deleteColour() 
-
-    /**
-     * Method deleteValue
-     * 
-     */
-    public void deleteValue()
-    {
-        this._has_value= false;
-    } //-- void deleteValue() 
-
-    /**
-     * Returns the value of field 'colour'.
-     * 
-     * @return int
-     * @return the value of field 'colour'.
-     */
-    public int getColour()
-    {
-        return this._colour;
-    } //-- int getColour() 
-
-    /**
-     * Returns the value of field 'label'.
-     * 
-     * @return String
-     * @return the value of field 'label'.
-     */
-    public java.lang.String getLabel()
-    {
-        return this._label;
-    } //-- java.lang.String getLabel() 
-
-    /**
-     * Returns the value of field 'value'.
-     * 
-     * @return float
-     * @return the value of field 'value'.
-     */
-    public float getValue()
-    {
-        return this._value;
-    } //-- float getValue() 
-
-    /**
-     * Method hasColour
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasColour()
-    {
-        return this._has_colour;
-    } //-- boolean hasColour() 
-
-    /**
-     * Method hasValue
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasValue()
-    {
-        return this._has_value;
-    } //-- boolean hasValue() 
-
-    /**
-     * Method isValid
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean isValid()
-    {
-        try {
-            validate();
-        }
-        catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    } //-- boolean isValid() 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param out
-     */
-    public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, out);
-    } //-- void marshal(java.io.Writer) 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param handler
-     */
-    public void marshal(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, handler);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
-
-    /**
-     * Sets the value of field 'colour'.
-     * 
-     * @param colour the value of field 'colour'.
-     */
-    public void setColour(int colour)
-    {
-        this._colour = colour;
-        this._has_colour = true;
-    } //-- void setColour(int) 
-
-    /**
-     * Sets the value of field 'label'.
-     * 
-     * @param label the value of field 'label'.
-     */
-    public void setLabel(java.lang.String label)
-    {
-        this._label = label;
-    } //-- void setLabel(java.lang.String) 
-
-    /**
-     * Sets the value of field 'value'.
-     * 
-     * @param value the value of field 'value'.
-     */
-    public void setValue(float value)
-    {
-        this._value = value;
-        this._has_value = true;
-    } //-- void setValue(float) 
-
-    /**
-     * Method unmarshal
-     * 
-     * 
-     * 
-     * @param reader
-     * @return Object
-     */
-    public static java.lang.Object unmarshal(java.io.Reader reader)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+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();
+  } //-- jalview.schemabinding.version2.ThresholdLine()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Method deleteColour
+   *
+   */
+  public void deleteColour()
+  {
+    this._has_colour = false;
+  } //-- void deleteColour()
+
+  /**
+   * Method deleteValue
+   *
+   */
+  public void deleteValue()
+  {
+    this._has_value = false;
+  } //-- void deleteValue()
+
+  /**
+   * Returns the value of field 'colour'.
+   *
+   * @return int
+   * @return the value of field 'colour'.
+   */
+  public int getColour()
+  {
+    return this._colour;
+  } //-- int getColour()
+
+  /**
+   * Returns the value of field 'label'.
+   *
+   * @return String
+   * @return the value of field 'label'.
+   */
+  public java.lang.String getLabel()
+  {
+    return this._label;
+  } //-- java.lang.String getLabel()
+
+  /**
+   * Returns the value of field 'value'.
+   *
+   * @return float
+   * @return the value of field 'value'.
+   */
+  public float getValue()
+  {
+    return this._value;
+  } //-- float getValue()
+
+  /**
+   * Method hasColour
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasColour()
+  {
+    return this._has_colour;
+  } //-- boolean hasColour()
+
+  /**
+   * Method hasValue
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasValue()
+  {
+    return this._has_value;
+  } //-- boolean hasValue()
+
+  /**
+   * Method isValid
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean isValid()
+  {
+    try
     {
-        return (jalview.schemabinding.version2.ThresholdLine) Unmarshaller.unmarshal(jalview.schemabinding.version2.ThresholdLine.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
-
-    /**
-     * Method validate
-     * 
-     */
-    public void validate()
-        throws org.exolab.castor.xml.ValidationException
+      validate();
+    }
+    catch (org.exolab.castor.xml.ValidationException vex)
     {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    } //-- void validate() 
+      return false;
+    }
+    return true;
+  } //-- boolean isValid()
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param out
+   */
+  public void marshal(java.io.Writer out)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, out);
+  } //-- void marshal(java.io.Writer)
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param handler
+   */
+  public void marshal(org.xml.sax.ContentHandler handler)
+      throws java.io.IOException, org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, handler);
+  } //-- void marshal(org.xml.sax.ContentHandler)
+
+  /**
+   * Sets the value of field 'colour'.
+   *
+   * @param colour the value of field 'colour'.
+   */
+  public void setColour(int colour)
+  {
+    this._colour = colour;
+    this._has_colour = true;
+  } //-- void setColour(int)
+
+  /**
+   * Sets the value of field 'label'.
+   *
+   * @param label the value of field 'label'.
+   */
+  public void setLabel(java.lang.String label)
+  {
+    this._label = label;
+  } //-- void setLabel(java.lang.String)
+
+  /**
+   * Sets the value of field 'value'.
+   *
+   * @param value the value of field 'value'.
+   */
+  public void setValue(float value)
+  {
+    this._value = value;
+    this._has_value = true;
+  } //-- void setValue(float)
+
+  /**
+   * Method unmarshal
+   *
+   *
+   *
+   * @param reader
+   * @return Object
+   */
+  public static java.lang.Object unmarshal(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);
+  } //-- java.lang.Object unmarshal(java.io.Reader)
+
+  /**
+   * Method validate
+   *
+   */
+  public void validate()
+      throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.
+        Validator();
+    validator.validate(this);
+  } //-- void validate()
 
 }
diff --git a/src/jalview/schemabinding/version2/ThresholdLineDescriptor.java b/src/jalview/schemabinding/version2/ThresholdLineDescriptor.java
index 9241003..a4cf76f 100755
--- a/src/jalview/schemabinding/version2/ThresholdLineDescriptor.java
+++ b/src/jalview/schemabinding/version2/ThresholdLineDescriptor.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,282 +7,308 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
-import org.exolab.castor.mapping.AccessMode;
-import org.exolab.castor.xml.TypeValidator;
-import org.exolab.castor.xml.XMLFieldDescriptor;
 import org.exolab.castor.xml.validators.*;
 
 /**
  * Class ThresholdLineDescriptor.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class ThresholdLineDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field nsPrefix
-     */
-    private java.lang.String nsPrefix;
-
-    /**
-     * Field nsURI
-     */
-    private java.lang.String nsURI;
-
-    /**
-     * Field xmlName
-     */
-    private java.lang.String xmlName;
-
-    /**
-     * Field identity
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor identity;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public ThresholdLineDescriptor() {
-        super();
-        nsURI = "www.vamsas.ac.uk/jalview/version2";
-        xmlName = "thresholdLine";
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.xml.XMLFieldHandler              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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _label
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            StringValidator typeValidator = new StringValidator();
-            typeValidator.setWhiteSpace("preserve");
-            fieldValidator.setValidator(typeValidator);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _value
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(float.class, "_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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _value
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            FloatValidator typeValidator = new FloatValidator();
-            fieldValidator.setValidator(typeValidator);
+public class ThresholdLineDescriptor
+    extends org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  //--------------------------/
+  //- Class/Member Variables -/
+  //--------------------------/
+
+  /**
+   * Field nsPrefix
+   */
+  private java.lang.String nsPrefix;
+
+  /**
+   * Field nsURI
+   */
+  private java.lang.String nsURI;
+
+  /**
+   * Field xmlName
+   */
+  private java.lang.String xmlName;
+
+  /**
+   * Field identity
+   */
+  private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+  //----------------/
+  //- Constructors -/
+  //----------------/
+
+  public ThresholdLineDescriptor()
+  {
+    super();
+    nsURI = "www.vamsas.ac.uk/jalview/version2";
+    xmlName = "thresholdLine";
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.xml.XMLFieldHandler 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);
         }
-        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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _colour
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            IntegerValidator typeValidator= new IntegerValidator();
-            fieldValidator.setValidator(typeValidator);
+        catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-    } //-- jalview.schemabinding.version2.ThresholdLineDescriptor()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method getAccessMode
-     * 
-     * 
-     * 
-     * @return AccessMode
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode()
-    {
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
-
-    /**
-     * Method getExtends
-     * 
-     * 
-     * 
-     * @return ClassDescriptor
-     */
-    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+      }
+    });
+    desc.setHandler(handler);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _label
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      StringValidator typeValidator = new StringValidator();
+      typeValidator.setWhiteSpace("preserve");
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    //-- _value
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(float.class,
+        "_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;
-    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
-
-    /**
-     * Method getIdentity
-     * 
-     * 
-     * 
-     * @return FieldDescriptor
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
-    {
-        return identity;
-    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
-
-    /**
-     * Method getJavaClass
-     * 
-     * 
-     * 
-     * @return Class
-     */
-    public java.lang.Class getJavaClass()
-    {
-        return jalview.schemabinding.version2.ThresholdLine.class;
-    } //-- java.lang.Class getJavaClass() 
-
-    /**
-     * Method getNameSpacePrefix
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpacePrefix()
-    {
-        return nsPrefix;
-    } //-- java.lang.String getNameSpacePrefix() 
-
-    /**
-     * Method getNameSpaceURI
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpaceURI()
-    {
-        return nsURI;
-    } //-- java.lang.String getNameSpaceURI() 
-
-    /**
-     * Method getValidator
-     * 
-     * 
-     * 
-     * @return TypeValidator
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator()
-    {
-        return this;
-    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
-
-    /**
-     * Method getXMLName
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getXMLName()
+      }
+    });
+    desc.setHandler(handler);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _value
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      FloatValidator typeValidator = new FloatValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    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()
     {
-        return xmlName;
-    } //-- java.lang.String getXMLName() 
+      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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _colour
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      IntegerValidator typeValidator = new IntegerValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    //-- initialize element descriptors
+
+  } //-- jalview.schemabinding.version2.ThresholdLineDescriptor()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Method getAccessMode
+   *
+   *
+   *
+   * @return AccessMode
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
+
+  /**
+   * Method getExtends
+   *
+   *
+   *
+   * @return ClassDescriptor
+   */
+  public org.exolab.castor.mapping.ClassDescriptor getExtends()
+  {
+    return null;
+  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
+
+  /**
+   * Method getIdentity
+   *
+   *
+   *
+   * @return FieldDescriptor
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return identity;
+  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
+
+  /**
+   * Method getJavaClass
+   *
+   *
+   *
+   * @return Class
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.ThresholdLine.class;
+  } //-- java.lang.Class getJavaClass()
+
+  /**
+   * Method getNameSpacePrefix
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return nsPrefix;
+  } //-- java.lang.String getNameSpacePrefix()
+
+  /**
+   * Method getNameSpaceURI
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return nsURI;
+  } //-- java.lang.String getNameSpaceURI()
+
+  /**
+   * Method getValidator
+   *
+   *
+   *
+   * @return TypeValidator
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  } //-- org.exolab.castor.xml.TypeValidator getValidator()
+
+  /**
+   * Method getXMLName
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getXMLName()
+  {
+    return xmlName;
+  } //-- java.lang.String getXMLName()
 
 }
diff --git a/src/jalview/schemabinding/version2/Tree.java b/src/jalview/schemabinding/version2/Tree.java
index 96b2e18..3f9098a 100755
--- a/src/jalview/schemabinding/version2/Tree.java
+++ b/src/jalview/schemabinding/version2/Tree.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,829 +7,828 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
+import org.exolab.castor.xml.*;
 
 /**
  * Class Tree.
- * 
+ *
  * @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();
-    } //-- jalview.schemabinding.version2.Tree()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method deleteCurrentTree
-     * 
-     */
-    public void deleteCurrentTree()
-    {
-        this._has_currentTree= false;
-    } //-- void deleteCurrentTree() 
-
-    /**
-     * Method deleteFitToWindow
-     * 
-     */
-    public void deleteFitToWindow()
-    {
-        this._has_fitToWindow= false;
-    } //-- void deleteFitToWindow() 
-
-    /**
-     * Method deleteFontSize
-     * 
-     */
-    public void deleteFontSize()
-    {
-        this._has_fontSize= false;
-    } //-- void deleteFontSize() 
-
-    /**
-     * Method deleteFontStyle
-     * 
-     */
-    public void deleteFontStyle()
-    {
-        this._has_fontStyle= false;
-    } //-- void deleteFontStyle() 
-
-    /**
-     * Method deleteHeight
-     * 
-     */
-    public void deleteHeight()
-    {
-        this._has_height= false;
-    } //-- void deleteHeight() 
-
-    /**
-     * Method deleteMarkUnlinked
-     * 
-     */
-    public void deleteMarkUnlinked()
-    {
-        this._has_markUnlinked= false;
-    } //-- void deleteMarkUnlinked() 
-
-    /**
-     * Method deleteShowBootstrap
-     * 
-     */
-    public void deleteShowBootstrap()
-    {
-        this._has_showBootstrap= false;
-    } //-- void deleteShowBootstrap() 
-
-    /**
-     * Method deleteShowDistances
-     * 
-     */
-    public void deleteShowDistances()
-    {
-        this._has_showDistances= false;
-    } //-- void deleteShowDistances() 
-
-    /**
-     * Method deleteThreshold
-     * 
-     */
-    public void deleteThreshold()
-    {
-        this._has_threshold= false;
-    } //-- void deleteThreshold() 
-
-    /**
-     * Method deleteWidth
-     * 
-     */
-    public void deleteWidth()
-    {
-        this._has_width= false;
-    } //-- void deleteWidth() 
-
-    /**
-     * Method deleteXpos
-     * 
-     */
-    public void deleteXpos()
-    {
-        this._has_xpos= false;
-    } //-- void deleteXpos() 
-
-    /**
-     * Method deleteYpos
-     * 
-     */
-    public void deleteYpos()
-    {
-        this._has_ypos= false;
-    } //-- void deleteYpos() 
-
-    /**
-     * Returns the value of field 'currentTree'.
-     * 
-     * @return boolean
-     * @return the value of field 'currentTree'.
-     */
-    public boolean getCurrentTree()
-    {
-        return this._currentTree;
-    } //-- boolean getCurrentTree() 
-
-    /**
-     * Returns the value of field 'fitToWindow'.
-     * 
-     * @return boolean
-     * @return the value of field 'fitToWindow'.
-     */
-    public boolean getFitToWindow()
-    {
-        return this._fitToWindow;
-    } //-- boolean getFitToWindow() 
-
-    /**
-     * Returns the value of field 'fontName'.
-     * 
-     * @return String
-     * @return the value of field 'fontName'.
-     */
-    public java.lang.String getFontName()
-    {
-        return this._fontName;
-    } //-- java.lang.String getFontName() 
-
-    /**
-     * Returns the value of field 'fontSize'.
-     * 
-     * @return int
-     * @return the value of field 'fontSize'.
-     */
-    public int getFontSize()
-    {
-        return this._fontSize;
-    } //-- int getFontSize() 
-
-    /**
-     * Returns the value of field 'fontStyle'.
-     * 
-     * @return int
-     * @return the value of field 'fontStyle'.
-     */
-    public int getFontStyle()
-    {
-        return this._fontStyle;
-    } //-- int getFontStyle() 
-
-    /**
-     * Returns the value of field 'height'.
-     * 
-     * @return int
-     * @return the value of field 'height'.
-     */
-    public int getHeight()
-    {
-        return this._height;
-    } //-- int getHeight() 
-
-    /**
-     * Returns the value of field 'markUnlinked'.
-     * 
-     * @return boolean
-     * @return the value of field 'markUnlinked'.
-     */
-    public boolean getMarkUnlinked()
-    {
-        return this._markUnlinked;
-    } //-- boolean getMarkUnlinked() 
-
-    /**
-     * Returns the value of field 'newick'.
-     * 
-     * @return String
-     * @return the value of field 'newick'.
-     */
-    public java.lang.String getNewick()
-    {
-        return this._newick;
-    } //-- java.lang.String getNewick() 
-
-    /**
-     * Returns the value of field 'showBootstrap'.
-     * 
-     * @return boolean
-     * @return the value of field 'showBootstrap'.
-     */
-    public boolean getShowBootstrap()
-    {
-        return this._showBootstrap;
-    } //-- boolean getShowBootstrap() 
-
-    /**
-     * Returns the value of field 'showDistances'.
-     * 
-     * @return boolean
-     * @return the value of field 'showDistances'.
-     */
-    public boolean getShowDistances()
-    {
-        return this._showDistances;
-    } //-- boolean getShowDistances() 
-
-    /**
-     * Returns the value of field 'threshold'.
-     * 
-     * @return float
-     * @return the value of field 'threshold'.
-     */
-    public float getThreshold()
-    {
-        return this._threshold;
-    } //-- float getThreshold() 
-
-    /**
-     * Returns the value of field 'title'.
-     * 
-     * @return String
-     * @return the value of field 'title'.
-     */
-    public java.lang.String getTitle()
-    {
-        return this._title;
-    } //-- java.lang.String getTitle() 
-
-    /**
-     * Returns the value of field 'width'.
-     * 
-     * @return int
-     * @return the value of field 'width'.
-     */
-    public int getWidth()
-    {
-        return this._width;
-    } //-- int getWidth() 
-
-    /**
-     * Returns the value of field 'xpos'.
-     * 
-     * @return int
-     * @return the value of field 'xpos'.
-     */
-    public int getXpos()
-    {
-        return this._xpos;
-    } //-- int getXpos() 
-
-    /**
-     * Returns the value of field 'ypos'.
-     * 
-     * @return int
-     * @return the value of field 'ypos'.
-     */
-    public int getYpos()
-    {
-        return this._ypos;
-    } //-- int getYpos() 
-
-    /**
-     * Method hasCurrentTree
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasCurrentTree()
-    {
-        return this._has_currentTree;
-    } //-- boolean hasCurrentTree() 
-
-    /**
-     * Method hasFitToWindow
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasFitToWindow()
-    {
-        return this._has_fitToWindow;
-    } //-- boolean hasFitToWindow() 
-
-    /**
-     * Method hasFontSize
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasFontSize()
-    {
-        return this._has_fontSize;
-    } //-- boolean hasFontSize() 
-
-    /**
-     * Method hasFontStyle
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasFontStyle()
-    {
-        return this._has_fontStyle;
-    } //-- boolean hasFontStyle() 
-
-    /**
-     * Method hasHeight
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasHeight()
-    {
-        return this._has_height;
-    } //-- boolean hasHeight() 
-
-    /**
-     * Method hasMarkUnlinked
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasMarkUnlinked()
-    {
-        return this._has_markUnlinked;
-    } //-- boolean hasMarkUnlinked() 
-
-    /**
-     * Method hasShowBootstrap
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasShowBootstrap()
-    {
-        return this._has_showBootstrap;
-    } //-- boolean hasShowBootstrap() 
-
-    /**
-     * Method hasShowDistances
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasShowDistances()
-    {
-        return this._has_showDistances;
-    } //-- boolean hasShowDistances() 
-
-    /**
-     * Method hasThreshold
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasThreshold()
-    {
-        return this._has_threshold;
-    } //-- boolean hasThreshold() 
-
-    /**
-     * Method hasWidth
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasWidth()
-    {
-        return this._has_width;
-    } //-- boolean hasWidth() 
-
-    /**
-     * Method hasXpos
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasXpos()
-    {
-        return this._has_xpos;
-    } //-- boolean hasXpos() 
-
-    /**
-     * Method hasYpos
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasYpos()
-    {
-        return this._has_ypos;
-    } //-- boolean hasYpos() 
-
-    /**
-     * Method isValid
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean isValid()
-    {
-        try {
-            validate();
-        }
-        catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    } //-- boolean isValid() 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param out
-     */
-    public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, out);
-    } //-- void marshal(java.io.Writer) 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param handler
-     */
-    public void marshal(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, handler);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
-
-    /**
-     * Sets the value of field 'currentTree'.
-     * 
-     * @param currentTree the value of field 'currentTree'.
-     */
-    public void setCurrentTree(boolean currentTree)
-    {
-        this._currentTree = currentTree;
-        this._has_currentTree = true;
-    } //-- void setCurrentTree(boolean) 
-
-    /**
-     * Sets the value of field 'fitToWindow'.
-     * 
-     * @param fitToWindow the value of field 'fitToWindow'.
-     */
-    public void setFitToWindow(boolean fitToWindow)
-    {
-        this._fitToWindow = fitToWindow;
-        this._has_fitToWindow = true;
-    } //-- void setFitToWindow(boolean) 
-
-    /**
-     * Sets the value of field 'fontName'.
-     * 
-     * @param fontName the value of field 'fontName'.
-     */
-    public void setFontName(java.lang.String fontName)
-    {
-        this._fontName = fontName;
-    } //-- void setFontName(java.lang.String) 
-
-    /**
-     * Sets the value of field 'fontSize'.
-     * 
-     * @param fontSize the value of field 'fontSize'.
-     */
-    public void setFontSize(int fontSize)
-    {
-        this._fontSize = fontSize;
-        this._has_fontSize = true;
-    } //-- void setFontSize(int) 
-
-    /**
-     * Sets the value of field 'fontStyle'.
-     * 
-     * @param fontStyle the value of field 'fontStyle'.
-     */
-    public void setFontStyle(int fontStyle)
-    {
-        this._fontStyle = fontStyle;
-        this._has_fontStyle = true;
-    } //-- void setFontStyle(int) 
-
-    /**
-     * Sets the value of field 'height'.
-     * 
-     * @param height the value of field 'height'.
-     */
-    public void setHeight(int height)
-    {
-        this._height = height;
-        this._has_height = true;
-    } //-- void setHeight(int) 
-
-    /**
-     * Sets the value of field 'markUnlinked'.
-     * 
-     * @param markUnlinked the value of field 'markUnlinked'.
-     */
-    public void setMarkUnlinked(boolean markUnlinked)
-    {
-        this._markUnlinked = markUnlinked;
-        this._has_markUnlinked = true;
-    } //-- void setMarkUnlinked(boolean) 
-
-    /**
-     * Sets the value of field 'newick'.
-     * 
-     * @param newick the value of field 'newick'.
-     */
-    public void setNewick(java.lang.String newick)
-    {
-        this._newick = newick;
-    } //-- void setNewick(java.lang.String) 
-
-    /**
-     * Sets the value of field 'showBootstrap'.
-     * 
-     * @param showBootstrap the value of field 'showBootstrap'.
-     */
-    public void setShowBootstrap(boolean showBootstrap)
-    {
-        this._showBootstrap = showBootstrap;
-        this._has_showBootstrap = true;
-    } //-- void setShowBootstrap(boolean) 
-
-    /**
-     * Sets the value of field 'showDistances'.
-     * 
-     * @param showDistances the value of field 'showDistances'.
-     */
-    public void setShowDistances(boolean showDistances)
-    {
-        this._showDistances = showDistances;
-        this._has_showDistances = true;
-    } //-- void setShowDistances(boolean) 
-
-    /**
-     * Sets the value of field 'threshold'.
-     * 
-     * @param threshold the value of field 'threshold'.
-     */
-    public void setThreshold(float threshold)
-    {
-        this._threshold = threshold;
-        this._has_threshold = true;
-    } //-- void setThreshold(float) 
-
-    /**
-     * Sets the value of field 'title'.
-     * 
-     * @param title the value of field 'title'.
-     */
-    public void setTitle(java.lang.String title)
-    {
-        this._title = title;
-    } //-- void setTitle(java.lang.String) 
-
-    /**
-     * Sets the value of field 'width'.
-     * 
-     * @param width the value of field 'width'.
-     */
-    public void setWidth(int width)
-    {
-        this._width = width;
-        this._has_width = true;
-    } //-- void setWidth(int) 
-
-    /**
-     * Sets the value of field 'xpos'.
-     * 
-     * @param xpos the value of field 'xpos'.
-     */
-    public void setXpos(int xpos)
-    {
-        this._xpos = xpos;
-        this._has_xpos = true;
-    } //-- void setXpos(int) 
-
-    /**
-     * Sets the value of field 'ypos'.
-     * 
-     * @param ypos the value of field 'ypos'.
-     */
-    public void setYpos(int ypos)
-    {
-        this._ypos = ypos;
-        this._has_ypos = true;
-    } //-- void setYpos(int) 
-
-    /**
-     * Method unmarshal
-     * 
-     * 
-     * 
-     * @param reader
-     * @return Object
-     */
-    public static java.lang.Object unmarshal(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);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
-
-    /**
-     * Method validate
-     * 
-     */
-    public void validate()
-        throws org.exolab.castor.xml.ValidationException
-    {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    } //-- void validate() 
+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();
+  } //-- jalview.schemabinding.version2.Tree()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Method deleteCurrentTree
+   *
+   */
+  public void deleteCurrentTree()
+  {
+    this._has_currentTree = false;
+  } //-- void deleteCurrentTree()
+
+  /**
+   * Method deleteFitToWindow
+   *
+   */
+  public void deleteFitToWindow()
+  {
+    this._has_fitToWindow = false;
+  } //-- void deleteFitToWindow()
+
+  /**
+   * Method deleteFontSize
+   *
+   */
+  public void deleteFontSize()
+  {
+    this._has_fontSize = false;
+  } //-- void deleteFontSize()
+
+  /**
+   * Method deleteFontStyle
+   *
+   */
+  public void deleteFontStyle()
+  {
+    this._has_fontStyle = false;
+  } //-- void deleteFontStyle()
+
+  /**
+   * Method deleteHeight
+   *
+   */
+  public void deleteHeight()
+  {
+    this._has_height = false;
+  } //-- void deleteHeight()
+
+  /**
+   * Method deleteMarkUnlinked
+   *
+   */
+  public void deleteMarkUnlinked()
+  {
+    this._has_markUnlinked = false;
+  } //-- void deleteMarkUnlinked()
+
+  /**
+   * Method deleteShowBootstrap
+   *
+   */
+  public void deleteShowBootstrap()
+  {
+    this._has_showBootstrap = false;
+  } //-- void deleteShowBootstrap()
+
+  /**
+   * Method deleteShowDistances
+   *
+   */
+  public void deleteShowDistances()
+  {
+    this._has_showDistances = false;
+  } //-- void deleteShowDistances()
+
+  /**
+   * Method deleteThreshold
+   *
+   */
+  public void deleteThreshold()
+  {
+    this._has_threshold = false;
+  } //-- void deleteThreshold()
+
+  /**
+   * Method deleteWidth
+   *
+   */
+  public void deleteWidth()
+  {
+    this._has_width = false;
+  } //-- void deleteWidth()
+
+  /**
+   * Method deleteXpos
+   *
+   */
+  public void deleteXpos()
+  {
+    this._has_xpos = false;
+  } //-- void deleteXpos()
+
+  /**
+   * Method deleteYpos
+   *
+   */
+  public void deleteYpos()
+  {
+    this._has_ypos = false;
+  } //-- void deleteYpos()
+
+  /**
+   * Returns the value of field 'currentTree'.
+   *
+   * @return boolean
+   * @return the value of field 'currentTree'.
+   */
+  public boolean getCurrentTree()
+  {
+    return this._currentTree;
+  } //-- boolean getCurrentTree()
+
+  /**
+   * Returns the value of field 'fitToWindow'.
+   *
+   * @return boolean
+   * @return the value of field 'fitToWindow'.
+   */
+  public boolean getFitToWindow()
+  {
+    return this._fitToWindow;
+  } //-- boolean getFitToWindow()
+
+  /**
+   * Returns the value of field 'fontName'.
+   *
+   * @return String
+   * @return the value of field 'fontName'.
+   */
+  public java.lang.String getFontName()
+  {
+    return this._fontName;
+  } //-- java.lang.String getFontName()
+
+  /**
+   * Returns the value of field 'fontSize'.
+   *
+   * @return int
+   * @return the value of field 'fontSize'.
+   */
+  public int getFontSize()
+  {
+    return this._fontSize;
+  } //-- int getFontSize()
+
+  /**
+   * Returns the value of field 'fontStyle'.
+   *
+   * @return int
+   * @return the value of field 'fontStyle'.
+   */
+  public int getFontStyle()
+  {
+    return this._fontStyle;
+  } //-- int getFontStyle()
+
+  /**
+   * Returns the value of field 'height'.
+   *
+   * @return int
+   * @return the value of field 'height'.
+   */
+  public int getHeight()
+  {
+    return this._height;
+  } //-- int getHeight()
+
+  /**
+   * Returns the value of field 'markUnlinked'.
+   *
+   * @return boolean
+   * @return the value of field 'markUnlinked'.
+   */
+  public boolean getMarkUnlinked()
+  {
+    return this._markUnlinked;
+  } //-- boolean getMarkUnlinked()
+
+  /**
+   * Returns the value of field 'newick'.
+   *
+   * @return String
+   * @return the value of field 'newick'.
+   */
+  public java.lang.String getNewick()
+  {
+    return this._newick;
+  } //-- java.lang.String getNewick()
+
+  /**
+   * Returns the value of field 'showBootstrap'.
+   *
+   * @return boolean
+   * @return the value of field 'showBootstrap'.
+   */
+  public boolean getShowBootstrap()
+  {
+    return this._showBootstrap;
+  } //-- boolean getShowBootstrap()
+
+  /**
+   * Returns the value of field 'showDistances'.
+   *
+   * @return boolean
+   * @return the value of field 'showDistances'.
+   */
+  public boolean getShowDistances()
+  {
+    return this._showDistances;
+  } //-- boolean getShowDistances()
+
+  /**
+   * Returns the value of field 'threshold'.
+   *
+   * @return float
+   * @return the value of field 'threshold'.
+   */
+  public float getThreshold()
+  {
+    return this._threshold;
+  } //-- float getThreshold()
+
+  /**
+   * Returns the value of field 'title'.
+   *
+   * @return String
+   * @return the value of field 'title'.
+   */
+  public java.lang.String getTitle()
+  {
+    return this._title;
+  } //-- java.lang.String getTitle()
+
+  /**
+   * Returns the value of field 'width'.
+   *
+   * @return int
+   * @return the value of field 'width'.
+   */
+  public int getWidth()
+  {
+    return this._width;
+  } //-- int getWidth()
+
+  /**
+   * Returns the value of field 'xpos'.
+   *
+   * @return int
+   * @return the value of field 'xpos'.
+   */
+  public int getXpos()
+  {
+    return this._xpos;
+  } //-- int getXpos()
+
+  /**
+   * Returns the value of field 'ypos'.
+   *
+   * @return int
+   * @return the value of field 'ypos'.
+   */
+  public int getYpos()
+  {
+    return this._ypos;
+  } //-- int getYpos()
+
+  /**
+   * Method hasCurrentTree
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasCurrentTree()
+  {
+    return this._has_currentTree;
+  } //-- boolean hasCurrentTree()
+
+  /**
+   * Method hasFitToWindow
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasFitToWindow()
+  {
+    return this._has_fitToWindow;
+  } //-- boolean hasFitToWindow()
+
+  /**
+   * Method hasFontSize
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasFontSize()
+  {
+    return this._has_fontSize;
+  } //-- boolean hasFontSize()
+
+  /**
+   * Method hasFontStyle
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasFontStyle()
+  {
+    return this._has_fontStyle;
+  } //-- boolean hasFontStyle()
+
+  /**
+   * Method hasHeight
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasHeight()
+  {
+    return this._has_height;
+  } //-- boolean hasHeight()
+
+  /**
+   * Method hasMarkUnlinked
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasMarkUnlinked()
+  {
+    return this._has_markUnlinked;
+  } //-- boolean hasMarkUnlinked()
+
+  /**
+   * Method hasShowBootstrap
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasShowBootstrap()
+  {
+    return this._has_showBootstrap;
+  } //-- boolean hasShowBootstrap()
+
+  /**
+   * Method hasShowDistances
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasShowDistances()
+  {
+    return this._has_showDistances;
+  } //-- boolean hasShowDistances()
+
+  /**
+   * Method hasThreshold
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasThreshold()
+  {
+    return this._has_threshold;
+  } //-- boolean hasThreshold()
+
+  /**
+   * Method hasWidth
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasWidth()
+  {
+    return this._has_width;
+  } //-- boolean hasWidth()
+
+  /**
+   * Method hasXpos
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasXpos()
+  {
+    return this._has_xpos;
+  } //-- boolean hasXpos()
+
+  /**
+   * Method hasYpos
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasYpos()
+  {
+    return this._has_ypos;
+  } //-- boolean hasYpos()
+
+  /**
+   * Method isValid
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    }
+    catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  } //-- boolean isValid()
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param out
+   */
+  public void marshal(java.io.Writer out)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, out);
+  } //-- void marshal(java.io.Writer)
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param handler
+   */
+  public void marshal(org.xml.sax.ContentHandler handler)
+      throws java.io.IOException, org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, handler);
+  } //-- void marshal(org.xml.sax.ContentHandler)
+
+  /**
+   * Sets the value of field 'currentTree'.
+   *
+   * @param currentTree the value of field 'currentTree'.
+   */
+  public void setCurrentTree(boolean currentTree)
+  {
+    this._currentTree = currentTree;
+    this._has_currentTree = true;
+  } //-- void setCurrentTree(boolean)
+
+  /**
+   * Sets the value of field 'fitToWindow'.
+   *
+   * @param fitToWindow the value of field 'fitToWindow'.
+   */
+  public void setFitToWindow(boolean fitToWindow)
+  {
+    this._fitToWindow = fitToWindow;
+    this._has_fitToWindow = true;
+  } //-- void setFitToWindow(boolean)
+
+  /**
+   * Sets the value of field 'fontName'.
+   *
+   * @param fontName the value of field 'fontName'.
+   */
+  public void setFontName(java.lang.String fontName)
+  {
+    this._fontName = fontName;
+  } //-- void setFontName(java.lang.String)
+
+  /**
+   * Sets the value of field 'fontSize'.
+   *
+   * @param fontSize the value of field 'fontSize'.
+   */
+  public void setFontSize(int fontSize)
+  {
+    this._fontSize = fontSize;
+    this._has_fontSize = true;
+  } //-- void setFontSize(int)
+
+  /**
+   * Sets the value of field 'fontStyle'.
+   *
+   * @param fontStyle the value of field 'fontStyle'.
+   */
+  public void setFontStyle(int fontStyle)
+  {
+    this._fontStyle = fontStyle;
+    this._has_fontStyle = true;
+  } //-- void setFontStyle(int)
+
+  /**
+   * Sets the value of field 'height'.
+   *
+   * @param height the value of field 'height'.
+   */
+  public void setHeight(int height)
+  {
+    this._height = height;
+    this._has_height = true;
+  } //-- void setHeight(int)
+
+  /**
+   * Sets the value of field 'markUnlinked'.
+   *
+   * @param markUnlinked the value of field 'markUnlinked'.
+   */
+  public void setMarkUnlinked(boolean markUnlinked)
+  {
+    this._markUnlinked = markUnlinked;
+    this._has_markUnlinked = true;
+  } //-- void setMarkUnlinked(boolean)
+
+  /**
+   * Sets the value of field 'newick'.
+   *
+   * @param newick the value of field 'newick'.
+   */
+  public void setNewick(java.lang.String newick)
+  {
+    this._newick = newick;
+  } //-- void setNewick(java.lang.String)
+
+  /**
+   * Sets the value of field 'showBootstrap'.
+   *
+   * @param showBootstrap the value of field 'showBootstrap'.
+   */
+  public void setShowBootstrap(boolean showBootstrap)
+  {
+    this._showBootstrap = showBootstrap;
+    this._has_showBootstrap = true;
+  } //-- void setShowBootstrap(boolean)
+
+  /**
+   * Sets the value of field 'showDistances'.
+   *
+   * @param showDistances the value of field 'showDistances'.
+   */
+  public void setShowDistances(boolean showDistances)
+  {
+    this._showDistances = showDistances;
+    this._has_showDistances = true;
+  } //-- void setShowDistances(boolean)
+
+  /**
+   * Sets the value of field 'threshold'.
+   *
+   * @param threshold the value of field 'threshold'.
+   */
+  public void setThreshold(float threshold)
+  {
+    this._threshold = threshold;
+    this._has_threshold = true;
+  } //-- void setThreshold(float)
+
+  /**
+   * Sets the value of field 'title'.
+   *
+   * @param title the value of field 'title'.
+   */
+  public void setTitle(java.lang.String title)
+  {
+    this._title = title;
+  } //-- void setTitle(java.lang.String)
+
+  /**
+   * Sets the value of field 'width'.
+   *
+   * @param width the value of field 'width'.
+   */
+  public void setWidth(int width)
+  {
+    this._width = width;
+    this._has_width = true;
+  } //-- void setWidth(int)
+
+  /**
+   * Sets the value of field 'xpos'.
+   *
+   * @param xpos the value of field 'xpos'.
+   */
+  public void setXpos(int xpos)
+  {
+    this._xpos = xpos;
+    this._has_xpos = true;
+  } //-- void setXpos(int)
+
+  /**
+   * Sets the value of field 'ypos'.
+   *
+   * @param ypos the value of field 'ypos'.
+   */
+  public void setYpos(int ypos)
+  {
+    this._ypos = ypos;
+    this._has_ypos = true;
+  } //-- void setYpos(int)
+
+  /**
+   * Method unmarshal
+   *
+   *
+   *
+   * @param reader
+   * @return Object
+   */
+  public static java.lang.Object unmarshal(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);
+  } //-- java.lang.Object unmarshal(java.io.Reader)
+
+  /**
+   * Method validate
+   *
+   */
+  public void validate()
+      throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.
+        Validator();
+    validator.validate(this);
+  } //-- void validate()
 
 }
diff --git a/src/jalview/schemabinding/version2/TreeDescriptor.java b/src/jalview/schemabinding/version2/TreeDescriptor.java
index 5232c12..1b7065e 100755
--- a/src/jalview/schemabinding/version2/TreeDescriptor.java
+++ b/src/jalview/schemabinding/version2/TreeDescriptor.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,771 +7,925 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
-import org.exolab.castor.mapping.AccessMode;
-import org.exolab.castor.xml.TypeValidator;
-import org.exolab.castor.xml.XMLFieldDescriptor;
 import org.exolab.castor.xml.validators.*;
 
 /**
  * Class TreeDescriptor.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class TreeDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field nsPrefix
-     */
-    private java.lang.String nsPrefix;
-
-    /**
-     * Field nsURI
-     */
-    private java.lang.String nsURI;
-
-    /**
-     * Field xmlName
-     */
-    private java.lang.String xmlName;
-
-    /**
-     * Field identity
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor identity;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public TreeDescriptor() {
-        super();
-        nsURI = "www.jalview.org";
-        xmlName = "tree";
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.xml.XMLFieldHandler              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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _width
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            IntegerValidator typeValidator= new IntegerValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _height
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            IntegerValidator typeValidator= new IntegerValidator();
-            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
-            {
-                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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _xpos
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            IntegerValidator typeValidator= new IntegerValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _ypos
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            IntegerValidator typeValidator= new IntegerValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _fontName
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            StringValidator typeValidator = new StringValidator();
-            typeValidator.setWhiteSpace("preserve");
-            fieldValidator.setValidator(typeValidator);
-        }
-        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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _fontSize
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            IntegerValidator typeValidator= new IntegerValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _fontStyle
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            IntegerValidator typeValidator= new IntegerValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _threshold
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(float.class, "_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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _threshold
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            FloatValidator typeValidator = new FloatValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _showBootstrap
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            BooleanValidator typeValidator = new 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());
-                }
-            }
-            public java.lang.Object newInstance( java.lang.Object parent ) {
-                return null;
-            }
-        } );
-        desc.setHandler(handler);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _showDistances
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            BooleanValidator typeValidator = new 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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _markUnlinked
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            BooleanValidator typeValidator = new 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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _fitToWindow
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            BooleanValidator typeValidator = new 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());
-                }
-            }
-            public java.lang.Object newInstance( java.lang.Object parent ) {
-                return null;
-            }
-        } );
-        desc.setHandler(handler);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _currentTree
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            BooleanValidator typeValidator = new 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();
-            }
-            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
-            StringValidator typeValidator = new StringValidator();
-            typeValidator.setWhiteSpace("preserve");
-            fieldValidator.setValidator(typeValidator);
-        }
-        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
-            StringValidator typeValidator = new StringValidator();
-            typeValidator.setWhiteSpace("preserve");
-            fieldValidator.setValidator(typeValidator);
-        }
-        desc.setValidator(fieldValidator);
-    } //-- jalview.schemabinding.version2.TreeDescriptor()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method getAccessMode
-     * 
-     * 
-     * 
-     * @return AccessMode
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode()
+public class TreeDescriptor
+    extends org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  //--------------------------/
+  //- Class/Member Variables -/
+  //--------------------------/
+
+  /**
+   * Field nsPrefix
+   */
+  private java.lang.String nsPrefix;
+
+  /**
+   * Field nsURI
+   */
+  private java.lang.String nsURI;
+
+  /**
+   * Field xmlName
+   */
+  private java.lang.String xmlName;
+
+  /**
+   * Field identity
+   */
+  private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+  //----------------/
+  //- Constructors -/
+  //----------------/
+
+  public TreeDescriptor()
+  {
+    super();
+    nsURI = "www.jalview.org";
+    xmlName = "tree";
+
+    //-- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.xml.XMLFieldHandler 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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _width
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      IntegerValidator typeValidator = new IntegerValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    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;
-    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
-
-    /**
-     * Method getExtends
-     * 
-     * 
-     * 
-     * @return ClassDescriptor
-     */
-    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+      }
+    });
+    desc.setHandler(handler);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _height
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      IntegerValidator typeValidator = new IntegerValidator();
+      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
+      {
+        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;
-    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
-
-    /**
-     * Method getIdentity
-     * 
-     * 
-     * 
-     * @return FieldDescriptor
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+      }
+    });
+    desc.setHandler(handler);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _xpos
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      IntegerValidator typeValidator = new IntegerValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    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()
     {
-        return identity;
-    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
-
-    /**
-     * Method getJavaClass
-     * 
-     * 
-     * 
-     * @return Class
-     */
-    public java.lang.Class getJavaClass()
+      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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _ypos
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      IntegerValidator typeValidator = new IntegerValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    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()
     {
-        return jalview.schemabinding.version2.Tree.class;
-    } //-- java.lang.Class getJavaClass() 
-
-    /**
-     * Method getNameSpacePrefix
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpacePrefix()
+      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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _fontName
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      StringValidator typeValidator = new StringValidator();
+      typeValidator.setWhiteSpace("preserve");
+      fieldValidator.setValidator(typeValidator);
+    }
+    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()
     {
-        return nsPrefix;
-    } //-- java.lang.String getNameSpacePrefix() 
-
-    /**
-     * Method getNameSpaceURI
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpaceURI()
+      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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _fontSize
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      IntegerValidator typeValidator = new IntegerValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    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()
     {
-        return nsURI;
-    } //-- java.lang.String getNameSpaceURI() 
-
-    /**
-     * Method getValidator
-     * 
-     * 
-     * 
-     * @return TypeValidator
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator()
+      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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _fontStyle
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      IntegerValidator typeValidator = new IntegerValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    //-- _threshold
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(float.class,
+        "_threshold", "threshold", org.exolab.castor.xml.NodeType.Attribute);
+    handler = (new org.exolab.castor.xml.XMLFieldHandler()
     {
-        return this;
-    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
-
-    /**
-     * Method getXMLName
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getXMLName()
+      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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _threshold
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      FloatValidator typeValidator = new FloatValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    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()
     {
-        return xmlName;
-    } //-- java.lang.String getXMLName() 
+      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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _showBootstrap
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      BooleanValidator typeValidator = new 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());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    });
+    desc.setHandler(handler);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _showDistances
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      BooleanValidator typeValidator = new 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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _markUnlinked
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      BooleanValidator typeValidator = new 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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _fitToWindow
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      BooleanValidator typeValidator = new 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());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    });
+    desc.setHandler(handler);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _currentTree
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      BooleanValidator typeValidator = new 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();
+      }
+
+      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
+      StringValidator typeValidator = new StringValidator();
+      typeValidator.setWhiteSpace("preserve");
+      fieldValidator.setValidator(typeValidator);
+    }
+    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
+      StringValidator typeValidator = new StringValidator();
+      typeValidator.setWhiteSpace("preserve");
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+  } //-- jalview.schemabinding.version2.TreeDescriptor()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Method getAccessMode
+   *
+   *
+   *
+   * @return AccessMode
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
+
+  /**
+   * Method getExtends
+   *
+   *
+   *
+   * @return ClassDescriptor
+   */
+  public org.exolab.castor.mapping.ClassDescriptor getExtends()
+  {
+    return null;
+  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
+
+  /**
+   * Method getIdentity
+   *
+   *
+   *
+   * @return FieldDescriptor
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return identity;
+  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
+
+  /**
+   * Method getJavaClass
+   *
+   *
+   *
+   * @return Class
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.Tree.class;
+  } //-- java.lang.Class getJavaClass()
+
+  /**
+   * Method getNameSpacePrefix
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return nsPrefix;
+  } //-- java.lang.String getNameSpacePrefix()
+
+  /**
+   * Method getNameSpaceURI
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return nsURI;
+  } //-- java.lang.String getNameSpaceURI()
+
+  /**
+   * Method getValidator
+   *
+   *
+   *
+   * @return TypeValidator
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  } //-- org.exolab.castor.xml.TypeValidator getValidator()
+
+  /**
+   * Method getXMLName
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getXMLName()
+  {
+    return xmlName;
+  } //-- java.lang.String getXMLName()
 
 }
diff --git a/src/jalview/schemabinding/version2/UserColourScheme.java b/src/jalview/schemabinding/version2/UserColourScheme.java
index 00bc181..d186608 100755
--- a/src/jalview/schemabinding/version2/UserColourScheme.java
+++ b/src/jalview/schemabinding/version2/UserColourScheme.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,112 +7,110 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
+import org.exolab.castor.xml.*;
 
 /**
  * Class UserColourScheme.
- * 
+ *
  * @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();
+  } //-- jalview.schemabinding.version2.UserColourScheme()
 
-    public UserColourScheme() {
-        super();
-    } //-- jalview.schemabinding.version2.UserColourScheme()
+  //-----------/
+  //- Methods -/
+  //-----------/
 
+  /**
+   * Method isValid
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    }
+    catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  } //-- boolean isValid()
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param out
+   */
+  public void marshal(java.io.Writer out)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
 
-    /**
-     * Method isValid
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean isValid()
-    {
-        try {
-            validate();
-        }
-        catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    } //-- boolean isValid() 
+    Marshaller.marshal(this, out);
+  } //-- void marshal(java.io.Writer)
 
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param out
-     */
-    public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, out);
-    } //-- void marshal(java.io.Writer) 
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param handler
+   */
+  public void marshal(org.xml.sax.ContentHandler handler)
+      throws java.io.IOException, org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
 
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param handler
-     */
-    public void marshal(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, handler);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
+    Marshaller.marshal(this, handler);
+  } //-- void marshal(org.xml.sax.ContentHandler)
 
-    /**
-     * Method unmarshal
-     * 
-     * 
-     * 
-     * @param reader
-     * @return Object
-     */
-    public static java.lang.Object unmarshal(java.io.Reader reader)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        return (jalview.schemabinding.version2.UserColourScheme) Unmarshaller.unmarshal(jalview.schemabinding.version2.UserColourScheme.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
+  /**
+   * Method unmarshal
+   *
+   *
+   *
+   * @param reader
+   * @return Object
+   */
+  public static java.lang.Object unmarshal(java.io.Reader reader)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.UserColourScheme) Unmarshaller.
+        unmarshal(jalview.schemabinding.version2.UserColourScheme.class, reader);
+  } //-- java.lang.Object unmarshal(java.io.Reader)
 
-    /**
-     * Method validate
-     * 
-     */
-    public void validate()
-        throws org.exolab.castor.xml.ValidationException
-    {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    } //-- void validate() 
+  /**
+   * Method validate
+   *
+   */
+  public void validate()
+      throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.
+        Validator();
+    validator.validate(this);
+  } //-- void validate()
 
 }
diff --git a/src/jalview/schemabinding/version2/UserColourSchemeDescriptor.java b/src/jalview/schemabinding/version2/UserColourSchemeDescriptor.java
index cf86a11..adcb59b 100755
--- a/src/jalview/schemabinding/version2/UserColourSchemeDescriptor.java
+++ b/src/jalview/schemabinding/version2/UserColourSchemeDescriptor.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,160 +7,159 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
 //---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
 
-import org.exolab.castor.mapping.AccessMode;
-import org.exolab.castor.xml.TypeValidator;
-import org.exolab.castor.xml.XMLFieldDescriptor;
-import org.exolab.castor.xml.validators.*;
 
 /**
  * Class UserColourSchemeDescriptor.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class UserColourSchemeDescriptor extends JalviewUserColoursDescriptor {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field nsPrefix
-     */
-    private java.lang.String nsPrefix;
-
-    /**
-     * Field nsURI
-     */
-    private java.lang.String nsURI;
-
-    /**
-     * Field xmlName
-     */
-    private java.lang.String xmlName;
-
-    /**
-     * Field identity
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor identity;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public UserColourSchemeDescriptor() {
-        super();
-        setExtendsWithoutFlatten(new JalviewUserColoursDescriptor());
-        nsURI = "www.jalview.org";
-        xmlName = "UserColourScheme";
-    } //-- jalview.schemabinding.version2.UserColourSchemeDescriptor()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method getAccessMode
-     * 
-     * 
-     * 
-     * @return AccessMode
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode()
-    {
-        return null;
-    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
-
-    /**
-     * Method getExtends
-     * 
-     * 
-     * 
-     * @return ClassDescriptor
-     */
-    public org.exolab.castor.mapping.ClassDescriptor getExtends()
-    {
-        return super.getExtends();
-    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
-
-    /**
-     * Method getIdentity
-     * 
-     * 
-     * 
-     * @return FieldDescriptor
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
-    {
-        if (identity == null)
-            return super.getIdentity();
-        return identity;
-    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
-
-    /**
-     * Method getJavaClass
-     * 
-     * 
-     * 
-     * @return Class
-     */
-    public java.lang.Class getJavaClass()
-    {
-        return jalview.schemabinding.version2.UserColourScheme.class;
-    } //-- java.lang.Class getJavaClass() 
-
-    /**
-     * Method getNameSpacePrefix
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpacePrefix()
-    {
-        return nsPrefix;
-    } //-- java.lang.String getNameSpacePrefix() 
-
-    /**
-     * Method getNameSpaceURI
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpaceURI()
-    {
-        return nsURI;
-    } //-- java.lang.String getNameSpaceURI() 
-
-    /**
-     * Method getValidator
-     * 
-     * 
-     * 
-     * @return TypeValidator
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator()
-    {
-        return this;
-    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
-
-    /**
-     * Method getXMLName
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getXMLName()
+public class UserColourSchemeDescriptor
+    extends JalviewUserColoursDescriptor
+{
+
+  //--------------------------/
+  //- Class/Member Variables -/
+  //--------------------------/
+
+  /**
+   * Field nsPrefix
+   */
+  private java.lang.String nsPrefix;
+
+  /**
+   * Field nsURI
+   */
+  private java.lang.String nsURI;
+
+  /**
+   * Field xmlName
+   */
+  private java.lang.String xmlName;
+
+  /**
+   * Field identity
+   */
+  private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+  //----------------/
+  //- Constructors -/
+  //----------------/
+
+  public UserColourSchemeDescriptor()
+  {
+    super();
+    setExtendsWithoutFlatten(new JalviewUserColoursDescriptor());
+    nsURI = "www.jalview.org";
+    xmlName = "UserColourScheme";
+  } //-- jalview.schemabinding.version2.UserColourSchemeDescriptor()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Method getAccessMode
+   *
+   *
+   *
+   * @return AccessMode
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
+
+  /**
+   * Method getExtends
+   *
+   *
+   *
+   * @return ClassDescriptor
+   */
+  public org.exolab.castor.mapping.ClassDescriptor getExtends()
+  {
+    return super.getExtends();
+  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
+
+  /**
+   * Method getIdentity
+   *
+   *
+   *
+   * @return FieldDescriptor
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    if (identity == null)
     {
-        return xmlName;
-    } //-- java.lang.String getXMLName() 
+      return super.getIdentity();
+    }
+    return identity;
+  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
+
+  /**
+   * Method getJavaClass
+   *
+   *
+   *
+   * @return Class
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.UserColourScheme.class;
+  } //-- java.lang.Class getJavaClass()
+
+  /**
+   * Method getNameSpacePrefix
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return nsPrefix;
+  } //-- java.lang.String getNameSpacePrefix()
+
+  /**
+   * Method getNameSpaceURI
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return nsURI;
+  } //-- java.lang.String getNameSpaceURI()
+
+  /**
+   * Method getValidator
+   *
+   *
+   *
+   * @return TypeValidator
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  } //-- org.exolab.castor.xml.TypeValidator getValidator()
+
+  /**
+   * Method getXMLName
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getXMLName()
+  {
+    return xmlName;
+  } //-- java.lang.String getXMLName()
 
 }
diff --git a/src/jalview/schemabinding/version2/UserColours.java b/src/jalview/schemabinding/version2/UserColours.java
index 28f2b39..fe77948 100755
--- a/src/jalview/schemabinding/version2/UserColours.java
+++ b/src/jalview/schemabinding/version2/UserColours.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,167 +7,167 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
+import org.exolab.castor.xml.*;
 
 /**
  * Class UserColours.
- * 
+ *
  * @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();
-    } //-- jalview.schemabinding.version2.UserColours()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Returns the value of field 'id'.
-     * 
-     * @return String
-     * @return the value of field 'id'.
-     */
-    public java.lang.String getId()
-    {
-        return this._id;
-    } //-- java.lang.String getId() 
-
-    /**
-     * Returns the value of field 'userColourScheme'.
-     * 
-     * @return UserColourScheme
-     * @return the value of field 'userColourScheme'.
-     */
-    public jalview.schemabinding.version2.UserColourScheme getUserColourScheme()
-    {
-        return this._userColourScheme;
-    } //-- jalview.schemabinding.version2.UserColourScheme getUserColourScheme() 
-
-    /**
-     * Method isValid
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean isValid()
-    {
-        try {
-            validate();
-        }
-        catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    } //-- boolean isValid() 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param out
-     */
-    public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, out);
-    } //-- void marshal(java.io.Writer) 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param handler
-     */
-    public void marshal(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, handler);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
-
-    /**
-     * Sets the value of field 'id'.
-     * 
-     * @param id the value of field 'id'.
-     */
-    public void setId(java.lang.String id)
-    {
-        this._id = id;
-    } //-- void setId(java.lang.String) 
-
-    /**
-     * Sets the value of field 'userColourScheme'.
-     * 
-     * @param userColourScheme the value of field 'userColourScheme'
-     */
-    public void setUserColourScheme(jalview.schemabinding.version2.UserColourScheme userColourScheme)
-    {
-        this._userColourScheme = userColourScheme;
-    } //-- void setUserColourScheme(jalview.schemabinding.version2.UserColourScheme) 
-
-    /**
-     * Method unmarshal
-     * 
-     * 
-     * 
-     * @param reader
-     * @return Object
-     */
-    public static java.lang.Object unmarshal(java.io.Reader reader)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+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();
+  } //-- jalview.schemabinding.version2.UserColours()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Returns the value of field 'id'.
+   *
+   * @return String
+   * @return the value of field 'id'.
+   */
+  public java.lang.String getId()
+  {
+    return this._id;
+  } //-- java.lang.String getId()
+
+  /**
+   * Returns the value of field 'userColourScheme'.
+   *
+   * @return UserColourScheme
+   * @return the value of field 'userColourScheme'.
+   */
+  public jalview.schemabinding.version2.UserColourScheme getUserColourScheme()
+  {
+    return this._userColourScheme;
+  } //-- jalview.schemabinding.version2.UserColourScheme getUserColourScheme()
+
+  /**
+   * Method isValid
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean isValid()
+  {
+    try
     {
-        return (jalview.schemabinding.version2.UserColours) Unmarshaller.unmarshal(jalview.schemabinding.version2.UserColours.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
-
-    /**
-     * Method validate
-     * 
-     */
-    public void validate()
-        throws org.exolab.castor.xml.ValidationException
+      validate();
+    }
+    catch (org.exolab.castor.xml.ValidationException vex)
     {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    } //-- void validate() 
+      return false;
+    }
+    return true;
+  } //-- boolean isValid()
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param out
+   */
+  public void marshal(java.io.Writer out)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, out);
+  } //-- void marshal(java.io.Writer)
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param handler
+   */
+  public void marshal(org.xml.sax.ContentHandler handler)
+      throws java.io.IOException, org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, handler);
+  } //-- void marshal(org.xml.sax.ContentHandler)
+
+  /**
+   * Sets the value of field 'id'.
+   *
+   * @param id the value of field 'id'.
+   */
+  public void setId(java.lang.String id)
+  {
+    this._id = id;
+  } //-- void setId(java.lang.String)
+
+  /**
+   * Sets the value of field 'userColourScheme'.
+   *
+   * @param userColourScheme the value of field 'userColourScheme'
+   */
+  public void setUserColourScheme(jalview.schemabinding.version2.
+                                  UserColourScheme userColourScheme)
+  {
+    this._userColourScheme = userColourScheme;
+  } //-- void setUserColourScheme(jalview.schemabinding.version2.UserColourScheme)
+
+  /**
+   * Method unmarshal
+   *
+   *
+   *
+   * @param reader
+   * @return Object
+   */
+  public static java.lang.Object unmarshal(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);
+  } //-- java.lang.Object unmarshal(java.io.Reader)
+
+  /**
+   * Method validate
+   *
+   */
+  public void validate()
+      throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.
+        Validator();
+    validator.validate(this);
+  } //-- void validate()
 
 }
diff --git a/src/jalview/schemabinding/version2/UserColoursDescriptor.java b/src/jalview/schemabinding/version2/UserColoursDescriptor.java
index 6c42d0b..29339a2 100755
--- a/src/jalview/schemabinding/version2/UserColoursDescriptor.java
+++ b/src/jalview/schemabinding/version2/UserColoursDescriptor.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,239 +7,252 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
-import org.exolab.castor.mapping.AccessMode;
-import org.exolab.castor.xml.TypeValidator;
-import org.exolab.castor.xml.XMLFieldDescriptor;
 import org.exolab.castor.xml.validators.*;
 
 /**
  * Class UserColoursDescriptor.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class UserColoursDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field nsPrefix
-     */
-    private java.lang.String nsPrefix;
-
-    /**
-     * Field nsURI
-     */
-    private java.lang.String nsURI;
-
-    /**
-     * Field xmlName
-     */
-    private java.lang.String xmlName;
-
-    /**
-     * Field identity
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor identity;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public UserColoursDescriptor() {
-        super();
-        nsURI = "www.jalview.org";
-        xmlName = "UserColours";
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.xml.XMLFieldHandler              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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _id
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            StringValidator typeValidator = new StringValidator();
-            typeValidator.setWhiteSpace("preserve");
-            fieldValidator.setValidator(typeValidator);
+public class UserColoursDescriptor
+    extends org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  //--------------------------/
+  //- Class/Member Variables -/
+  //--------------------------/
+
+  /**
+   * Field nsPrefix
+   */
+  private java.lang.String nsPrefix;
+
+  /**
+   * Field nsURI
+   */
+  private java.lang.String nsURI;
+
+  /**
+   * Field xmlName
+   */
+  private java.lang.String xmlName;
+
+  /**
+   * Field identity
+   */
+  private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+  //----------------/
+  //- Constructors -/
+  //----------------/
+
+  public UserColoursDescriptor()
+  {
+    super();
+    nsURI = "www.jalview.org";
+    xmlName = "UserColours";
+
+    //-- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.xml.XMLFieldHandler 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);
         }
-        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
+        catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-    } //-- jalview.schemabinding.version2.UserColoursDescriptor()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method getAccessMode
-     * 
-     * 
-     * 
-     * @return AccessMode
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode()
-    {
-        return null;
-    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
-
-    /**
-     * Method getExtends
-     * 
-     * 
-     * 
-     * @return ClassDescriptor
-     */
-    public org.exolab.castor.mapping.ClassDescriptor getExtends()
-    {
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
-
-    /**
-     * Method getIdentity
-     * 
-     * 
-     * 
-     * @return FieldDescriptor
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
-    {
-        return identity;
-    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
-
-    /**
-     * Method getJavaClass
-     * 
-     * 
-     * 
-     * @return Class
-     */
-    public java.lang.Class getJavaClass()
-    {
-        return jalview.schemabinding.version2.UserColours.class;
-    } //-- java.lang.Class getJavaClass() 
-
-    /**
-     * Method getNameSpacePrefix
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpacePrefix()
-    {
-        return nsPrefix;
-    } //-- java.lang.String getNameSpacePrefix() 
-
-    /**
-     * Method getNameSpaceURI
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpaceURI()
-    {
-        return nsURI;
-    } //-- java.lang.String getNameSpaceURI() 
-
-    /**
-     * Method getValidator
-     * 
-     * 
-     * 
-     * @return TypeValidator
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator()
-    {
-        return this;
-    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
-
-    /**
-     * Method getXMLName
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getXMLName()
+      }
+    });
+    desc.setHandler(handler);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _id
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      StringValidator typeValidator = new StringValidator();
+      typeValidator.setWhiteSpace("preserve");
+      fieldValidator.setValidator(typeValidator);
+    }
+    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()
     {
-        return xmlName;
-    } //-- java.lang.String getXMLName() 
+      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);
+  } //-- jalview.schemabinding.version2.UserColoursDescriptor()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Method getAccessMode
+   *
+   *
+   *
+   * @return AccessMode
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
+
+  /**
+   * Method getExtends
+   *
+   *
+   *
+   * @return ClassDescriptor
+   */
+  public org.exolab.castor.mapping.ClassDescriptor getExtends()
+  {
+    return null;
+  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
+
+  /**
+   * Method getIdentity
+   *
+   *
+   *
+   * @return FieldDescriptor
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return identity;
+  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
+
+  /**
+   * Method getJavaClass
+   *
+   *
+   *
+   * @return Class
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.UserColours.class;
+  } //-- java.lang.Class getJavaClass()
+
+  /**
+   * Method getNameSpacePrefix
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return nsPrefix;
+  } //-- java.lang.String getNameSpacePrefix()
+
+  /**
+   * Method getNameSpaceURI
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return nsURI;
+  } //-- java.lang.String getNameSpaceURI()
+
+  /**
+   * Method getValidator
+   *
+   *
+   *
+   * @return TypeValidator
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  } //-- org.exolab.castor.xml.TypeValidator getValidator()
+
+  /**
+   * Method getXMLName
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getXMLName()
+  {
+    return xmlName;
+  } //-- java.lang.String getXMLName()
 
 }
diff --git a/src/jalview/schemabinding/version2/VAMSAS.java b/src/jalview/schemabinding/version2/VAMSAS.java
index 03633d6..8a4803c 100755
--- a/src/jalview/schemabinding/version2/VAMSAS.java
+++ b/src/jalview/schemabinding/version2/VAMSAS.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,419 +7,435 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
 //---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import java.util.*;
 
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import java.util.Enumeration;
-import java.util.Vector;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
+import org.exolab.castor.xml.*;
 
 /**
  * Class VAMSAS.
- * 
+ *
  * @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();
-        _treeList = new Vector();
-        _sequenceSetList = new Vector();
-    } //-- jalview.schemabinding.version2.VAMSAS()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method addSequenceSet
-     * 
-     * 
-     * 
-     * @param vSequenceSet
-     */
-    public void addSequenceSet(jalview.schemabinding.version2.SequenceSet vSequenceSet)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _sequenceSetList.addElement(vSequenceSet);
-    } //-- void addSequenceSet(jalview.schemabinding.version2.SequenceSet) 
-
-    /**
-     * Method addSequenceSet
-     * 
-     * 
-     * 
-     * @param index
-     * @param vSequenceSet
-     */
-    public void addSequenceSet(int index, jalview.schemabinding.version2.SequenceSet vSequenceSet)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _sequenceSetList.insertElementAt(vSequenceSet, index);
-    } //-- void addSequenceSet(int, jalview.schemabinding.version2.SequenceSet) 
-
-    /**
-     * Method addTree
-     * 
-     * 
-     * 
-     * @param vTree
-     */
-    public void addTree(java.lang.String vTree)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _treeList.addElement(vTree);
-    } //-- void addTree(java.lang.String) 
-
-    /**
-     * Method addTree
-     * 
-     * 
-     * 
-     * @param index
-     * @param vTree
-     */
-    public void addTree(int index, java.lang.String vTree)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _treeList.insertElementAt(vTree, index);
-    } //-- void addTree(int, java.lang.String) 
-
-    /**
-     * Method enumerateSequenceSet
-     * 
-     * 
-     * 
-     * @return Enumeration
-     */
-    public java.util.Enumeration enumerateSequenceSet()
-    {
-        return _sequenceSetList.elements();
-    } //-- java.util.Enumeration enumerateSequenceSet() 
-
-    /**
-     * Method enumerateTree
-     * 
-     * 
-     * 
-     * @return Enumeration
-     */
-    public java.util.Enumeration enumerateTree()
-    {
-        return _treeList.elements();
-    } //-- java.util.Enumeration enumerateTree() 
-
-    /**
-     * Method getSequenceSet
-     * 
-     * 
-     * 
-     * @param index
-     * @return SequenceSet
-     */
-    public jalview.schemabinding.version2.SequenceSet getSequenceSet(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _sequenceSetList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        
-        return (jalview.schemabinding.version2.SequenceSet) _sequenceSetList.elementAt(index);
-    } //-- jalview.schemabinding.version2.SequenceSet getSequenceSet(int) 
-
-    /**
-     * Method getSequenceSet
-     * 
-     * 
-     * 
-     * @return SequenceSet
-     */
-    public jalview.schemabinding.version2.SequenceSet[] getSequenceSet()
-    {
-        int size = _sequenceSetList.size();
-        jalview.schemabinding.version2.SequenceSet[] mArray = new jalview.schemabinding.version2.SequenceSet[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = (jalview.schemabinding.version2.SequenceSet) _sequenceSetList.elementAt(index);
-        }
-        return mArray;
-    } //-- jalview.schemabinding.version2.SequenceSet[] getSequenceSet() 
-
-    /**
-     * Method getSequenceSetCount
-     * 
-     * 
-     * 
-     * @return int
-     */
-    public int getSequenceSetCount()
-    {
-        return _sequenceSetList.size();
-    } //-- int getSequenceSetCount() 
-
-    /**
-     * Method getTree
-     * 
-     * 
-     * 
-     * @param index
-     * @return String
-     */
-    public java.lang.String getTree(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _treeList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        
-        return (String)_treeList.elementAt(index);
-    } //-- java.lang.String getTree(int) 
-
-    /**
-     * Method getTree
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String[] getTree()
-    {
-        int size = _treeList.size();
-        java.lang.String[] mArray = new java.lang.String[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = (String)_treeList.elementAt(index);
-        }
-        return mArray;
-    } //-- java.lang.String[] getTree() 
-
-    /**
-     * Method getTreeCount
-     * 
-     * 
-     * 
-     * @return int
-     */
-    public int getTreeCount()
-    {
-        return _treeList.size();
-    } //-- int getTreeCount() 
-
-    /**
-     * Method isValid
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean isValid()
-    {
-        try {
-            validate();
-        }
-        catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    } //-- boolean isValid() 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param out
-     */
-    public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, out);
-    } //-- void marshal(java.io.Writer) 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param handler
-     */
-    public void marshal(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, handler);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
-
-    /**
-     * Method removeAllSequenceSet
-     * 
-     */
-    public void removeAllSequenceSet()
+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();
+    _treeList = new Vector();
+    _sequenceSetList = new Vector();
+  } //-- jalview.schemabinding.version2.VAMSAS()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Method addSequenceSet
+   *
+   *
+   *
+   * @param vSequenceSet
+   */
+  public void addSequenceSet(jalview.schemabinding.version2.SequenceSet
+                             vSequenceSet)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _sequenceSetList.addElement(vSequenceSet);
+  } //-- void addSequenceSet(jalview.schemabinding.version2.SequenceSet)
+
+  /**
+   * Method addSequenceSet
+   *
+   *
+   *
+   * @param index
+   * @param vSequenceSet
+   */
+  public void addSequenceSet(int index,
+                             jalview.schemabinding.version2.SequenceSet
+                             vSequenceSet)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _sequenceSetList.insertElementAt(vSequenceSet, index);
+  } //-- void addSequenceSet(int, jalview.schemabinding.version2.SequenceSet)
+
+  /**
+   * Method addTree
+   *
+   *
+   *
+   * @param vTree
+   */
+  public void addTree(java.lang.String vTree)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _treeList.addElement(vTree);
+  } //-- void addTree(java.lang.String)
+
+  /**
+   * Method addTree
+   *
+   *
+   *
+   * @param index
+   * @param vTree
+   */
+  public void addTree(int index, java.lang.String vTree)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _treeList.insertElementAt(vTree, index);
+  } //-- void addTree(int, java.lang.String)
+
+  /**
+   * Method enumerateSequenceSet
+   *
+   *
+   *
+   * @return Enumeration
+   */
+  public java.util.Enumeration enumerateSequenceSet()
+  {
+    return _sequenceSetList.elements();
+  } //-- java.util.Enumeration enumerateSequenceSet()
+
+  /**
+   * Method enumerateTree
+   *
+   *
+   *
+   * @return Enumeration
+   */
+  public java.util.Enumeration enumerateTree()
+  {
+    return _treeList.elements();
+  } //-- java.util.Enumeration enumerateTree()
+
+  /**
+   * Method getSequenceSet
+   *
+   *
+   *
+   * @param index
+   * @return SequenceSet
+   */
+  public jalview.schemabinding.version2.SequenceSet getSequenceSet(int index)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _sequenceSetList.size()))
     {
-        _sequenceSetList.removeAllElements();
-    } //-- void removeAllSequenceSet() 
-
-    /**
-     * Method removeAllTree
-     * 
-     */
-    public void removeAllTree()
+      throw new IndexOutOfBoundsException();
+    }
+
+    return (jalview.schemabinding.version2.SequenceSet) _sequenceSetList.
+        elementAt(index);
+  } //-- jalview.schemabinding.version2.SequenceSet getSequenceSet(int)
+
+  /**
+   * Method getSequenceSet
+   *
+   *
+   *
+   * @return SequenceSet
+   */
+  public jalview.schemabinding.version2.SequenceSet[] getSequenceSet()
+  {
+    int size = _sequenceSetList.size();
+    jalview.schemabinding.version2.SequenceSet[] mArray = new jalview.
+        schemabinding.version2.SequenceSet[size];
+    for (int index = 0; index < size; index++)
     {
-        _treeList.removeAllElements();
-    } //-- void removeAllTree() 
-
-    /**
-     * Method removeSequenceSet
-     * 
-     * 
-     * 
-     * @param index
-     * @return SequenceSet
-     */
-    public jalview.schemabinding.version2.SequenceSet removeSequenceSet(int index)
+      mArray[index] = (jalview.schemabinding.version2.SequenceSet)
+          _sequenceSetList.elementAt(index);
+    }
+    return mArray;
+  } //-- jalview.schemabinding.version2.SequenceSet[] getSequenceSet()
+
+  /**
+   * Method getSequenceSetCount
+   *
+   *
+   *
+   * @return int
+   */
+  public int getSequenceSetCount()
+  {
+    return _sequenceSetList.size();
+  } //-- int getSequenceSetCount()
+
+  /**
+   * Method getTree
+   *
+   *
+   *
+   * @param index
+   * @return String
+   */
+  public java.lang.String getTree(int index)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _treeList.size()))
     {
-        java.lang.Object obj = _sequenceSetList.elementAt(index);
-        _sequenceSetList.removeElementAt(index);
-        return (jalview.schemabinding.version2.SequenceSet) obj;
-    } //-- jalview.schemabinding.version2.SequenceSet removeSequenceSet(int) 
-
-    /**
-     * Method removeTree
-     * 
-     * 
-     * 
-     * @param index
-     * @return String
-     */
-    public java.lang.String removeTree(int index)
+      throw new IndexOutOfBoundsException();
+    }
+
+    return (String) _treeList.elementAt(index);
+  } //-- java.lang.String getTree(int)
+
+  /**
+   * Method getTree
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String[] getTree()
+  {
+    int size = _treeList.size();
+    java.lang.String[] mArray = new java.lang.String[size];
+    for (int index = 0; index < size; index++)
     {
-        java.lang.Object obj = _treeList.elementAt(index);
-        _treeList.removeElementAt(index);
-        return (String)obj;
-    } //-- java.lang.String removeTree(int) 
-
-    /**
-     * Method setSequenceSet
-     * 
-     * 
-     * 
-     * @param index
-     * @param vSequenceSet
-     */
-    public void setSequenceSet(int index, jalview.schemabinding.version2.SequenceSet vSequenceSet)
-        throws java.lang.IndexOutOfBoundsException
+      mArray[index] = (String) _treeList.elementAt(index);
+    }
+    return mArray;
+  } //-- java.lang.String[] getTree()
+
+  /**
+   * Method getTreeCount
+   *
+   *
+   *
+   * @return int
+   */
+  public int getTreeCount()
+  {
+    return _treeList.size();
+  } //-- int getTreeCount()
+
+  /**
+   * Method isValid
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean isValid()
+  {
+    try
     {
-        //-- check bounds for index
-        if ((index < 0) || (index > _sequenceSetList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        _sequenceSetList.setElementAt(vSequenceSet, index);
-    } //-- void setSequenceSet(int, jalview.schemabinding.version2.SequenceSet) 
-
-    /**
-     * Method setSequenceSet
-     * 
-     * 
-     * 
-     * @param sequenceSetArray
-     */
-    public void setSequenceSet(jalview.schemabinding.version2.SequenceSet[] sequenceSetArray)
+      validate();
+    }
+    catch (org.exolab.castor.xml.ValidationException vex)
     {
-        //-- copy array
-        _sequenceSetList.removeAllElements();
-        for (int i = 0; i < sequenceSetArray.length; i++) {
-            _sequenceSetList.addElement(sequenceSetArray[i]);
-        }
-    } //-- void setSequenceSet(jalview.schemabinding.version2.SequenceSet) 
-
-    /**
-     * Method setTree
-     * 
-     * 
-     * 
-     * @param index
-     * @param vTree
-     */
-    public void setTree(int index, java.lang.String vTree)
-        throws java.lang.IndexOutOfBoundsException
+      return false;
+    }
+    return true;
+  } //-- boolean isValid()
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param out
+   */
+  public void marshal(java.io.Writer out)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, out);
+  } //-- void marshal(java.io.Writer)
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param handler
+   */
+  public void marshal(org.xml.sax.ContentHandler handler)
+      throws java.io.IOException, org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, handler);
+  } //-- void marshal(org.xml.sax.ContentHandler)
+
+  /**
+   * Method removeAllSequenceSet
+   *
+   */
+  public void removeAllSequenceSet()
+  {
+    _sequenceSetList.removeAllElements();
+  } //-- void removeAllSequenceSet()
+
+  /**
+   * Method removeAllTree
+   *
+   */
+  public void removeAllTree()
+  {
+    _treeList.removeAllElements();
+  } //-- void removeAllTree()
+
+  /**
+   * Method removeSequenceSet
+   *
+   *
+   *
+   * @param index
+   * @return SequenceSet
+   */
+  public jalview.schemabinding.version2.SequenceSet removeSequenceSet(int index)
+  {
+    java.lang.Object obj = _sequenceSetList.elementAt(index);
+    _sequenceSetList.removeElementAt(index);
+    return (jalview.schemabinding.version2.SequenceSet) obj;
+  } //-- jalview.schemabinding.version2.SequenceSet removeSequenceSet(int)
+
+  /**
+   * Method removeTree
+   *
+   *
+   *
+   * @param index
+   * @return String
+   */
+  public java.lang.String removeTree(int index)
+  {
+    java.lang.Object obj = _treeList.elementAt(index);
+    _treeList.removeElementAt(index);
+    return (String) obj;
+  } //-- java.lang.String removeTree(int)
+
+  /**
+   * Method setSequenceSet
+   *
+   *
+   *
+   * @param index
+   * @param vSequenceSet
+   */
+  public void setSequenceSet(int index,
+                             jalview.schemabinding.version2.SequenceSet
+                             vSequenceSet)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _sequenceSetList.size()))
     {
-        //-- check bounds for index
-        if ((index < 0) || (index > _treeList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        _treeList.setElementAt(vTree, index);
-    } //-- void setTree(int, java.lang.String) 
-
-    /**
-     * Method setTree
-     * 
-     * 
-     * 
-     * @param treeArray
-     */
-    public void setTree(java.lang.String[] treeArray)
+      throw new IndexOutOfBoundsException();
+    }
+    _sequenceSetList.setElementAt(vSequenceSet, index);
+  } //-- void setSequenceSet(int, jalview.schemabinding.version2.SequenceSet)
+
+  /**
+   * Method setSequenceSet
+   *
+   *
+   *
+   * @param sequenceSetArray
+   */
+  public void setSequenceSet(jalview.schemabinding.version2.SequenceSet[]
+                             sequenceSetArray)
+  {
+    //-- copy array
+    _sequenceSetList.removeAllElements();
+    for (int i = 0; i < sequenceSetArray.length; i++)
     {
-        //-- copy array
-        _treeList.removeAllElements();
-        for (int i = 0; i < treeArray.length; i++) {
-            _treeList.addElement(treeArray[i]);
-        }
-    } //-- void setTree(java.lang.String) 
-
-    /**
-     * Method unmarshal
-     * 
-     * 
-     * 
-     * @param reader
-     * @return Object
-     */
-    public static java.lang.Object unmarshal(java.io.Reader reader)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+      _sequenceSetList.addElement(sequenceSetArray[i]);
+    }
+  } //-- void setSequenceSet(jalview.schemabinding.version2.SequenceSet)
+
+  /**
+   * Method setTree
+   *
+   *
+   *
+   * @param index
+   * @param vTree
+   */
+  public void setTree(int index, java.lang.String vTree)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _treeList.size()))
     {
-        return (jalview.schemabinding.version2.VAMSAS) Unmarshaller.unmarshal(jalview.schemabinding.version2.VAMSAS.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
-
-    /**
-     * Method validate
-     * 
-     */
-    public void validate()
-        throws org.exolab.castor.xml.ValidationException
+      throw new IndexOutOfBoundsException();
+    }
+    _treeList.setElementAt(vTree, index);
+  } //-- void setTree(int, java.lang.String)
+
+  /**
+   * Method setTree
+   *
+   *
+   *
+   * @param treeArray
+   */
+  public void setTree(java.lang.String[] treeArray)
+  {
+    //-- copy array
+    _treeList.removeAllElements();
+    for (int i = 0; i < treeArray.length; i++)
     {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    } //-- void validate() 
+      _treeList.addElement(treeArray[i]);
+    }
+  } //-- void setTree(java.lang.String)
+
+  /**
+   * Method unmarshal
+   *
+   *
+   *
+   * @param reader
+   * @return Object
+   */
+  public static java.lang.Object unmarshal(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);
+  } //-- java.lang.Object unmarshal(java.io.Reader)
+
+  /**
+   * Method validate
+   *
+   */
+  public void validate()
+      throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.
+        Validator();
+    validator.validate(this);
+  } //-- void validate()
 
 }
diff --git a/src/jalview/schemabinding/version2/VAMSASDescriptor.java b/src/jalview/schemabinding/version2/VAMSASDescriptor.java
index fad185b..89d4157 100755
--- a/src/jalview/schemabinding/version2/VAMSASDescriptor.java
+++ b/src/jalview/schemabinding/version2/VAMSASDescriptor.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,241 +7,255 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
-import org.exolab.castor.mapping.AccessMode;
-import org.exolab.castor.xml.TypeValidator;
-import org.exolab.castor.xml.XMLFieldDescriptor;
 import org.exolab.castor.xml.validators.*;
 
 /**
  * Class VAMSASDescriptor.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class VAMSASDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field nsPrefix
-     */
-    private java.lang.String nsPrefix;
-
-    /**
-     * Field nsURI
-     */
-    private java.lang.String nsURI;
-
-    /**
-     * Field xmlName
-     */
-    private java.lang.String xmlName;
-
-    /**
-     * Field identity
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor identity;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public VAMSASDescriptor() {
-        super();
-        nsURI = "www.vamsas.ac.uk/jalview/version2";
-        xmlName = "VAMSAS";
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.xml.XMLFieldHandler              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 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
-            StringValidator typeValidator = new StringValidator();
-            typeValidator.setWhiteSpace("preserve");
-            fieldValidator.setValidator(typeValidator);
+public class VAMSASDescriptor
+    extends org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  //--------------------------/
+  //- Class/Member Variables -/
+  //--------------------------/
+
+  /**
+   * Field nsPrefix
+   */
+  private java.lang.String nsPrefix;
+
+  /**
+   * Field nsURI
+   */
+  private java.lang.String nsURI;
+
+  /**
+   * Field xmlName
+   */
+  private java.lang.String xmlName;
+
+  /**
+   * Field identity
+   */
+  private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+  //----------------/
+  //- Constructors -/
+  //----------------/
+
+  public VAMSASDescriptor()
+  {
+    super();
+    nsURI = "www.vamsas.ac.uk/jalview/version2";
+    xmlName = "VAMSAS";
+
+    //-- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.xml.XMLFieldHandler 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);
         }
-        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 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
+        catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
         }
-        desc.setValidator(fieldValidator);
-    } //-- jalview.schemabinding.version2.VAMSASDescriptor()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method getAccessMode
-     * 
-     * 
-     * 
-     * @return AccessMode
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode()
-    {
-        return null;
-    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
-
-    /**
-     * Method getExtends
-     * 
-     * 
-     * 
-     * @return ClassDescriptor
-     */
-    public org.exolab.castor.mapping.ClassDescriptor getExtends()
-    {
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
         return null;
-    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
-
-    /**
-     * Method getIdentity
-     * 
-     * 
-     * 
-     * @return FieldDescriptor
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
-    {
-        return identity;
-    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
-
-    /**
-     * Method getJavaClass
-     * 
-     * 
-     * 
-     * @return Class
-     */
-    public java.lang.Class getJavaClass()
-    {
-        return jalview.schemabinding.version2.VAMSAS.class;
-    } //-- java.lang.Class getJavaClass() 
-
-    /**
-     * Method getNameSpacePrefix
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpacePrefix()
-    {
-        return nsPrefix;
-    } //-- java.lang.String getNameSpacePrefix() 
-
-    /**
-     * Method getNameSpaceURI
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpaceURI()
-    {
-        return nsURI;
-    } //-- java.lang.String getNameSpaceURI() 
-
-    /**
-     * Method getValidator
-     * 
-     * 
-     * 
-     * @return TypeValidator
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator()
-    {
-        return this;
-    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
-
-    /**
-     * Method getXMLName
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getXMLName()
+      }
+    });
+    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
+      StringValidator typeValidator = new StringValidator();
+      typeValidator.setWhiteSpace("preserve");
+      fieldValidator.setValidator(typeValidator);
+    }
+    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()
     {
-        return xmlName;
-    } //-- java.lang.String getXMLName() 
+      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 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
+    }
+    desc.setValidator(fieldValidator);
+  } //-- jalview.schemabinding.version2.VAMSASDescriptor()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Method getAccessMode
+   *
+   *
+   *
+   * @return AccessMode
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
+
+  /**
+   * Method getExtends
+   *
+   *
+   *
+   * @return ClassDescriptor
+   */
+  public org.exolab.castor.mapping.ClassDescriptor getExtends()
+  {
+    return null;
+  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
+
+  /**
+   * Method getIdentity
+   *
+   *
+   *
+   * @return FieldDescriptor
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return identity;
+  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
+
+  /**
+   * Method getJavaClass
+   *
+   *
+   *
+   * @return Class
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.VAMSAS.class;
+  } //-- java.lang.Class getJavaClass()
+
+  /**
+   * Method getNameSpacePrefix
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return nsPrefix;
+  } //-- java.lang.String getNameSpacePrefix()
+
+  /**
+   * Method getNameSpaceURI
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return nsURI;
+  } //-- java.lang.String getNameSpaceURI()
+
+  /**
+   * Method getValidator
+   *
+   *
+   *
+   * @return TypeValidator
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  } //-- org.exolab.castor.xml.TypeValidator getValidator()
+
+  /**
+   * Method getXMLName
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getXMLName()
+  {
+    return xmlName;
+  } //-- java.lang.String getXMLName()
 
 }
diff --git a/src/jalview/schemabinding/version2/VamsasModel.java b/src/jalview/schemabinding/version2/VamsasModel.java
index 4617903..abd267f 100755
--- a/src/jalview/schemabinding/version2/VamsasModel.java
+++ b/src/jalview/schemabinding/version2/VamsasModel.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,112 +7,110 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
+import org.exolab.castor.xml.*;
 
 /**
  * Class VamsasModel.
- * 
+ *
  * @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();
+  } //-- jalview.schemabinding.version2.VamsasModel()
 
-    public VamsasModel() {
-        super();
-    } //-- jalview.schemabinding.version2.VamsasModel()
+  //-----------/
+  //- Methods -/
+  //-----------/
 
+  /**
+   * Method isValid
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    }
+    catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  } //-- boolean isValid()
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param out
+   */
+  public void marshal(java.io.Writer out)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
 
-    /**
-     * Method isValid
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean isValid()
-    {
-        try {
-            validate();
-        }
-        catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    } //-- boolean isValid() 
+    Marshaller.marshal(this, out);
+  } //-- void marshal(java.io.Writer)
 
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param out
-     */
-    public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, out);
-    } //-- void marshal(java.io.Writer) 
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param handler
+   */
+  public void marshal(org.xml.sax.ContentHandler handler)
+      throws java.io.IOException, org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
 
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param handler
-     */
-    public void marshal(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, handler);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
+    Marshaller.marshal(this, handler);
+  } //-- void marshal(org.xml.sax.ContentHandler)
 
-    /**
-     * Method unmarshal
-     * 
-     * 
-     * 
-     * @param reader
-     * @return Object
-     */
-    public static java.lang.Object unmarshal(java.io.Reader reader)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        return (jalview.schemabinding.version2.VamsasModel) Unmarshaller.unmarshal(jalview.schemabinding.version2.VamsasModel.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
+  /**
+   * Method unmarshal
+   *
+   *
+   *
+   * @param reader
+   * @return Object
+   */
+  public static java.lang.Object unmarshal(java.io.Reader reader)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.VamsasModel) Unmarshaller.unmarshal(
+        jalview.schemabinding.version2.VamsasModel.class, reader);
+  } //-- java.lang.Object unmarshal(java.io.Reader)
 
-    /**
-     * Method validate
-     * 
-     */
-    public void validate()
-        throws org.exolab.castor.xml.ValidationException
-    {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    } //-- void validate() 
+  /**
+   * Method validate
+   *
+   */
+  public void validate()
+      throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.
+        Validator();
+    validator.validate(this);
+  } //-- void validate()
 
 }
diff --git a/src/jalview/schemabinding/version2/VamsasModelDescriptor.java b/src/jalview/schemabinding/version2/VamsasModelDescriptor.java
index e40d9c8..95adf50 100755
--- a/src/jalview/schemabinding/version2/VamsasModelDescriptor.java
+++ b/src/jalview/schemabinding/version2/VamsasModelDescriptor.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,160 +7,159 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
 //---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
 
-import org.exolab.castor.mapping.AccessMode;
-import org.exolab.castor.xml.TypeValidator;
-import org.exolab.castor.xml.XMLFieldDescriptor;
-import org.exolab.castor.xml.validators.*;
 
 /**
  * Class VamsasModelDescriptor.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class VamsasModelDescriptor extends VAMSASDescriptor {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field nsPrefix
-     */
-    private java.lang.String nsPrefix;
-
-    /**
-     * Field nsURI
-     */
-    private java.lang.String nsURI;
-
-    /**
-     * Field xmlName
-     */
-    private java.lang.String xmlName;
-
-    /**
-     * Field identity
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor identity;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public VamsasModelDescriptor() {
-        super();
-        setExtendsWithoutFlatten(new VAMSASDescriptor());
-        nsURI = "www.jalview.org";
-        xmlName = "vamsasModel";
-    } //-- jalview.schemabinding.version2.VamsasModelDescriptor()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method getAccessMode
-     * 
-     * 
-     * 
-     * @return AccessMode
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode()
-    {
-        return null;
-    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
-
-    /**
-     * Method getExtends
-     * 
-     * 
-     * 
-     * @return ClassDescriptor
-     */
-    public org.exolab.castor.mapping.ClassDescriptor getExtends()
-    {
-        return super.getExtends();
-    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
-
-    /**
-     * Method getIdentity
-     * 
-     * 
-     * 
-     * @return FieldDescriptor
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
-    {
-        if (identity == null)
-            return super.getIdentity();
-        return identity;
-    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
-
-    /**
-     * Method getJavaClass
-     * 
-     * 
-     * 
-     * @return Class
-     */
-    public java.lang.Class getJavaClass()
-    {
-        return jalview.schemabinding.version2.VamsasModel.class;
-    } //-- java.lang.Class getJavaClass() 
-
-    /**
-     * Method getNameSpacePrefix
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpacePrefix()
-    {
-        return nsPrefix;
-    } //-- java.lang.String getNameSpacePrefix() 
-
-    /**
-     * Method getNameSpaceURI
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpaceURI()
-    {
-        return nsURI;
-    } //-- java.lang.String getNameSpaceURI() 
-
-    /**
-     * Method getValidator
-     * 
-     * 
-     * 
-     * @return TypeValidator
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator()
-    {
-        return this;
-    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
-
-    /**
-     * Method getXMLName
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getXMLName()
+public class VamsasModelDescriptor
+    extends VAMSASDescriptor
+{
+
+  //--------------------------/
+  //- Class/Member Variables -/
+  //--------------------------/
+
+  /**
+   * Field nsPrefix
+   */
+  private java.lang.String nsPrefix;
+
+  /**
+   * Field nsURI
+   */
+  private java.lang.String nsURI;
+
+  /**
+   * Field xmlName
+   */
+  private java.lang.String xmlName;
+
+  /**
+   * Field identity
+   */
+  private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+  //----------------/
+  //- Constructors -/
+  //----------------/
+
+  public VamsasModelDescriptor()
+  {
+    super();
+    setExtendsWithoutFlatten(new VAMSASDescriptor());
+    nsURI = "www.jalview.org";
+    xmlName = "vamsasModel";
+  } //-- jalview.schemabinding.version2.VamsasModelDescriptor()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Method getAccessMode
+   *
+   *
+   *
+   * @return AccessMode
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
+
+  /**
+   * Method getExtends
+   *
+   *
+   *
+   * @return ClassDescriptor
+   */
+  public org.exolab.castor.mapping.ClassDescriptor getExtends()
+  {
+    return super.getExtends();
+  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
+
+  /**
+   * Method getIdentity
+   *
+   *
+   *
+   * @return FieldDescriptor
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    if (identity == null)
     {
-        return xmlName;
-    } //-- java.lang.String getXMLName() 
+      return super.getIdentity();
+    }
+    return identity;
+  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
+
+  /**
+   * Method getJavaClass
+   *
+   *
+   *
+   * @return Class
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.VamsasModel.class;
+  } //-- java.lang.Class getJavaClass()
+
+  /**
+   * Method getNameSpacePrefix
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return nsPrefix;
+  } //-- java.lang.String getNameSpacePrefix()
+
+  /**
+   * Method getNameSpaceURI
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return nsURI;
+  } //-- java.lang.String getNameSpaceURI()
+
+  /**
+   * Method getValidator
+   *
+   *
+   *
+   * @return TypeValidator
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  } //-- org.exolab.castor.xml.TypeValidator getValidator()
+
+  /**
+   * Method getXMLName
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getXMLName()
+  {
+    return xmlName;
+  } //-- java.lang.String getXMLName()
 
 }
diff --git a/src/jalview/schemabinding/version2/Viewport.java b/src/jalview/schemabinding/version2/Viewport.java
index 6dfb14f..978ab5c 100755
--- a/src/jalview/schemabinding/version2/Viewport.java
+++ b/src/jalview/schemabinding/version2/Viewport.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,1752 +7,1767 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
 //---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import java.util.*;
 
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import java.util.Enumeration;
-import java.util.Vector;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
+import org.exolab.castor.xml.*;
 
 /**
  * Class Viewport.
- * 
+ *
  * @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();
-        _hiddenColumnsList = new Vector();
-    } //-- jalview.schemabinding.version2.Viewport()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method addHiddenColumns
-     * 
-     * 
-     * 
-     * @param vHiddenColumns
-     */
-    public void addHiddenColumns(jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _hiddenColumnsList.addElement(vHiddenColumns);
-    } //-- void addHiddenColumns(jalview.schemabinding.version2.HiddenColumns) 
-
-    /**
-     * Method addHiddenColumns
-     * 
-     * 
-     * 
-     * @param index
-     * @param vHiddenColumns
-     */
-    public void addHiddenColumns(int index, jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _hiddenColumnsList.insertElementAt(vHiddenColumns, index);
-    } //-- void addHiddenColumns(int, jalview.schemabinding.version2.HiddenColumns) 
-
-    /**
-     * Method deleteConsThreshold
-     * 
-     */
-    public void deleteConsThreshold()
-    {
-        this._has_consThreshold= false;
-    } //-- void deleteConsThreshold() 
-
-    /**
-     * Method deleteConservationSelected
-     * 
-     */
-    public void deleteConservationSelected()
-    {
-        this._has_conservationSelected= false;
-    } //-- void deleteConservationSelected() 
-
-    /**
-     * Method deleteFontSize
-     * 
-     */
-    public void deleteFontSize()
-    {
-        this._has_fontSize= false;
-    } //-- void deleteFontSize() 
-
-    /**
-     * Method deleteFontStyle
-     * 
-     */
-    public void deleteFontStyle()
-    {
-        this._has_fontStyle= false;
-    } //-- void deleteFontStyle() 
-
-    /**
-     * Method deleteGatheredViews
-     * 
-     */
-    public void deleteGatheredViews()
-    {
-        this._has_gatheredViews= false;
-    } //-- void deleteGatheredViews() 
-
-    /**
-     * Method deleteHeight
-     * 
-     */
-    public void deleteHeight()
-    {
-        this._has_height= false;
-    } //-- void deleteHeight() 
-
-    /**
-     * Method deletePidSelected
-     * 
-     */
-    public void deletePidSelected()
-    {
-        this._has_pidSelected= false;
-    } //-- void deletePidSelected() 
-
-    /**
-     * Method deletePidThreshold
-     * 
-     */
-    public void deletePidThreshold()
-    {
-        this._has_pidThreshold= false;
-    } //-- void deletePidThreshold() 
-
-    /**
-     * Method deleteRenderGaps
-     * 
-     */
-    public void deleteRenderGaps()
-    {
-        this._has_renderGaps= false;
-    } //-- void deleteRenderGaps() 
-
-    /**
-     * Method deleteRightAlignIds
-     * 
-     */
-    public void deleteRightAlignIds()
-    {
-        this._has_rightAlignIds= false;
-    } //-- void deleteRightAlignIds() 
-
-    /**
-     * Method deleteShowAnnotation
-     * 
-     */
-    public void deleteShowAnnotation()
-    {
-        this._has_showAnnotation= false;
-    } //-- void deleteShowAnnotation() 
-
-    /**
-     * Method deleteShowBoxes
-     * 
-     */
-    public void deleteShowBoxes()
-    {
-        this._has_showBoxes= false;
-    } //-- void deleteShowBoxes() 
-
-    /**
-     * Method deleteShowColourText
-     * 
-     */
-    public void deleteShowColourText()
-    {
-        this._has_showColourText= false;
-    } //-- void deleteShowColourText() 
-
-    /**
-     * Method deleteShowFullId
-     * 
-     */
-    public void deleteShowFullId()
-    {
-        this._has_showFullId= false;
-    } //-- void deleteShowFullId() 
-
-    /**
-     * Method deleteShowSequenceFeatures
-     * 
-     */
-    public void deleteShowSequenceFeatures()
-    {
-        this._has_showSequenceFeatures= false;
-    } //-- void deleteShowSequenceFeatures() 
-
-    /**
-     * Method deleteShowText
-     * 
-     */
-    public void deleteShowText()
-    {
-        this._has_showText= false;
-    } //-- void deleteShowText() 
-
-    /**
-     * Method deleteStartRes
-     * 
-     */
-    public void deleteStartRes()
-    {
-        this._has_startRes= false;
-    } //-- void deleteStartRes() 
-
-    /**
-     * Method deleteStartSeq
-     * 
-     */
-    public void deleteStartSeq()
-    {
-        this._has_startSeq= false;
-    } //-- void deleteStartSeq() 
-
-    /**
-     * Method deleteTextCol1
-     * 
-     */
-    public void deleteTextCol1()
-    {
-        this._has_textCol1= false;
-    } //-- void deleteTextCol1() 
-
-    /**
-     * Method deleteTextCol2
-     * 
-     */
-    public void deleteTextCol2()
-    {
-        this._has_textCol2= false;
-    } //-- void deleteTextCol2() 
-
-    /**
-     * Method deleteTextColThreshold
-     * 
-     */
-    public void deleteTextColThreshold()
-    {
-        this._has_textColThreshold= false;
-    } //-- void deleteTextColThreshold() 
-
-    /**
-     * Method deleteWidth
-     * 
-     */
-    public void deleteWidth()
-    {
-        this._has_width= false;
-    } //-- void deleteWidth() 
-
-    /**
-     * Method deleteWrapAlignment
-     * 
-     */
-    public void deleteWrapAlignment()
-    {
-        this._has_wrapAlignment= false;
-    } //-- void deleteWrapAlignment() 
-
-    /**
-     * Method deleteXpos
-     * 
-     */
-    public void deleteXpos()
-    {
-        this._has_xpos= false;
-    } //-- void deleteXpos() 
-
-    /**
-     * Method deleteYpos
-     * 
-     */
-    public void deleteYpos()
-    {
-        this._has_ypos= false;
-    } //-- void deleteYpos() 
-
-    /**
-     * Method enumerateHiddenColumns
-     * 
-     * 
-     * 
-     * @return Enumeration
-     */
-    public java.util.Enumeration enumerateHiddenColumns()
-    {
-        return _hiddenColumnsList.elements();
-    } //-- java.util.Enumeration enumerateHiddenColumns() 
-
-    /**
-     * Returns the value of field 'annotationColours'.
-     * 
-     * @return AnnotationColours
-     * @return the value of field 'annotationColours'.
-     */
-    public jalview.schemabinding.version2.AnnotationColours getAnnotationColours()
-    {
-        return this._annotationColours;
-    } //-- jalview.schemabinding.version2.AnnotationColours getAnnotationColours() 
-
-    /**
-     * Returns the value of field 'bgColour'.
-     * 
-     * @return String
-     * @return the value of field 'bgColour'.
-     */
-    public java.lang.String getBgColour()
-    {
-        return this._bgColour;
-    } //-- java.lang.String getBgColour() 
-
-    /**
-     * Returns the value of field 'consThreshold'.
-     * 
-     * @return int
-     * @return the value of field 'consThreshold'.
-     */
-    public int getConsThreshold()
-    {
-        return this._consThreshold;
-    } //-- int getConsThreshold() 
-
-    /**
-     * Returns the value of field 'conservationSelected'.
-     * 
-     * @return boolean
-     * @return the value of field 'conservationSelected'.
-     */
-    public boolean getConservationSelected()
-    {
-        return this._conservationSelected;
-    } //-- boolean getConservationSelected() 
-
-    /**
-     * Returns the value of field 'fontName'.
-     * 
-     * @return String
-     * @return the value of field 'fontName'.
-     */
-    public java.lang.String getFontName()
-    {
-        return this._fontName;
-    } //-- java.lang.String getFontName() 
-
-    /**
-     * Returns the value of field 'fontSize'.
-     * 
-     * @return int
-     * @return the value of field 'fontSize'.
-     */
-    public int getFontSize()
-    {
-        return this._fontSize;
-    } //-- int getFontSize() 
-
-    /**
-     * Returns the value of field 'fontStyle'.
-     * 
-     * @return int
-     * @return the value of field 'fontStyle'.
-     */
-    public int getFontStyle()
-    {
-        return this._fontStyle;
-    } //-- int getFontStyle() 
-
-    /**
-     * Returns the value of field 'gatheredViews'.
-     * 
-     * @return boolean
-     * @return the value of field 'gatheredViews'.
-     */
-    public boolean getGatheredViews()
-    {
-        return this._gatheredViews;
-    } //-- boolean getGatheredViews() 
-
-    /**
-     * Returns the value of field 'height'.
-     * 
-     * @return int
-     * @return the value of field 'height'.
-     */
-    public int getHeight()
-    {
-        return this._height;
-    } //-- int getHeight() 
-
-    /**
-     * Method getHiddenColumns
-     * 
-     * 
-     * 
-     * @param index
-     * @return HiddenColumns
-     */
-    public jalview.schemabinding.version2.HiddenColumns getHiddenColumns(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _hiddenColumnsList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        
-        return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList.elementAt(index);
-    } //-- jalview.schemabinding.version2.HiddenColumns getHiddenColumns(int) 
-
-    /**
-     * Method getHiddenColumns
-     * 
-     * 
-     * 
-     * @return HiddenColumns
-     */
-    public jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns()
-    {
-        int size = _hiddenColumnsList.size();
-        jalview.schemabinding.version2.HiddenColumns[] mArray = new jalview.schemabinding.version2.HiddenColumns[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList.elementAt(index);
-        }
-        return mArray;
-    } //-- jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns() 
-
-    /**
-     * Method getHiddenColumnsCount
-     * 
-     * 
-     * 
-     * @return int
-     */
-    public int getHiddenColumnsCount()
-    {
-        return _hiddenColumnsList.size();
-    } //-- int getHiddenColumnsCount() 
-
-    /**
-     * Returns the value of field 'pidSelected'.
-     * 
-     * @return boolean
-     * @return the value of field 'pidSelected'.
-     */
-    public boolean getPidSelected()
-    {
-        return this._pidSelected;
-    } //-- boolean getPidSelected() 
-
-    /**
-     * Returns the value of field 'pidThreshold'.
-     * 
-     * @return int
-     * @return the value of field 'pidThreshold'.
-     */
-    public int getPidThreshold()
-    {
-        return this._pidThreshold;
-    } //-- int getPidThreshold() 
-
-    /**
-     * Returns the value of field 'renderGaps'.
-     * 
-     * @return boolean
-     * @return the value of field 'renderGaps'.
-     */
-    public boolean getRenderGaps()
-    {
-        return this._renderGaps;
-    } //-- boolean getRenderGaps() 
-
-    /**
-     * Returns the value of field 'rightAlignIds'.
-     * 
-     * @return boolean
-     * @return the value of field 'rightAlignIds'.
-     */
-    public boolean getRightAlignIds()
-    {
-        return this._rightAlignIds;
-    } //-- boolean getRightAlignIds() 
-
-    /**
-     * Returns the value of field 'sequenceSetId'.
-     * 
-     * @return String
-     * @return the value of field 'sequenceSetId'.
-     */
-    public java.lang.String getSequenceSetId()
-    {
-        return this._sequenceSetId;
-    } //-- java.lang.String getSequenceSetId() 
-
-    /**
-     * Returns the value of field 'showAnnotation'.
-     * 
-     * @return boolean
-     * @return the value of field 'showAnnotation'.
-     */
-    public boolean getShowAnnotation()
-    {
-        return this._showAnnotation;
-    } //-- boolean getShowAnnotation() 
-
-    /**
-     * Returns the value of field 'showBoxes'.
-     * 
-     * @return boolean
-     * @return the value of field 'showBoxes'.
-     */
-    public boolean getShowBoxes()
-    {
-        return this._showBoxes;
-    } //-- boolean getShowBoxes() 
-
-    /**
-     * Returns the value of field 'showColourText'.
-     * 
-     * @return boolean
-     * @return the value of field 'showColourText'.
-     */
-    public boolean getShowColourText()
-    {
-        return this._showColourText;
-    } //-- boolean getShowColourText() 
-
-    /**
-     * Returns the value of field 'showFullId'.
-     * 
-     * @return boolean
-     * @return the value of field 'showFullId'.
-     */
-    public boolean getShowFullId()
-    {
-        return this._showFullId;
-    } //-- boolean getShowFullId() 
-
-    /**
-     * Returns the value of field 'showSequenceFeatures'.
-     * 
-     * @return boolean
-     * @return the value of field 'showSequenceFeatures'.
-     */
-    public boolean getShowSequenceFeatures()
-    {
-        return this._showSequenceFeatures;
-    } //-- boolean getShowSequenceFeatures() 
-
-    /**
-     * Returns the value of field 'showText'.
-     * 
-     * @return boolean
-     * @return the value of field 'showText'.
-     */
-    public boolean getShowText()
-    {
-        return this._showText;
-    } //-- boolean getShowText() 
-
-    /**
-     * Returns the value of field 'startRes'.
-     * 
-     * @return int
-     * @return the value of field 'startRes'.
-     */
-    public int getStartRes()
-    {
-        return this._startRes;
-    } //-- int getStartRes() 
-
-    /**
-     * Returns the value of field 'startSeq'.
-     * 
-     * @return int
-     * @return the value of field 'startSeq'.
-     */
-    public int getStartSeq()
-    {
-        return this._startSeq;
-    } //-- int getStartSeq() 
-
-    /**
-     * Returns the value of field 'textCol1'.
-     * 
-     * @return int
-     * @return the value of field 'textCol1'.
-     */
-    public int getTextCol1()
-    {
-        return this._textCol1;
-    } //-- int getTextCol1() 
-
-    /**
-     * Returns the value of field 'textCol2'.
-     * 
-     * @return int
-     * @return the value of field 'textCol2'.
-     */
-    public int getTextCol2()
-    {
-        return this._textCol2;
-    } //-- int getTextCol2() 
-
-    /**
-     * Returns the value of field 'textColThreshold'.
-     * 
-     * @return int
-     * @return the value of field 'textColThreshold'.
-     */
-    public int getTextColThreshold()
-    {
-        return this._textColThreshold;
-    } //-- int getTextColThreshold() 
-
-    /**
-     * Returns the value of field 'title'.
-     * 
-     * @return String
-     * @return the value of field 'title'.
-     */
-    public java.lang.String getTitle()
-    {
-        return this._title;
-    } //-- java.lang.String getTitle() 
-
-    /**
-     * Returns the value of field 'viewName'.
-     * 
-     * @return String
-     * @return the value of field 'viewName'.
-     */
-    public java.lang.String getViewName()
-    {
-        return this._viewName;
-    } //-- java.lang.String getViewName() 
-
-    /**
-     * Returns the value of field 'width'.
-     * 
-     * @return int
-     * @return the value of field 'width'.
-     */
-    public int getWidth()
-    {
-        return this._width;
-    } //-- int getWidth() 
-
-    /**
-     * Returns the value of field 'wrapAlignment'.
-     * 
-     * @return boolean
-     * @return the value of field 'wrapAlignment'.
-     */
-    public boolean getWrapAlignment()
-    {
-        return this._wrapAlignment;
-    } //-- boolean getWrapAlignment() 
-
-    /**
-     * Returns the value of field 'xpos'.
-     * 
-     * @return int
-     * @return the value of field 'xpos'.
-     */
-    public int getXpos()
-    {
-        return this._xpos;
-    } //-- int getXpos() 
-
-    /**
-     * Returns the value of field 'ypos'.
-     * 
-     * @return int
-     * @return the value of field 'ypos'.
-     */
-    public int getYpos()
-    {
-        return this._ypos;
-    } //-- int getYpos() 
-
-    /**
-     * Method hasConsThreshold
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasConsThreshold()
-    {
-        return this._has_consThreshold;
-    } //-- boolean hasConsThreshold() 
-
-    /**
-     * Method hasConservationSelected
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasConservationSelected()
-    {
-        return this._has_conservationSelected;
-    } //-- boolean hasConservationSelected() 
-
-    /**
-     * Method hasFontSize
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasFontSize()
-    {
-        return this._has_fontSize;
-    } //-- boolean hasFontSize() 
-
-    /**
-     * Method hasFontStyle
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasFontStyle()
-    {
-        return this._has_fontStyle;
-    } //-- boolean hasFontStyle() 
-
-    /**
-     * Method hasGatheredViews
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasGatheredViews()
-    {
-        return this._has_gatheredViews;
-    } //-- boolean hasGatheredViews() 
-
-    /**
-     * Method hasHeight
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasHeight()
-    {
-        return this._has_height;
-    } //-- boolean hasHeight() 
-
-    /**
-     * Method hasPidSelected
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasPidSelected()
-    {
-        return this._has_pidSelected;
-    } //-- boolean hasPidSelected() 
-
-    /**
-     * Method hasPidThreshold
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasPidThreshold()
-    {
-        return this._has_pidThreshold;
-    } //-- boolean hasPidThreshold() 
-
-    /**
-     * Method hasRenderGaps
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasRenderGaps()
-    {
-        return this._has_renderGaps;
-    } //-- boolean hasRenderGaps() 
-
-    /**
-     * Method hasRightAlignIds
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasRightAlignIds()
-    {
-        return this._has_rightAlignIds;
-    } //-- boolean hasRightAlignIds() 
-
-    /**
-     * Method hasShowAnnotation
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasShowAnnotation()
-    {
-        return this._has_showAnnotation;
-    } //-- boolean hasShowAnnotation() 
-
-    /**
-     * Method hasShowBoxes
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasShowBoxes()
-    {
-        return this._has_showBoxes;
-    } //-- boolean hasShowBoxes() 
-
-    /**
-     * Method hasShowColourText
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasShowColourText()
-    {
-        return this._has_showColourText;
-    } //-- boolean hasShowColourText() 
-
-    /**
-     * Method hasShowFullId
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasShowFullId()
-    {
-        return this._has_showFullId;
-    } //-- boolean hasShowFullId() 
-
-    /**
-     * Method hasShowSequenceFeatures
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasShowSequenceFeatures()
-    {
-        return this._has_showSequenceFeatures;
-    } //-- boolean hasShowSequenceFeatures() 
-
-    /**
-     * Method hasShowText
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasShowText()
-    {
-        return this._has_showText;
-    } //-- boolean hasShowText() 
-
-    /**
-     * Method hasStartRes
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasStartRes()
-    {
-        return this._has_startRes;
-    } //-- boolean hasStartRes() 
-
-    /**
-     * Method hasStartSeq
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasStartSeq()
-    {
-        return this._has_startSeq;
-    } //-- boolean hasStartSeq() 
-
-    /**
-     * Method hasTextCol1
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasTextCol1()
-    {
-        return this._has_textCol1;
-    } //-- boolean hasTextCol1() 
-
-    /**
-     * Method hasTextCol2
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasTextCol2()
-    {
-        return this._has_textCol2;
-    } //-- boolean hasTextCol2() 
-
-    /**
-     * Method hasTextColThreshold
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasTextColThreshold()
-    {
-        return this._has_textColThreshold;
-    } //-- boolean hasTextColThreshold() 
-
-    /**
-     * Method hasWidth
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasWidth()
-    {
-        return this._has_width;
-    } //-- boolean hasWidth() 
-
-    /**
-     * Method hasWrapAlignment
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasWrapAlignment()
-    {
-        return this._has_wrapAlignment;
-    } //-- boolean hasWrapAlignment() 
-
-    /**
-     * Method hasXpos
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasXpos()
-    {
-        return this._has_xpos;
-    } //-- boolean hasXpos() 
-
-    /**
-     * Method hasYpos
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasYpos()
-    {
-        return this._has_ypos;
-    } //-- boolean hasYpos() 
-
-    /**
-     * Method isValid
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean isValid()
-    {
-        try {
-            validate();
-        }
-        catch (org.exolab.castor.xml.ValidationException vex) {
-            return false;
-        }
-        return true;
-    } //-- boolean isValid() 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param out
-     */
-    public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, out);
-    } //-- void marshal(java.io.Writer) 
-
-    /**
-     * Method marshal
-     * 
-     * 
-     * 
-     * @param handler
-     */
-    public void marshal(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        
-        Marshaller.marshal(this, handler);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
-
-    /**
-     * Method removeAllHiddenColumns
-     * 
-     */
-    public void removeAllHiddenColumns()
-    {
-        _hiddenColumnsList.removeAllElements();
-    } //-- void removeAllHiddenColumns() 
-
-    /**
-     * Method removeHiddenColumns
-     * 
-     * 
-     * 
-     * @param index
-     * @return HiddenColumns
-     */
-    public jalview.schemabinding.version2.HiddenColumns removeHiddenColumns(int index)
-    {
-        java.lang.Object obj = _hiddenColumnsList.elementAt(index);
-        _hiddenColumnsList.removeElementAt(index);
-        return (jalview.schemabinding.version2.HiddenColumns) obj;
-    } //-- jalview.schemabinding.version2.HiddenColumns removeHiddenColumns(int) 
-
-    /**
-     * Sets the value of field 'annotationColours'.
-     * 
-     * @param annotationColours the value of field
-     * 'annotationColours'.
-     */
-    public void setAnnotationColours(jalview.schemabinding.version2.AnnotationColours annotationColours)
-    {
-        this._annotationColours = annotationColours;
-    } //-- void setAnnotationColours(jalview.schemabinding.version2.AnnotationColours) 
-
-    /**
-     * Sets the value of field 'bgColour'.
-     * 
-     * @param bgColour the value of field 'bgColour'.
-     */
-    public void setBgColour(java.lang.String bgColour)
-    {
-        this._bgColour = bgColour;
-    } //-- void setBgColour(java.lang.String) 
-
-    /**
-     * Sets the value of field 'consThreshold'.
-     * 
-     * @param consThreshold the value of field 'consThreshold'.
-     */
-    public void setConsThreshold(int consThreshold)
-    {
-        this._consThreshold = consThreshold;
-        this._has_consThreshold = true;
-    } //-- void setConsThreshold(int) 
-
-    /**
-     * Sets the value of field 'conservationSelected'.
-     * 
-     * @param conservationSelected the value of field
-     * 'conservationSelected'.
-     */
-    public void setConservationSelected(boolean conservationSelected)
-    {
-        this._conservationSelected = conservationSelected;
-        this._has_conservationSelected = true;
-    } //-- void setConservationSelected(boolean) 
-
-    /**
-     * Sets the value of field 'fontName'.
-     * 
-     * @param fontName the value of field 'fontName'.
-     */
-    public void setFontName(java.lang.String fontName)
-    {
-        this._fontName = fontName;
-    } //-- void setFontName(java.lang.String) 
-
-    /**
-     * Sets the value of field 'fontSize'.
-     * 
-     * @param fontSize the value of field 'fontSize'.
-     */
-    public void setFontSize(int fontSize)
-    {
-        this._fontSize = fontSize;
-        this._has_fontSize = true;
-    } //-- void setFontSize(int) 
-
-    /**
-     * Sets the value of field 'fontStyle'.
-     * 
-     * @param fontStyle the value of field 'fontStyle'.
-     */
-    public void setFontStyle(int fontStyle)
-    {
-        this._fontStyle = fontStyle;
-        this._has_fontStyle = true;
-    } //-- void setFontStyle(int) 
-
-    /**
-     * Sets the value of field 'gatheredViews'.
-     * 
-     * @param gatheredViews the value of field 'gatheredViews'.
-     */
-    public void setGatheredViews(boolean gatheredViews)
-    {
-        this._gatheredViews = gatheredViews;
-        this._has_gatheredViews = true;
-    } //-- void setGatheredViews(boolean) 
-
-    /**
-     * Sets the value of field 'height'.
-     * 
-     * @param height the value of field 'height'.
-     */
-    public void setHeight(int height)
-    {
-        this._height = height;
-        this._has_height = true;
-    } //-- void setHeight(int) 
-
-    /**
-     * Method setHiddenColumns
-     * 
-     * 
-     * 
-     * @param index
-     * @param vHiddenColumns
-     */
-    public void setHiddenColumns(int index, jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _hiddenColumnsList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        _hiddenColumnsList.setElementAt(vHiddenColumns, index);
-    } //-- void setHiddenColumns(int, jalview.schemabinding.version2.HiddenColumns) 
-
-    /**
-     * Method setHiddenColumns
-     * 
-     * 
-     * 
-     * @param hiddenColumnsArray
-     */
-    public void setHiddenColumns(jalview.schemabinding.version2.HiddenColumns[] hiddenColumnsArray)
-    {
-        //-- copy array
-        _hiddenColumnsList.removeAllElements();
-        for (int i = 0; i < hiddenColumnsArray.length; i++) {
-            _hiddenColumnsList.addElement(hiddenColumnsArray[i]);
-        }
-    } //-- void setHiddenColumns(jalview.schemabinding.version2.HiddenColumns) 
-
-    /**
-     * Sets the value of field 'pidSelected'.
-     * 
-     * @param pidSelected the value of field 'pidSelected'.
-     */
-    public void setPidSelected(boolean pidSelected)
-    {
-        this._pidSelected = pidSelected;
-        this._has_pidSelected = true;
-    } //-- void setPidSelected(boolean) 
-
-    /**
-     * Sets the value of field 'pidThreshold'.
-     * 
-     * @param pidThreshold the value of field 'pidThreshold'.
-     */
-    public void setPidThreshold(int pidThreshold)
-    {
-        this._pidThreshold = pidThreshold;
-        this._has_pidThreshold = true;
-    } //-- void setPidThreshold(int) 
-
-    /**
-     * Sets the value of field 'renderGaps'.
-     * 
-     * @param renderGaps the value of field 'renderGaps'.
-     */
-    public void setRenderGaps(boolean renderGaps)
-    {
-        this._renderGaps = renderGaps;
-        this._has_renderGaps = true;
-    } //-- void setRenderGaps(boolean) 
-
-    /**
-     * Sets the value of field 'rightAlignIds'.
-     * 
-     * @param rightAlignIds the value of field 'rightAlignIds'.
-     */
-    public void setRightAlignIds(boolean rightAlignIds)
-    {
-        this._rightAlignIds = rightAlignIds;
-        this._has_rightAlignIds = true;
-    } //-- void setRightAlignIds(boolean) 
-
-    /**
-     * Sets the value of field 'sequenceSetId'.
-     * 
-     * @param sequenceSetId the value of field 'sequenceSetId'.
-     */
-    public void setSequenceSetId(java.lang.String sequenceSetId)
-    {
-        this._sequenceSetId = sequenceSetId;
-    } //-- void setSequenceSetId(java.lang.String) 
-
-    /**
-     * Sets the value of field 'showAnnotation'.
-     * 
-     * @param showAnnotation the value of field 'showAnnotation'.
-     */
-    public void setShowAnnotation(boolean showAnnotation)
-    {
-        this._showAnnotation = showAnnotation;
-        this._has_showAnnotation = true;
-    } //-- void setShowAnnotation(boolean) 
-
-    /**
-     * Sets the value of field 'showBoxes'.
-     * 
-     * @param showBoxes the value of field 'showBoxes'.
-     */
-    public void setShowBoxes(boolean showBoxes)
-    {
-        this._showBoxes = showBoxes;
-        this._has_showBoxes = true;
-    } //-- void setShowBoxes(boolean) 
-
-    /**
-     * Sets the value of field 'showColourText'.
-     * 
-     * @param showColourText the value of field 'showColourText'.
-     */
-    public void setShowColourText(boolean showColourText)
-    {
-        this._showColourText = showColourText;
-        this._has_showColourText = true;
-    } //-- void setShowColourText(boolean) 
-
-    /**
-     * Sets the value of field 'showFullId'.
-     * 
-     * @param showFullId the value of field 'showFullId'.
-     */
-    public void setShowFullId(boolean showFullId)
-    {
-        this._showFullId = showFullId;
-        this._has_showFullId = true;
-    } //-- void setShowFullId(boolean) 
-
-    /**
-     * Sets the value of field 'showSequenceFeatures'.
-     * 
-     * @param showSequenceFeatures the value of field
-     * 'showSequenceFeatures'.
-     */
-    public void setShowSequenceFeatures(boolean showSequenceFeatures)
-    {
-        this._showSequenceFeatures = showSequenceFeatures;
-        this._has_showSequenceFeatures = true;
-    } //-- void setShowSequenceFeatures(boolean) 
-
-    /**
-     * Sets the value of field 'showText'.
-     * 
-     * @param showText the value of field 'showText'.
-     */
-    public void setShowText(boolean showText)
-    {
-        this._showText = showText;
-        this._has_showText = true;
-    } //-- void setShowText(boolean) 
-
-    /**
-     * Sets the value of field 'startRes'.
-     * 
-     * @param startRes the value of field 'startRes'.
-     */
-    public void setStartRes(int startRes)
-    {
-        this._startRes = startRes;
-        this._has_startRes = true;
-    } //-- void setStartRes(int) 
-
-    /**
-     * Sets the value of field 'startSeq'.
-     * 
-     * @param startSeq the value of field 'startSeq'.
-     */
-    public void setStartSeq(int startSeq)
-    {
-        this._startSeq = startSeq;
-        this._has_startSeq = true;
-    } //-- void setStartSeq(int) 
-
-    /**
-     * Sets the value of field 'textCol1'.
-     * 
-     * @param textCol1 the value of field 'textCol1'.
-     */
-    public void setTextCol1(int textCol1)
-    {
-        this._textCol1 = textCol1;
-        this._has_textCol1 = true;
-    } //-- void setTextCol1(int) 
-
-    /**
-     * Sets the value of field 'textCol2'.
-     * 
-     * @param textCol2 the value of field 'textCol2'.
-     */
-    public void setTextCol2(int textCol2)
-    {
-        this._textCol2 = textCol2;
-        this._has_textCol2 = true;
-    } //-- void setTextCol2(int) 
-
-    /**
-     * Sets the value of field 'textColThreshold'.
-     * 
-     * @param textColThreshold the value of field 'textColThreshold'
-     */
-    public void setTextColThreshold(int textColThreshold)
-    {
-        this._textColThreshold = textColThreshold;
-        this._has_textColThreshold = true;
-    } //-- void setTextColThreshold(int) 
-
-    /**
-     * Sets the value of field 'title'.
-     * 
-     * @param title the value of field 'title'.
-     */
-    public void setTitle(java.lang.String title)
-    {
-        this._title = title;
-    } //-- void setTitle(java.lang.String) 
-
-    /**
-     * Sets the value of field 'viewName'.
-     * 
-     * @param viewName the value of field 'viewName'.
-     */
-    public void setViewName(java.lang.String viewName)
-    {
-        this._viewName = viewName;
-    } //-- void setViewName(java.lang.String) 
-
-    /**
-     * Sets the value of field 'width'.
-     * 
-     * @param width the value of field 'width'.
-     */
-    public void setWidth(int width)
-    {
-        this._width = width;
-        this._has_width = true;
-    } //-- void setWidth(int) 
-
-    /**
-     * Sets the value of field 'wrapAlignment'.
-     * 
-     * @param wrapAlignment the value of field 'wrapAlignment'.
-     */
-    public void setWrapAlignment(boolean wrapAlignment)
-    {
-        this._wrapAlignment = wrapAlignment;
-        this._has_wrapAlignment = true;
-    } //-- void setWrapAlignment(boolean) 
-
-    /**
-     * Sets the value of field 'xpos'.
-     * 
-     * @param xpos the value of field 'xpos'.
-     */
-    public void setXpos(int xpos)
-    {
-        this._xpos = xpos;
-        this._has_xpos = true;
-    } //-- void setXpos(int) 
-
-    /**
-     * Sets the value of field 'ypos'.
-     * 
-     * @param ypos the value of field 'ypos'.
-     */
-    public void setYpos(int ypos)
-    {
-        this._ypos = ypos;
-        this._has_ypos = true;
-    } //-- void setYpos(int) 
-
-    /**
-     * Method unmarshal
-     * 
-     * 
-     * 
-     * @param reader
-     * @return Object
-     */
-    public static java.lang.Object unmarshal(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);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
-
-    /**
-     * Method validate
-     * 
-     */
-    public void validate()
-        throws org.exolab.castor.xml.ValidationException
-    {
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-        validator.validate(this);
-    } //-- void validate() 
+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();
+    _hiddenColumnsList = new Vector();
+  } //-- jalview.schemabinding.version2.Viewport()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Method addHiddenColumns
+   *
+   *
+   *
+   * @param vHiddenColumns
+   */
+  public void addHiddenColumns(jalview.schemabinding.version2.HiddenColumns
+                               vHiddenColumns)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _hiddenColumnsList.addElement(vHiddenColumns);
+  } //-- void addHiddenColumns(jalview.schemabinding.version2.HiddenColumns)
+
+  /**
+   * Method addHiddenColumns
+   *
+   *
+   *
+   * @param index
+   * @param vHiddenColumns
+   */
+  public void addHiddenColumns(int index,
+                               jalview.schemabinding.version2.HiddenColumns
+                               vHiddenColumns)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    _hiddenColumnsList.insertElementAt(vHiddenColumns, index);
+  } //-- void addHiddenColumns(int, jalview.schemabinding.version2.HiddenColumns)
+
+  /**
+   * Method deleteConsThreshold
+   *
+   */
+  public void deleteConsThreshold()
+  {
+    this._has_consThreshold = false;
+  } //-- void deleteConsThreshold()
+
+  /**
+   * Method deleteConservationSelected
+   *
+   */
+  public void deleteConservationSelected()
+  {
+    this._has_conservationSelected = false;
+  } //-- void deleteConservationSelected()
+
+  /**
+   * Method deleteFontSize
+   *
+   */
+  public void deleteFontSize()
+  {
+    this._has_fontSize = false;
+  } //-- void deleteFontSize()
+
+  /**
+   * Method deleteFontStyle
+   *
+   */
+  public void deleteFontStyle()
+  {
+    this._has_fontStyle = false;
+  } //-- void deleteFontStyle()
+
+  /**
+   * Method deleteGatheredViews
+   *
+   */
+  public void deleteGatheredViews()
+  {
+    this._has_gatheredViews = false;
+  } //-- void deleteGatheredViews()
+
+  /**
+   * Method deleteHeight
+   *
+   */
+  public void deleteHeight()
+  {
+    this._has_height = false;
+  } //-- void deleteHeight()
+
+  /**
+   * Method deletePidSelected
+   *
+   */
+  public void deletePidSelected()
+  {
+    this._has_pidSelected = false;
+  } //-- void deletePidSelected()
+
+  /**
+   * Method deletePidThreshold
+   *
+   */
+  public void deletePidThreshold()
+  {
+    this._has_pidThreshold = false;
+  } //-- void deletePidThreshold()
+
+  /**
+   * Method deleteRenderGaps
+   *
+   */
+  public void deleteRenderGaps()
+  {
+    this._has_renderGaps = false;
+  } //-- void deleteRenderGaps()
+
+  /**
+   * Method deleteRightAlignIds
+   *
+   */
+  public void deleteRightAlignIds()
+  {
+    this._has_rightAlignIds = false;
+  } //-- void deleteRightAlignIds()
+
+  /**
+   * Method deleteShowAnnotation
+   *
+   */
+  public void deleteShowAnnotation()
+  {
+    this._has_showAnnotation = false;
+  } //-- void deleteShowAnnotation()
+
+  /**
+   * Method deleteShowBoxes
+   *
+   */
+  public void deleteShowBoxes()
+  {
+    this._has_showBoxes = false;
+  } //-- void deleteShowBoxes()
+
+  /**
+   * Method deleteShowColourText
+   *
+   */
+  public void deleteShowColourText()
+  {
+    this._has_showColourText = false;
+  } //-- void deleteShowColourText()
+
+  /**
+   * Method deleteShowFullId
+   *
+   */
+  public void deleteShowFullId()
+  {
+    this._has_showFullId = false;
+  } //-- void deleteShowFullId()
+
+  /**
+   * Method deleteShowSequenceFeatures
+   *
+   */
+  public void deleteShowSequenceFeatures()
+  {
+    this._has_showSequenceFeatures = false;
+  } //-- void deleteShowSequenceFeatures()
+
+  /**
+   * Method deleteShowText
+   *
+   */
+  public void deleteShowText()
+  {
+    this._has_showText = false;
+  } //-- void deleteShowText()
+
+  /**
+   * Method deleteStartRes
+   *
+   */
+  public void deleteStartRes()
+  {
+    this._has_startRes = false;
+  } //-- void deleteStartRes()
+
+  /**
+   * Method deleteStartSeq
+   *
+   */
+  public void deleteStartSeq()
+  {
+    this._has_startSeq = false;
+  } //-- void deleteStartSeq()
+
+  /**
+   * Method deleteTextCol1
+   *
+   */
+  public void deleteTextCol1()
+  {
+    this._has_textCol1 = false;
+  } //-- void deleteTextCol1()
+
+  /**
+   * Method deleteTextCol2
+   *
+   */
+  public void deleteTextCol2()
+  {
+    this._has_textCol2 = false;
+  } //-- void deleteTextCol2()
+
+  /**
+   * Method deleteTextColThreshold
+   *
+   */
+  public void deleteTextColThreshold()
+  {
+    this._has_textColThreshold = false;
+  } //-- void deleteTextColThreshold()
+
+  /**
+   * Method deleteWidth
+   *
+   */
+  public void deleteWidth()
+  {
+    this._has_width = false;
+  } //-- void deleteWidth()
+
+  /**
+   * Method deleteWrapAlignment
+   *
+   */
+  public void deleteWrapAlignment()
+  {
+    this._has_wrapAlignment = false;
+  } //-- void deleteWrapAlignment()
+
+  /**
+   * Method deleteXpos
+   *
+   */
+  public void deleteXpos()
+  {
+    this._has_xpos = false;
+  } //-- void deleteXpos()
+
+  /**
+   * Method deleteYpos
+   *
+   */
+  public void deleteYpos()
+  {
+    this._has_ypos = false;
+  } //-- void deleteYpos()
+
+  /**
+   * Method enumerateHiddenColumns
+   *
+   *
+   *
+   * @return Enumeration
+   */
+  public java.util.Enumeration enumerateHiddenColumns()
+  {
+    return _hiddenColumnsList.elements();
+  } //-- java.util.Enumeration enumerateHiddenColumns()
+
+  /**
+   * Returns the value of field 'annotationColours'.
+   *
+   * @return AnnotationColours
+   * @return the value of field 'annotationColours'.
+   */
+  public jalview.schemabinding.version2.AnnotationColours getAnnotationColours()
+  {
+    return this._annotationColours;
+  } //-- jalview.schemabinding.version2.AnnotationColours getAnnotationColours()
+
+  /**
+   * Returns the value of field 'bgColour'.
+   *
+   * @return String
+   * @return the value of field 'bgColour'.
+   */
+  public java.lang.String getBgColour()
+  {
+    return this._bgColour;
+  } //-- java.lang.String getBgColour()
+
+  /**
+   * Returns the value of field 'consThreshold'.
+   *
+   * @return int
+   * @return the value of field 'consThreshold'.
+   */
+  public int getConsThreshold()
+  {
+    return this._consThreshold;
+  } //-- int getConsThreshold()
+
+  /**
+   * Returns the value of field 'conservationSelected'.
+   *
+   * @return boolean
+   * @return the value of field 'conservationSelected'.
+   */
+  public boolean getConservationSelected()
+  {
+    return this._conservationSelected;
+  } //-- boolean getConservationSelected()
+
+  /**
+   * Returns the value of field 'fontName'.
+   *
+   * @return String
+   * @return the value of field 'fontName'.
+   */
+  public java.lang.String getFontName()
+  {
+    return this._fontName;
+  } //-- java.lang.String getFontName()
+
+  /**
+   * Returns the value of field 'fontSize'.
+   *
+   * @return int
+   * @return the value of field 'fontSize'.
+   */
+  public int getFontSize()
+  {
+    return this._fontSize;
+  } //-- int getFontSize()
+
+  /**
+   * Returns the value of field 'fontStyle'.
+   *
+   * @return int
+   * @return the value of field 'fontStyle'.
+   */
+  public int getFontStyle()
+  {
+    return this._fontStyle;
+  } //-- int getFontStyle()
+
+  /**
+   * Returns the value of field 'gatheredViews'.
+   *
+   * @return boolean
+   * @return the value of field 'gatheredViews'.
+   */
+  public boolean getGatheredViews()
+  {
+    return this._gatheredViews;
+  } //-- boolean getGatheredViews()
+
+  /**
+   * Returns the value of field 'height'.
+   *
+   * @return int
+   * @return the value of field 'height'.
+   */
+  public int getHeight()
+  {
+    return this._height;
+  } //-- int getHeight()
+
+  /**
+   * Method getHiddenColumns
+   *
+   *
+   *
+   * @param index
+   * @return HiddenColumns
+   */
+  public jalview.schemabinding.version2.HiddenColumns getHiddenColumns(int
+      index)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _hiddenColumnsList.size()))
+    {
+      throw new IndexOutOfBoundsException();
+    }
+
+    return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList.
+        elementAt(index);
+  } //-- jalview.schemabinding.version2.HiddenColumns getHiddenColumns(int)
+
+  /**
+   * Method getHiddenColumns
+   *
+   *
+   *
+   * @return HiddenColumns
+   */
+  public jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns()
+  {
+    int size = _hiddenColumnsList.size();
+    jalview.schemabinding.version2.HiddenColumns[] mArray = new jalview.
+        schemabinding.version2.HiddenColumns[size];
+    for (int index = 0; index < size; index++)
+    {
+      mArray[index] = (jalview.schemabinding.version2.HiddenColumns)
+          _hiddenColumnsList.elementAt(index);
+    }
+    return mArray;
+  } //-- jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns()
+
+  /**
+   * Method getHiddenColumnsCount
+   *
+   *
+   *
+   * @return int
+   */
+  public int getHiddenColumnsCount()
+  {
+    return _hiddenColumnsList.size();
+  } //-- int getHiddenColumnsCount()
+
+  /**
+   * Returns the value of field 'pidSelected'.
+   *
+   * @return boolean
+   * @return the value of field 'pidSelected'.
+   */
+  public boolean getPidSelected()
+  {
+    return this._pidSelected;
+  } //-- boolean getPidSelected()
+
+  /**
+   * Returns the value of field 'pidThreshold'.
+   *
+   * @return int
+   * @return the value of field 'pidThreshold'.
+   */
+  public int getPidThreshold()
+  {
+    return this._pidThreshold;
+  } //-- int getPidThreshold()
+
+  /**
+   * Returns the value of field 'renderGaps'.
+   *
+   * @return boolean
+   * @return the value of field 'renderGaps'.
+   */
+  public boolean getRenderGaps()
+  {
+    return this._renderGaps;
+  } //-- boolean getRenderGaps()
+
+  /**
+   * Returns the value of field 'rightAlignIds'.
+   *
+   * @return boolean
+   * @return the value of field 'rightAlignIds'.
+   */
+  public boolean getRightAlignIds()
+  {
+    return this._rightAlignIds;
+  } //-- boolean getRightAlignIds()
+
+  /**
+   * Returns the value of field 'sequenceSetId'.
+   *
+   * @return String
+   * @return the value of field 'sequenceSetId'.
+   */
+  public java.lang.String getSequenceSetId()
+  {
+    return this._sequenceSetId;
+  } //-- java.lang.String getSequenceSetId()
+
+  /**
+   * Returns the value of field 'showAnnotation'.
+   *
+   * @return boolean
+   * @return the value of field 'showAnnotation'.
+   */
+  public boolean getShowAnnotation()
+  {
+    return this._showAnnotation;
+  } //-- boolean getShowAnnotation()
+
+  /**
+   * Returns the value of field 'showBoxes'.
+   *
+   * @return boolean
+   * @return the value of field 'showBoxes'.
+   */
+  public boolean getShowBoxes()
+  {
+    return this._showBoxes;
+  } //-- boolean getShowBoxes()
+
+  /**
+   * Returns the value of field 'showColourText'.
+   *
+   * @return boolean
+   * @return the value of field 'showColourText'.
+   */
+  public boolean getShowColourText()
+  {
+    return this._showColourText;
+  } //-- boolean getShowColourText()
+
+  /**
+   * Returns the value of field 'showFullId'.
+   *
+   * @return boolean
+   * @return the value of field 'showFullId'.
+   */
+  public boolean getShowFullId()
+  {
+    return this._showFullId;
+  } //-- boolean getShowFullId()
+
+  /**
+   * Returns the value of field 'showSequenceFeatures'.
+   *
+   * @return boolean
+   * @return the value of field 'showSequenceFeatures'.
+   */
+  public boolean getShowSequenceFeatures()
+  {
+    return this._showSequenceFeatures;
+  } //-- boolean getShowSequenceFeatures()
+
+  /**
+   * Returns the value of field 'showText'.
+   *
+   * @return boolean
+   * @return the value of field 'showText'.
+   */
+  public boolean getShowText()
+  {
+    return this._showText;
+  } //-- boolean getShowText()
+
+  /**
+   * Returns the value of field 'startRes'.
+   *
+   * @return int
+   * @return the value of field 'startRes'.
+   */
+  public int getStartRes()
+  {
+    return this._startRes;
+  } //-- int getStartRes()
+
+  /**
+   * Returns the value of field 'startSeq'.
+   *
+   * @return int
+   * @return the value of field 'startSeq'.
+   */
+  public int getStartSeq()
+  {
+    return this._startSeq;
+  } //-- int getStartSeq()
+
+  /**
+   * Returns the value of field 'textCol1'.
+   *
+   * @return int
+   * @return the value of field 'textCol1'.
+   */
+  public int getTextCol1()
+  {
+    return this._textCol1;
+  } //-- int getTextCol1()
+
+  /**
+   * Returns the value of field 'textCol2'.
+   *
+   * @return int
+   * @return the value of field 'textCol2'.
+   */
+  public int getTextCol2()
+  {
+    return this._textCol2;
+  } //-- int getTextCol2()
+
+  /**
+   * Returns the value of field 'textColThreshold'.
+   *
+   * @return int
+   * @return the value of field 'textColThreshold'.
+   */
+  public int getTextColThreshold()
+  {
+    return this._textColThreshold;
+  } //-- int getTextColThreshold()
+
+  /**
+   * Returns the value of field 'title'.
+   *
+   * @return String
+   * @return the value of field 'title'.
+   */
+  public java.lang.String getTitle()
+  {
+    return this._title;
+  } //-- java.lang.String getTitle()
+
+  /**
+   * Returns the value of field 'viewName'.
+   *
+   * @return String
+   * @return the value of field 'viewName'.
+   */
+  public java.lang.String getViewName()
+  {
+    return this._viewName;
+  } //-- java.lang.String getViewName()
+
+  /**
+   * Returns the value of field 'width'.
+   *
+   * @return int
+   * @return the value of field 'width'.
+   */
+  public int getWidth()
+  {
+    return this._width;
+  } //-- int getWidth()
+
+  /**
+   * Returns the value of field 'wrapAlignment'.
+   *
+   * @return boolean
+   * @return the value of field 'wrapAlignment'.
+   */
+  public boolean getWrapAlignment()
+  {
+    return this._wrapAlignment;
+  } //-- boolean getWrapAlignment()
+
+  /**
+   * Returns the value of field 'xpos'.
+   *
+   * @return int
+   * @return the value of field 'xpos'.
+   */
+  public int getXpos()
+  {
+    return this._xpos;
+  } //-- int getXpos()
+
+  /**
+   * Returns the value of field 'ypos'.
+   *
+   * @return int
+   * @return the value of field 'ypos'.
+   */
+  public int getYpos()
+  {
+    return this._ypos;
+  } //-- int getYpos()
+
+  /**
+   * Method hasConsThreshold
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasConsThreshold()
+  {
+    return this._has_consThreshold;
+  } //-- boolean hasConsThreshold()
+
+  /**
+   * Method hasConservationSelected
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasConservationSelected()
+  {
+    return this._has_conservationSelected;
+  } //-- boolean hasConservationSelected()
+
+  /**
+   * Method hasFontSize
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasFontSize()
+  {
+    return this._has_fontSize;
+  } //-- boolean hasFontSize()
+
+  /**
+   * Method hasFontStyle
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasFontStyle()
+  {
+    return this._has_fontStyle;
+  } //-- boolean hasFontStyle()
+
+  /**
+   * Method hasGatheredViews
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasGatheredViews()
+  {
+    return this._has_gatheredViews;
+  } //-- boolean hasGatheredViews()
+
+  /**
+   * Method hasHeight
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasHeight()
+  {
+    return this._has_height;
+  } //-- boolean hasHeight()
+
+  /**
+   * Method hasPidSelected
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasPidSelected()
+  {
+    return this._has_pidSelected;
+  } //-- boolean hasPidSelected()
+
+  /**
+   * Method hasPidThreshold
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasPidThreshold()
+  {
+    return this._has_pidThreshold;
+  } //-- boolean hasPidThreshold()
+
+  /**
+   * Method hasRenderGaps
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasRenderGaps()
+  {
+    return this._has_renderGaps;
+  } //-- boolean hasRenderGaps()
+
+  /**
+   * Method hasRightAlignIds
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasRightAlignIds()
+  {
+    return this._has_rightAlignIds;
+  } //-- boolean hasRightAlignIds()
+
+  /**
+   * Method hasShowAnnotation
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasShowAnnotation()
+  {
+    return this._has_showAnnotation;
+  } //-- boolean hasShowAnnotation()
+
+  /**
+   * Method hasShowBoxes
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasShowBoxes()
+  {
+    return this._has_showBoxes;
+  } //-- boolean hasShowBoxes()
+
+  /**
+   * Method hasShowColourText
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasShowColourText()
+  {
+    return this._has_showColourText;
+  } //-- boolean hasShowColourText()
+
+  /**
+   * Method hasShowFullId
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasShowFullId()
+  {
+    return this._has_showFullId;
+  } //-- boolean hasShowFullId()
+
+  /**
+   * Method hasShowSequenceFeatures
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasShowSequenceFeatures()
+  {
+    return this._has_showSequenceFeatures;
+  } //-- boolean hasShowSequenceFeatures()
+
+  /**
+   * Method hasShowText
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasShowText()
+  {
+    return this._has_showText;
+  } //-- boolean hasShowText()
+
+  /**
+   * Method hasStartRes
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasStartRes()
+  {
+    return this._has_startRes;
+  } //-- boolean hasStartRes()
+
+  /**
+   * Method hasStartSeq
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasStartSeq()
+  {
+    return this._has_startSeq;
+  } //-- boolean hasStartSeq()
+
+  /**
+   * Method hasTextCol1
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasTextCol1()
+  {
+    return this._has_textCol1;
+  } //-- boolean hasTextCol1()
+
+  /**
+   * Method hasTextCol2
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasTextCol2()
+  {
+    return this._has_textCol2;
+  } //-- boolean hasTextCol2()
+
+  /**
+   * Method hasTextColThreshold
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasTextColThreshold()
+  {
+    return this._has_textColThreshold;
+  } //-- boolean hasTextColThreshold()
+
+  /**
+   * Method hasWidth
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasWidth()
+  {
+    return this._has_width;
+  } //-- boolean hasWidth()
+
+  /**
+   * Method hasWrapAlignment
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasWrapAlignment()
+  {
+    return this._has_wrapAlignment;
+  } //-- boolean hasWrapAlignment()
+
+  /**
+   * Method hasXpos
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasXpos()
+  {
+    return this._has_xpos;
+  } //-- boolean hasXpos()
+
+  /**
+   * Method hasYpos
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean hasYpos()
+  {
+    return this._has_ypos;
+  } //-- boolean hasYpos()
+
+  /**
+   * Method isValid
+   *
+   *
+   *
+   * @return boolean
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    }
+    catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  } //-- boolean isValid()
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param out
+   */
+  public void marshal(java.io.Writer out)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, out);
+  } //-- void marshal(java.io.Writer)
+
+  /**
+   * Method marshal
+   *
+   *
+   *
+   * @param handler
+   */
+  public void marshal(org.xml.sax.ContentHandler handler)
+      throws java.io.IOException, org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException
+  {
+
+    Marshaller.marshal(this, handler);
+  } //-- void marshal(org.xml.sax.ContentHandler)
+
+  /**
+   * Method removeAllHiddenColumns
+   *
+   */
+  public void removeAllHiddenColumns()
+  {
+    _hiddenColumnsList.removeAllElements();
+  } //-- void removeAllHiddenColumns()
+
+  /**
+   * Method removeHiddenColumns
+   *
+   *
+   *
+   * @param index
+   * @return HiddenColumns
+   */
+  public jalview.schemabinding.version2.HiddenColumns removeHiddenColumns(int
+      index)
+  {
+    java.lang.Object obj = _hiddenColumnsList.elementAt(index);
+    _hiddenColumnsList.removeElementAt(index);
+    return (jalview.schemabinding.version2.HiddenColumns) obj;
+  } //-- jalview.schemabinding.version2.HiddenColumns removeHiddenColumns(int)
+
+  /**
+   * Sets the value of field 'annotationColours'.
+   *
+   * @param annotationColours the value of field
+   * 'annotationColours'.
+   */
+  public void setAnnotationColours(jalview.schemabinding.version2.
+                                   AnnotationColours annotationColours)
+  {
+    this._annotationColours = annotationColours;
+  } //-- void setAnnotationColours(jalview.schemabinding.version2.AnnotationColours)
+
+  /**
+   * Sets the value of field 'bgColour'.
+   *
+   * @param bgColour the value of field 'bgColour'.
+   */
+  public void setBgColour(java.lang.String bgColour)
+  {
+    this._bgColour = bgColour;
+  } //-- void setBgColour(java.lang.String)
+
+  /**
+   * Sets the value of field 'consThreshold'.
+   *
+   * @param consThreshold the value of field 'consThreshold'.
+   */
+  public void setConsThreshold(int consThreshold)
+  {
+    this._consThreshold = consThreshold;
+    this._has_consThreshold = true;
+  } //-- void setConsThreshold(int)
+
+  /**
+   * Sets the value of field 'conservationSelected'.
+   *
+   * @param conservationSelected the value of field
+   * 'conservationSelected'.
+   */
+  public void setConservationSelected(boolean conservationSelected)
+  {
+    this._conservationSelected = conservationSelected;
+    this._has_conservationSelected = true;
+  } //-- void setConservationSelected(boolean)
+
+  /**
+   * Sets the value of field 'fontName'.
+   *
+   * @param fontName the value of field 'fontName'.
+   */
+  public void setFontName(java.lang.String fontName)
+  {
+    this._fontName = fontName;
+  } //-- void setFontName(java.lang.String)
+
+  /**
+   * Sets the value of field 'fontSize'.
+   *
+   * @param fontSize the value of field 'fontSize'.
+   */
+  public void setFontSize(int fontSize)
+  {
+    this._fontSize = fontSize;
+    this._has_fontSize = true;
+  } //-- void setFontSize(int)
+
+  /**
+   * Sets the value of field 'fontStyle'.
+   *
+   * @param fontStyle the value of field 'fontStyle'.
+   */
+  public void setFontStyle(int fontStyle)
+  {
+    this._fontStyle = fontStyle;
+    this._has_fontStyle = true;
+  } //-- void setFontStyle(int)
+
+  /**
+   * Sets the value of field 'gatheredViews'.
+   *
+   * @param gatheredViews the value of field 'gatheredViews'.
+   */
+  public void setGatheredViews(boolean gatheredViews)
+  {
+    this._gatheredViews = gatheredViews;
+    this._has_gatheredViews = true;
+  } //-- void setGatheredViews(boolean)
+
+  /**
+   * Sets the value of field 'height'.
+   *
+   * @param height the value of field 'height'.
+   */
+  public void setHeight(int height)
+  {
+    this._height = height;
+    this._has_height = true;
+  } //-- void setHeight(int)
+
+  /**
+   * Method setHiddenColumns
+   *
+   *
+   *
+   * @param index
+   * @param vHiddenColumns
+   */
+  public void setHiddenColumns(int index,
+                               jalview.schemabinding.version2.HiddenColumns
+                               vHiddenColumns)
+      throws java.lang.IndexOutOfBoundsException
+  {
+    //-- check bounds for index
+    if ( (index < 0) || (index > _hiddenColumnsList.size()))
+    {
+      throw new IndexOutOfBoundsException();
+    }
+    _hiddenColumnsList.setElementAt(vHiddenColumns, index);
+  } //-- void setHiddenColumns(int, jalview.schemabinding.version2.HiddenColumns)
+
+  /**
+   * Method setHiddenColumns
+   *
+   *
+   *
+   * @param hiddenColumnsArray
+   */
+  public void setHiddenColumns(jalview.schemabinding.version2.HiddenColumns[]
+                               hiddenColumnsArray)
+  {
+    //-- copy array
+    _hiddenColumnsList.removeAllElements();
+    for (int i = 0; i < hiddenColumnsArray.length; i++)
+    {
+      _hiddenColumnsList.addElement(hiddenColumnsArray[i]);
+    }
+  } //-- void setHiddenColumns(jalview.schemabinding.version2.HiddenColumns)
+
+  /**
+   * Sets the value of field 'pidSelected'.
+   *
+   * @param pidSelected the value of field 'pidSelected'.
+   */
+  public void setPidSelected(boolean pidSelected)
+  {
+    this._pidSelected = pidSelected;
+    this._has_pidSelected = true;
+  } //-- void setPidSelected(boolean)
+
+  /**
+   * Sets the value of field 'pidThreshold'.
+   *
+   * @param pidThreshold the value of field 'pidThreshold'.
+   */
+  public void setPidThreshold(int pidThreshold)
+  {
+    this._pidThreshold = pidThreshold;
+    this._has_pidThreshold = true;
+  } //-- void setPidThreshold(int)
+
+  /**
+   * Sets the value of field 'renderGaps'.
+   *
+   * @param renderGaps the value of field 'renderGaps'.
+   */
+  public void setRenderGaps(boolean renderGaps)
+  {
+    this._renderGaps = renderGaps;
+    this._has_renderGaps = true;
+  } //-- void setRenderGaps(boolean)
+
+  /**
+   * Sets the value of field 'rightAlignIds'.
+   *
+   * @param rightAlignIds the value of field 'rightAlignIds'.
+   */
+  public void setRightAlignIds(boolean rightAlignIds)
+  {
+    this._rightAlignIds = rightAlignIds;
+    this._has_rightAlignIds = true;
+  } //-- void setRightAlignIds(boolean)
+
+  /**
+   * Sets the value of field 'sequenceSetId'.
+   *
+   * @param sequenceSetId the value of field 'sequenceSetId'.
+   */
+  public void setSequenceSetId(java.lang.String sequenceSetId)
+  {
+    this._sequenceSetId = sequenceSetId;
+  } //-- void setSequenceSetId(java.lang.String)
+
+  /**
+   * Sets the value of field 'showAnnotation'.
+   *
+   * @param showAnnotation the value of field 'showAnnotation'.
+   */
+  public void setShowAnnotation(boolean showAnnotation)
+  {
+    this._showAnnotation = showAnnotation;
+    this._has_showAnnotation = true;
+  } //-- void setShowAnnotation(boolean)
+
+  /**
+   * Sets the value of field 'showBoxes'.
+   *
+   * @param showBoxes the value of field 'showBoxes'.
+   */
+  public void setShowBoxes(boolean showBoxes)
+  {
+    this._showBoxes = showBoxes;
+    this._has_showBoxes = true;
+  } //-- void setShowBoxes(boolean)
+
+  /**
+   * Sets the value of field 'showColourText'.
+   *
+   * @param showColourText the value of field 'showColourText'.
+   */
+  public void setShowColourText(boolean showColourText)
+  {
+    this._showColourText = showColourText;
+    this._has_showColourText = true;
+  } //-- void setShowColourText(boolean)
+
+  /**
+   * Sets the value of field 'showFullId'.
+   *
+   * @param showFullId the value of field 'showFullId'.
+   */
+  public void setShowFullId(boolean showFullId)
+  {
+    this._showFullId = showFullId;
+    this._has_showFullId = true;
+  } //-- void setShowFullId(boolean)
+
+  /**
+   * Sets the value of field 'showSequenceFeatures'.
+   *
+   * @param showSequenceFeatures the value of field
+   * 'showSequenceFeatures'.
+   */
+  public void setShowSequenceFeatures(boolean showSequenceFeatures)
+  {
+    this._showSequenceFeatures = showSequenceFeatures;
+    this._has_showSequenceFeatures = true;
+  } //-- void setShowSequenceFeatures(boolean)
+
+  /**
+   * Sets the value of field 'showText'.
+   *
+   * @param showText the value of field 'showText'.
+   */
+  public void setShowText(boolean showText)
+  {
+    this._showText = showText;
+    this._has_showText = true;
+  } //-- void setShowText(boolean)
+
+  /**
+   * Sets the value of field 'startRes'.
+   *
+   * @param startRes the value of field 'startRes'.
+   */
+  public void setStartRes(int startRes)
+  {
+    this._startRes = startRes;
+    this._has_startRes = true;
+  } //-- void setStartRes(int)
+
+  /**
+   * Sets the value of field 'startSeq'.
+   *
+   * @param startSeq the value of field 'startSeq'.
+   */
+  public void setStartSeq(int startSeq)
+  {
+    this._startSeq = startSeq;
+    this._has_startSeq = true;
+  } //-- void setStartSeq(int)
+
+  /**
+   * Sets the value of field 'textCol1'.
+   *
+   * @param textCol1 the value of field 'textCol1'.
+   */
+  public void setTextCol1(int textCol1)
+  {
+    this._textCol1 = textCol1;
+    this._has_textCol1 = true;
+  } //-- void setTextCol1(int)
+
+  /**
+   * Sets the value of field 'textCol2'.
+   *
+   * @param textCol2 the value of field 'textCol2'.
+   */
+  public void setTextCol2(int textCol2)
+  {
+    this._textCol2 = textCol2;
+    this._has_textCol2 = true;
+  } //-- void setTextCol2(int)
+
+  /**
+   * Sets the value of field 'textColThreshold'.
+   *
+   * @param textColThreshold the value of field 'textColThreshold'
+   */
+  public void setTextColThreshold(int textColThreshold)
+  {
+    this._textColThreshold = textColThreshold;
+    this._has_textColThreshold = true;
+  } //-- void setTextColThreshold(int)
+
+  /**
+   * Sets the value of field 'title'.
+   *
+   * @param title the value of field 'title'.
+   */
+  public void setTitle(java.lang.String title)
+  {
+    this._title = title;
+  } //-- void setTitle(java.lang.String)
+
+  /**
+   * Sets the value of field 'viewName'.
+   *
+   * @param viewName the value of field 'viewName'.
+   */
+  public void setViewName(java.lang.String viewName)
+  {
+    this._viewName = viewName;
+  } //-- void setViewName(java.lang.String)
+
+  /**
+   * Sets the value of field 'width'.
+   *
+   * @param width the value of field 'width'.
+   */
+  public void setWidth(int width)
+  {
+    this._width = width;
+    this._has_width = true;
+  } //-- void setWidth(int)
+
+  /**
+   * Sets the value of field 'wrapAlignment'.
+   *
+   * @param wrapAlignment the value of field 'wrapAlignment'.
+   */
+  public void setWrapAlignment(boolean wrapAlignment)
+  {
+    this._wrapAlignment = wrapAlignment;
+    this._has_wrapAlignment = true;
+  } //-- void setWrapAlignment(boolean)
+
+  /**
+   * Sets the value of field 'xpos'.
+   *
+   * @param xpos the value of field 'xpos'.
+   */
+  public void setXpos(int xpos)
+  {
+    this._xpos = xpos;
+    this._has_xpos = true;
+  } //-- void setXpos(int)
+
+  /**
+   * Sets the value of field 'ypos'.
+   *
+   * @param ypos the value of field 'ypos'.
+   */
+  public void setYpos(int ypos)
+  {
+    this._ypos = ypos;
+    this._has_ypos = true;
+  } //-- void setYpos(int)
+
+  /**
+   * Method unmarshal
+   *
+   *
+   *
+   * @param reader
+   * @return Object
+   */
+  public static java.lang.Object unmarshal(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);
+  } //-- java.lang.Object unmarshal(java.io.Reader)
+
+  /**
+   * Method validate
+   *
+   */
+  public void validate()
+      throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.
+        Validator();
+    validator.validate(this);
+  } //-- void validate()
 
 }
diff --git a/src/jalview/schemabinding/version2/ViewportDescriptor.java b/src/jalview/schemabinding/version2/ViewportDescriptor.java
index 09544ef..5b2e45c 100755
--- a/src/jalview/schemabinding/version2/ViewportDescriptor.java
+++ b/src/jalview/schemabinding/version2/ViewportDescriptor.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,1441 +7,1783 @@
 
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
-import org.exolab.castor.mapping.AccessMode;
-import org.exolab.castor.xml.TypeValidator;
-import org.exolab.castor.xml.XMLFieldDescriptor;
 import org.exolab.castor.xml.validators.*;
 
 /**
  * Class ViewportDescriptor.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class ViewportDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field nsPrefix
-     */
-    private java.lang.String nsPrefix;
-
-    /**
-     * Field nsURI
-     */
-    private java.lang.String nsURI;
-
-    /**
-     * Field xmlName
-     */
-    private java.lang.String xmlName;
-
-    /**
-     * Field identity
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor identity;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public ViewportDescriptor() {
-        super();
-        nsURI = "www.jalview.org";
-        xmlName = "Viewport";
-        
-        //-- set grouping compositor
-        setCompositorAsSequence();
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
-        org.exolab.castor.xml.XMLFieldHandler              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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _conservationSelected
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            BooleanValidator typeValidator = new 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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _pidSelected
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            BooleanValidator typeValidator = new 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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _bgColour
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            StringValidator typeValidator = new StringValidator();
-            typeValidator.setWhiteSpace("preserve");
-            fieldValidator.setValidator(typeValidator);
-        }
-        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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _consThreshold
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            IntegerValidator typeValidator= new IntegerValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _pidThreshold
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            IntegerValidator typeValidator= new IntegerValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _title
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            StringValidator typeValidator = new StringValidator();
-            typeValidator.setWhiteSpace("preserve");
-            fieldValidator.setValidator(typeValidator);
-        }
-        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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _showFullId
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            BooleanValidator typeValidator = new 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;
-                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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _rightAlignIds
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            BooleanValidator typeValidator = new 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;
-                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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _showText
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            BooleanValidator typeValidator = new 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;
-                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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _showColourText
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            BooleanValidator typeValidator = new 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;
-                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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _showBoxes
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            BooleanValidator typeValidator = new 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;
-                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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _wrapAlignment
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            BooleanValidator typeValidator = new 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;
-                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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _renderGaps
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            BooleanValidator typeValidator = new 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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _showSequenceFeatures
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            BooleanValidator typeValidator = new 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;
-                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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _showAnnotation
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            BooleanValidator typeValidator = new 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;
-                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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _xpos
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            IntegerValidator typeValidator= new IntegerValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _ypos
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            IntegerValidator typeValidator= new IntegerValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _width
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            IntegerValidator typeValidator= new IntegerValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _height
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            IntegerValidator typeValidator= new IntegerValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _startRes
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            IntegerValidator typeValidator= new IntegerValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _startSeq
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            IntegerValidator typeValidator= new IntegerValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _fontName
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            StringValidator typeValidator = new StringValidator();
-            typeValidator.setWhiteSpace("preserve");
-            fieldValidator.setValidator(typeValidator);
-        }
-        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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _fontSize
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            IntegerValidator typeValidator= new IntegerValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _fontStyle
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            IntegerValidator typeValidator= new IntegerValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _viewName
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            StringValidator typeValidator = new StringValidator();
-            typeValidator.setWhiteSpace("preserve");
-            fieldValidator.setValidator(typeValidator);
-        }
-        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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _sequenceSetId
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            StringValidator typeValidator = new StringValidator();
-            typeValidator.setWhiteSpace("preserve");
-            fieldValidator.setValidator(typeValidator);
-        }
-        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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _gatheredViews
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            BooleanValidator typeValidator = new 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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _textCol1
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            IntegerValidator typeValidator= new IntegerValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _textCol2
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            IntegerValidator typeValidator= new IntegerValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        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);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _textColThreshold
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-            IntegerValidator typeValidator= new IntegerValidator();
-            fieldValidator.setValidator(typeValidator);
-        }
-        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
-        }
-        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 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);
-    } //-- jalview.schemabinding.version2.ViewportDescriptor()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method getAccessMode
-     * 
-     * 
-     * 
-     * @return AccessMode
-     */
-    public org.exolab.castor.mapping.AccessMode getAccessMode()
+public class ViewportDescriptor
+    extends org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  //--------------------------/
+  //- Class/Member Variables -/
+  //--------------------------/
+
+  /**
+   * Field nsPrefix
+   */
+  private java.lang.String nsPrefix;
+
+  /**
+   * Field nsURI
+   */
+  private java.lang.String nsURI;
+
+  /**
+   * Field xmlName
+   */
+  private java.lang.String xmlName;
+
+  /**
+   * Field identity
+   */
+  private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+  //----------------/
+  //- Constructors -/
+  //----------------/
+
+  public ViewportDescriptor()
+  {
+    super();
+    nsURI = "www.jalview.org";
+    xmlName = "Viewport";
+
+    //-- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.xml.XMLFieldHandler 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;
-    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
-
-    /**
-     * Method getExtends
-     * 
-     * 
-     * 
-     * @return ClassDescriptor
-     */
-    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+      }
+    });
+    desc.setHandler(handler);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _conservationSelected
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      BooleanValidator typeValidator = new 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;
-    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
-
-    /**
-     * Method getIdentity
-     * 
-     * 
-     * 
-     * @return FieldDescriptor
-     */
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+      }
+    });
+    desc.setHandler(handler);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _pidSelected
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      BooleanValidator typeValidator = new 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()
     {
-        return identity;
-    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
-
-    /**
-     * Method getJavaClass
-     * 
-     * 
-     * 
-     * @return Class
-     */
-    public java.lang.Class getJavaClass()
+      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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _bgColour
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      StringValidator typeValidator = new StringValidator();
+      typeValidator.setWhiteSpace("preserve");
+      fieldValidator.setValidator(typeValidator);
+    }
+    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()
     {
-        return jalview.schemabinding.version2.Viewport.class;
-    } //-- java.lang.Class getJavaClass() 
-
-    /**
-     * Method getNameSpacePrefix
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpacePrefix()
+      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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _consThreshold
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      IntegerValidator typeValidator = new IntegerValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _pidThreshold
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      IntegerValidator typeValidator = new IntegerValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    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()
     {
-        return nsPrefix;
-    } //-- java.lang.String getNameSpacePrefix() 
-
-    /**
-     * Method getNameSpaceURI
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getNameSpaceURI()
+      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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _title
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      StringValidator typeValidator = new StringValidator();
+      typeValidator.setWhiteSpace("preserve");
+      fieldValidator.setValidator(typeValidator);
+    }
+    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()
     {
-        return nsURI;
-    } //-- java.lang.String getNameSpaceURI() 
-
-    /**
-     * Method getValidator
-     * 
-     * 
-     * 
-     * @return TypeValidator
-     */
-    public org.exolab.castor.xml.TypeValidator getValidator()
+      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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _showFullId
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      BooleanValidator typeValidator = new 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()
     {
-        return this;
-    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
-
-    /**
-     * Method getXMLName
-     * 
-     * 
-     * 
-     * @return String
-     */
-    public java.lang.String getXMLName()
+      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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _rightAlignIds
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      BooleanValidator typeValidator = new 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()
     {
-        return xmlName;
-    } //-- java.lang.String getXMLName() 
+      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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _showText
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      BooleanValidator typeValidator = new 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;
+        }
+        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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _showColourText
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      BooleanValidator typeValidator = new 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;
+        }
+        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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _showBoxes
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      BooleanValidator typeValidator = new 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;
+        }
+        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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _wrapAlignment
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      BooleanValidator typeValidator = new 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;
+        }
+        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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _renderGaps
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      BooleanValidator typeValidator = new 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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _showSequenceFeatures
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      BooleanValidator typeValidator = new 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;
+        }
+        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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _showAnnotation
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      BooleanValidator typeValidator = new 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;
+        }
+        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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _xpos
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      IntegerValidator typeValidator = new IntegerValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _ypos
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      IntegerValidator typeValidator = new IntegerValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _width
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      IntegerValidator typeValidator = new IntegerValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _height
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      IntegerValidator typeValidator = new IntegerValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _startRes
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      IntegerValidator typeValidator = new IntegerValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _startSeq
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      IntegerValidator typeValidator = new IntegerValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _fontName
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      StringValidator typeValidator = new StringValidator();
+      typeValidator.setWhiteSpace("preserve");
+      fieldValidator.setValidator(typeValidator);
+    }
+    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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _fontSize
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      IntegerValidator typeValidator = new IntegerValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _fontStyle
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      IntegerValidator typeValidator = new IntegerValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _viewName
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      StringValidator typeValidator = new StringValidator();
+      typeValidator.setWhiteSpace("preserve");
+      fieldValidator.setValidator(typeValidator);
+    }
+    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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _sequenceSetId
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      StringValidator typeValidator = new StringValidator();
+      typeValidator.setWhiteSpace("preserve");
+      fieldValidator.setValidator(typeValidator);
+    }
+    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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _gatheredViews
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      BooleanValidator typeValidator = new 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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _textCol1
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      IntegerValidator typeValidator = new IntegerValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _textCol2
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      IntegerValidator typeValidator = new IntegerValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    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);
+    addFieldDescriptor(desc);
+
+    //-- validation code for: _textColThreshold
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { //-- local scope
+      IntegerValidator typeValidator = new IntegerValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    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
+    }
+    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 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);
+  } //-- jalview.schemabinding.version2.ViewportDescriptor()
+
+  //-----------/
+  //- Methods -/
+  //-----------/
+
+  /**
+   * Method getAccessMode
+   *
+   *
+   *
+   * @return AccessMode
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
+
+  /**
+   * Method getExtends
+   *
+   *
+   *
+   * @return ClassDescriptor
+   */
+  public org.exolab.castor.mapping.ClassDescriptor getExtends()
+  {
+    return null;
+  } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
+
+  /**
+   * Method getIdentity
+   *
+   *
+   *
+   * @return FieldDescriptor
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return identity;
+  } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
+
+  /**
+   * Method getJavaClass
+   *
+   *
+   *
+   * @return Class
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.Viewport.class;
+  } //-- java.lang.Class getJavaClass()
+
+  /**
+   * Method getNameSpacePrefix
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return nsPrefix;
+  } //-- java.lang.String getNameSpacePrefix()
+
+  /**
+   * Method getNameSpaceURI
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return nsURI;
+  } //-- java.lang.String getNameSpaceURI()
+
+  /**
+   * Method getValidator
+   *
+   *
+   *
+   * @return TypeValidator
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  } //-- org.exolab.castor.xml.TypeValidator getValidator()
+
+  /**
+   * Method getXMLName
+   *
+   *
+   *
+   * @return String
+   */
+  public java.lang.String getXMLName()
+  {
+    return xmlName;
+  } //-- java.lang.String getXMLName()
 
 }
diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index 20b0885..06085da 100755
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -1,186 +1,203 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 jalview.schemes;
 
 import java.awt.*;
 
 import jalview.datamodel.*;
 
-public class AnnotationColourGradient extends ResidueColourScheme
+public class AnnotationColourGradient
+    extends ResidueColourScheme
 {
-    public static int NO_THRESHOLD = -1;
-    public static int BELOW_THRESHOLD = 0;
-    public static int ABOVE_THRESHOLD = 1;
+  public static int NO_THRESHOLD = -1;
+  public static int BELOW_THRESHOLD = 0;
+  public static int ABOVE_THRESHOLD = 1;
 
-    AlignmentAnnotation annotation;
-    int aboveAnnotationThreshold = -1;
+  AlignmentAnnotation annotation;
+  int aboveAnnotationThreshold = -1;
 
-    GraphLine annotationThreshold;
+  GraphLine annotationThreshold;
 
-    float r1, g1, b1, rr, gg, bb, dr, dg, db;
-    float range = 0;
+  float r1, g1, b1, rr, gg, bb, dr, dg, db;
+  float range = 0;
 
-    ColourSchemeI colourScheme;
+  ColourSchemeI colourScheme;
 
-    /**
-     * Creates a new AnnotationColourGradient object.
-     */
-    public AnnotationColourGradient(AlignmentAnnotation annotation,
-                                    ColourSchemeI originalColour,
-                                    int aboveThreshold)
+  /**
+   * Creates a new AnnotationColourGradient object.
+   */
+  public AnnotationColourGradient(AlignmentAnnotation annotation,
+                                  ColourSchemeI originalColour,
+                                  int aboveThreshold)
+  {
+    if (originalColour instanceof AnnotationColourGradient)
     {
-      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;
+      colourScheme = ( (AnnotationColourGradient) originalColour).colourScheme;
     }
-
-    /**
-     * Creates a new AnnotationColourGradient object.
-     */
-    public AnnotationColourGradient(AlignmentAnnotation annotation,
-        Color minColour, Color maxColour, int aboveThreshold)
+    else
     {
-      this.annotation = annotation;
+      colourScheme = originalColour;
+    }
 
-      aboveAnnotationThreshold = aboveThreshold;
+    this.annotation = annotation;
 
-      if(aboveThreshold!=NO_THRESHOLD && annotation.threshold!=null)
-        annotationThreshold = annotation.threshold;
+    aboveAnnotationThreshold = aboveThreshold;
 
-      r1 = minColour.getRed();
-      g1 = minColour.getGreen();
-      b1 = minColour.getBlue();
+    if (aboveThreshold != NO_THRESHOLD && annotation.threshold != null)
+    {
+      annotationThreshold = annotation.threshold;
+    }
+  }
 
-      rr = maxColour.getRed() - r1;
-      gg = maxColour.getGreen() - g1;
-      bb = maxColour.getBlue() - b1;
+  /**
+   * Creates a new AnnotationColourGradient object.
+   */
+  public AnnotationColourGradient(AlignmentAnnotation annotation,
+                                  Color minColour, Color maxColour,
+                                  int aboveThreshold)
+  {
+    this.annotation = annotation;
 
-      range = annotation.graphMax - annotation.graphMin;
+    aboveAnnotationThreshold = aboveThreshold;
 
+    if (aboveThreshold != NO_THRESHOLD && annotation.threshold != null)
+    {
+      annotationThreshold = annotation.threshold;
     }
 
+    r1 = minColour.getRed();
+    g1 = minColour.getGreen();
+    b1 = minColour.getBlue();
 
-    public String getAnnotation()
-    {
-      return annotation.label;
-    }
+    rr = maxColour.getRed() - r1;
+    gg = maxColour.getGreen() - g1;
+    bb = maxColour.getBlue() - b1;
 
-    public int getAboveThreshold()
-    {
-      return aboveAnnotationThreshold;
-    }
+    range = annotation.graphMax - annotation.graphMin;
 
-    public float getAnnotationThreshold()
-    {
-      if(annotationThreshold==null)
-        return 0;
-      else
-        return annotationThreshold.value;
-    }
+  }
 
-    public ColourSchemeI getBaseColour()
-    {
-      return colourScheme;
-    }
+  public String getAnnotation()
+  {
+    return annotation.label;
+  }
 
-    public Color getMinColour()
-    {
-      return new Color( (int) r1, (int) g1, (int) b1);
-    }
+  public int getAboveThreshold()
+  {
+    return aboveAnnotationThreshold;
+  }
 
-    public Color getMaxColour()
+  public float getAnnotationThreshold()
+  {
+    if (annotationThreshold == null)
     {
-      return new Color( (int) (r1 + rr), (int) (g1 + gg), (int) (b1 + bb));
+      return 0;
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param n DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Color findColour(char c)
+    else
     {
-        return Color.red;
+      return annotationThreshold.value;
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param n DOCUMENT ME!
-     * @param j DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Color findColour(char c, int j)
+  }
+
+  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))
     {
-        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 (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))
         {
-          if( j<annotation.annotations.length
-              && annotation.annotations[j]!=null
-              && !jalview.util.Comparison.isGap(c))
+          if (colourScheme != null)
           {
-            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))
-            {
-              if(colourScheme!=null)
-              {
-                currentColour = colourScheme.findColour(c, j);
-              }
-              else if(range!=0)
-              {
-                dr = rr *
-                    ( (annotation.annotations[j].value - annotation.graphMin) /
-                     range)
-                    + r1;
-                dg = gg *
-                    ( (annotation.annotations[j].value - annotation.graphMin) /
-                     range)
-                    + g1;
-                db = bb *
-                    ( (annotation.annotations[j].value - annotation.graphMin) /
-                     range)
-                    + b1;
-
-                currentColour = new Color( (int) dr, (int) dg, (int) db);
-              }
-            }
+            currentColour = colourScheme.findColour(c, j);
+          }
+          else if (range != 0)
+          {
+            dr = rr *
+                ( (annotation.annotations[j].value - annotation.graphMin) /
+                 range)
+                + r1;
+            dg = gg *
+                ( (annotation.annotations[j].value - annotation.graphMin) /
+                 range)
+                + g1;
+            db = bb *
+                ( (annotation.annotations[j].value - annotation.graphMin) /
+                 range)
+                + b1;
+
+            currentColour = new Color( (int) dr, (int) dg, (int) db);
           }
         }
+      }
+    }
 
-        if(conservationColouring)
-         currentColour = applyConservation(currentColour, j);
-
-       return currentColour;
+    if (conservationColouring)
+    {
+      currentColour = applyConservation(currentColour, j);
     }
+
+    return currentColour;
+  }
 }
diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index 02545a3..0db55c0 100755
--- a/src/jalview/schemes/Blosum62ColourScheme.java
+++ b/src/jalview/schemes/Blosum62ColourScheme.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,9 +18,9 @@
  */
 package jalview.schemes;
 
-
 import java.awt.*;
-import jalview.analysis.AAFrequency;
+
+import jalview.analysis.*;
 
 public class Blosum62ColourScheme
     extends ResidueColourScheme
@@ -32,10 +32,10 @@ public class Blosum62ColourScheme
 
   public Color findColour(char res, int j)
   {
-    if ('a' <= res && res <= 'z' )
+    if ('a' <= res && res <= 'z')
     {
-       // TO UPPERCASE !!!
-       res -= ('a' - 'A');
+      // TO UPPERCASE !!!
+      res -= ('a' - 'A');
     }
 
     if (consensus == null ||
@@ -48,7 +48,7 @@ public class Blosum62ColourScheme
 
     Color currentColour;
 
-    if (!jalview.util.Comparison.isGap( res ))
+    if (!jalview.util.Comparison.isGap(res))
     {
       String max = (String) consensus[j].get(AAFrequency.MAXRESIDUE);
 
@@ -79,8 +79,10 @@ public class Blosum62ColourScheme
         }
       }
 
-      if(conservationColouring)
-       currentColour =  applyConservation(currentColour, j);
+      if (conservationColouring)
+      {
+        currentColour = applyConservation(currentColour, j);
+      }
     }
     else
     {
diff --git a/src/jalview/schemes/BuriedColourScheme.java b/src/jalview/schemes/BuriedColourScheme.java
index 9fe1173..c973035 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) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 jalview.schemes;
 
 import java.awt.*;
 
-
 /**
  * DOCUMENT ME!
  *
  * @author $author$
  * @version $Revision$
  */
-public class BuriedColourScheme extends ScoreColourScheme
+public class BuriedColourScheme
+    extends ScoreColourScheme
 {
-    /**
-     * Creates a new BuriedColourScheme object.
-     */
-    public BuriedColourScheme()
-    {
-        super(ResidueProperties.buried, ResidueProperties.buriedmin,
-            ResidueProperties.buriedmax);
-    }
+  /**
+   * 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);
-    }
+  /**
+   * 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 eaf2a5f..8dd8994 100755
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -70,7 +70,7 @@ public class ClustalxColourScheme
     int res;
     int i;
     int j = 0;
-    char [] seq;
+    char[] seq;
 
     while (j < seqs.size())
     {
@@ -86,7 +86,7 @@ public class ClustalxColourScheme
         }
         else
         {
-          res =  ResidueProperties.aaIndex[seq[i]];
+          res = ResidueProperties.aaIndex[seq[i]];
         }
 
         cons2[i][res]++;
@@ -249,8 +249,7 @@ public class ClustalxColourScheme
   {
     Color currentColour;
 
-
-    if ( cons2.length<=j || (threshold != 0 && !aboveThreshold(c, j)))
+    if (cons2.length <= j || (threshold != 0 && !aboveThreshold(c, j)))
     {
       return Color.white;
     }
@@ -264,13 +263,13 @@ public class ClustalxColourScheme
       return currentColour;
     }
 
-  for (int k = 0; k < ResidueColour[i].conses.length; k++)
-  {
-    if (ResidueColour[i].conses[k].isConserved(cons2, j, size))
+    for (int k = 0; k < ResidueColour[i].conses.length; k++)
     {
-      currentColour = ResidueColour[i].c;
+      if (ResidueColour[i].conses[k].isConserved(cons2, j, size))
+      {
+        currentColour = ResidueColour[i].c;
+      }
     }
-  }
 
     if (i == 4)
     {
@@ -280,8 +279,10 @@ public class ClustalxColourScheme
       }
     }
 
-    if(conservationColouring)
+    if (conservationColouring)
+    {
       currentColour = applyConservation(currentColour, j);
+    }
 
     return currentColour;
   }
diff --git a/src/jalview/schemes/ColourSchemeI.java b/src/jalview/schemes/ColourSchemeI.java
index 6afa3ef..96699c6 100755
--- a/src/jalview/schemes/ColourSchemeI.java
+++ b/src/jalview/schemes/ColourSchemeI.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -26,7 +26,7 @@ public interface ColourSchemeI
 
   public Color findColour(char c, int j);
 
-  public void setConsensus(java.util.Hashtable [] h);
+  public void setConsensus(java.util.Hashtable[] h);
 
   public void setConservation(jalview.analysis.Conservation c);
 
@@ -40,5 +40,4 @@ public interface ColourSchemeI
 
   public void setThreshold(int ct, boolean ignoreGaps);
 
-
 }
diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index 278cf6a..d3325ca 100755
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@ -1,24 +1,25 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 jalview.schemes;
 
 import java.awt.*;
+
 /**
  * DOCUMENT ME!
  *
@@ -27,398 +28,425 @@ import java.awt.*;
  */
 public class ColourSchemeProperty
 {
-    /** DOCUMENT ME!! */
-    public static final int CLUSTAL = 0;
+  /** DOCUMENT ME!! */
+  public static final int CLUSTAL = 0;
 
-    /** DOCUMENT ME!! */
-    public static final int BLOSUM = 1;
+  /** DOCUMENT ME!! */
+  public static final int BLOSUM = 1;
 
-    /** DOCUMENT ME!! */
-    public static final int PID = 2;
+  /** DOCUMENT ME!! */
+  public static final int PID = 2;
 
-    /** DOCUMENT ME!! */
-    public static final int ZAPPO = 3;
+  /** DOCUMENT ME!! */
+  public static final int ZAPPO = 3;
 
-    /** DOCUMENT ME!! */
-    public static final int TAYLOR = 4;
+  /** DOCUMENT ME!! */
+  public static final int TAYLOR = 4;
 
-    /** DOCUMENT ME!! */
-    public static final int HYDROPHOBIC = 5;
+  /** DOCUMENT ME!! */
+  public static final int HYDROPHOBIC = 5;
 
-    /** DOCUMENT ME!! */
-    public static final int HELIX = 6;
+  /** DOCUMENT ME!! */
+  public static final int HELIX = 6;
 
-    /** DOCUMENT ME!! */
-    public static final int STRAND = 7;
+  /** DOCUMENT ME!! */
+  public static final int STRAND = 7;
 
-    /** DOCUMENT ME!! */
-    public static final int TURN = 8;
+  /** DOCUMENT ME!! */
+  public static final int TURN = 8;
 
-    /** DOCUMENT ME!! */
-    public static final int BURIED = 9;
+  /** DOCUMENT ME!! */
+  public static final int BURIED = 9;
 
-    /** DOCUMENT ME!! */
-    public static final int NUCLEOTIDE = 10;
+  /** DOCUMENT ME!! */
+  public static final int NUCLEOTIDE = 10;
 
-    /** DOCUMENT ME!! */
-    public static final int USER_DEFINED = 11;
+  /** DOCUMENT ME!! */
+  public static final int USER_DEFINED = 11;
 
+  /** DOCUMENT ME!! */
+  public static final int NONE = 12;
 
-    /** DOCUMENT ME!! */
-    public static final int NONE = 12;
+  /**
+   * DOCUMENT ME!
+   *
+   * @param name DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public static int getColourIndexFromName(String name)
+  {
+    int ret = 12;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param name DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public static int getColourIndexFromName(String name)
+    if (name.equalsIgnoreCase("Clustal"))
     {
-        int ret = 12;
-
-        if (name.equalsIgnoreCase("Clustal"))
-        {
-            ret = CLUSTAL;
-        }
-        else if (name.equalsIgnoreCase("Blosum62"))
-        {
-            ret = BLOSUM;
-        }
-        else if (name.equalsIgnoreCase("% Identity"))
-        {
-            ret = PID;
-        }
-        else if (name.equalsIgnoreCase("Zappo"))
-        {
-            ret = ZAPPO;
-        }
-        else if (name.equalsIgnoreCase("Taylor"))
-        {
-          ret = TAYLOR;
-        }
-        else if (name.equalsIgnoreCase("Hydrophobic"))
-        {
-            ret = HYDROPHOBIC;
-        }
-        else if (name.equalsIgnoreCase("Helix Propensity"))
-        {
-            ret = HELIX;
-        }
-        else if (name.equalsIgnoreCase("Strand Propensity"))
-        {
-            ret = STRAND;
-        }
-        else if (name.equalsIgnoreCase("Turn Propensity"))
-        {
-            ret = TURN;
-        }
-        else if (name.equalsIgnoreCase("Buried Index"))
-        {
-            ret = BURIED;
-        }
-        else if (name.equalsIgnoreCase("Nucleotide"))
-        {
-            ret = NUCLEOTIDE;
-        }
-        else if (name.equalsIgnoreCase("User Defined"))
-        {
-            ret = USER_DEFINED;
-        }
-
-        return ret;
+      ret = CLUSTAL;
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param cs DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public static String getColourName(ColourSchemeI cs)
+    else if (name.equalsIgnoreCase("Blosum62"))
+    {
+      ret = BLOSUM;
+    }
+    else if (name.equalsIgnoreCase("% Identity"))
     {
+      ret = PID;
+    }
+    else if (name.equalsIgnoreCase("Zappo"))
+    {
+      ret = ZAPPO;
+    }
+    else if (name.equalsIgnoreCase("Taylor"))
+    {
+      ret = TAYLOR;
+    }
+    else if (name.equalsIgnoreCase("Hydrophobic"))
+    {
+      ret = HYDROPHOBIC;
+    }
+    else if (name.equalsIgnoreCase("Helix Propensity"))
+    {
+      ret = HELIX;
+    }
+    else if (name.equalsIgnoreCase("Strand Propensity"))
+    {
+      ret = STRAND;
+    }
+    else if (name.equalsIgnoreCase("Turn Propensity"))
+    {
+      ret = TURN;
+    }
+    else if (name.equalsIgnoreCase("Buried Index"))
+    {
+      ret = BURIED;
+    }
+    else if (name.equalsIgnoreCase("Nucleotide"))
+    {
+      ret = NUCLEOTIDE;
+    }
+    else if (name.equalsIgnoreCase("User Defined"))
+    {
+      ret = USER_DEFINED;
+    }
 
-        int index = 12;
+    return ret;
+  }
 
-        if (cs instanceof ClustalxColourScheme)
-        {
-            index = CLUSTAL;
-        }
-        else if (cs instanceof Blosum62ColourScheme)
-        {
-            index = BLOSUM;
-        }
-        else if (cs instanceof PIDColourScheme)
-        {
-            index = PID;
-        }
-        else if (cs instanceof ZappoColourScheme)
-        {
-            index = ZAPPO;
-        }
-        else if (cs instanceof TaylorColourScheme)
-        {
-            index = TAYLOR;
-        }
-        else if (cs instanceof HydrophobicColourScheme)
-        {
-            index = HYDROPHOBIC;
-        }
-        else if (cs instanceof HelixColourScheme)
-        {
-            index = HELIX;
-        }
-        else if (cs instanceof StrandColourScheme)
-        {
-            index = STRAND;
-        }
-        else if (cs instanceof TurnColourScheme)
-        {
-            index = TURN;
-        }
-        else if (cs instanceof BuriedColourScheme)
-        {
-            index = BURIED;
-        }
-        else if (cs instanceof NucleotideColourScheme)
-        {
-            index = NUCLEOTIDE;
-        }
-        else if (cs instanceof UserColourScheme)
-        {
-            index = USER_DEFINED;
-        }
+  /**
+   * DOCUMENT ME!
+   *
+   * @param cs DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public static String getColourName(ColourSchemeI cs)
+  {
 
-        return getColourName(index);
+    int index = 12;
+
+    if (cs instanceof ClustalxColourScheme)
+    {
+      index = CLUSTAL;
+    }
+    else if (cs instanceof Blosum62ColourScheme)
+    {
+      index = BLOSUM;
+    }
+    else if (cs instanceof PIDColourScheme)
+    {
+      index = PID;
+    }
+    else if (cs instanceof ZappoColourScheme)
+    {
+      index = ZAPPO;
+    }
+    else if (cs instanceof TaylorColourScheme)
+    {
+      index = TAYLOR;
+    }
+    else if (cs instanceof HydrophobicColourScheme)
+    {
+      index = HYDROPHOBIC;
+    }
+    else if (cs instanceof HelixColourScheme)
+    {
+      index = HELIX;
+    }
+    else if (cs instanceof StrandColourScheme)
+    {
+      index = STRAND;
+    }
+    else if (cs instanceof TurnColourScheme)
+    {
+      index = TURN;
+    }
+    else if (cs instanceof BuriedColourScheme)
+    {
+      index = BURIED;
+    }
+    else if (cs instanceof NucleotideColourScheme)
+    {
+      index = NUCLEOTIDE;
+    }
+    else if (cs instanceof UserColourScheme)
+    {
+      index = USER_DEFINED;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param index DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public static String getColourName(int index)
+    return getColourName(index);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param index DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public static String getColourName(int index)
+  {
+    String ret = null;
+
+    switch (index)
     {
-        String ret = null;
+      case CLUSTAL:
+        ret = "Clustal";
 
-        switch (index)
-        {
-        case CLUSTAL:
-            ret = "Clustal";
+        break;
 
-            break;
+      case BLOSUM:
+        ret = "Blosum62";
 
-        case BLOSUM:
-            ret = "Blosum62";
+        break;
 
-            break;
+      case PID:
+        ret = "% Identity";
 
-        case PID:
-            ret = "% Identity";
+        break;
 
-            break;
+      case ZAPPO:
+        ret = "Zappo";
 
-        case ZAPPO:
-            ret = "Zappo";
+        break;
 
-            break;
+      case TAYLOR:
+        ret = "Taylor";
+        break;
 
-        case TAYLOR:
-            ret = "Taylor";
-            break;
+      case HYDROPHOBIC:
+        ret = "Hydrophobic";
 
-        case HYDROPHOBIC:
-            ret = "Hydrophobic";
+        break;
 
-            break;
+      case HELIX:
+        ret = "Helix Propensity";
 
-        case HELIX:
-            ret = "Helix Propensity";
+        break;
 
-            break;
+      case STRAND:
+        ret = "Strand Propensity";
 
-        case STRAND:
-            ret = "Strand Propensity";
+        break;
 
-            break;
+      case TURN:
+        ret = "Turn Propensity";
 
-        case TURN:
-            ret = "Turn Propensity";
+        break;
 
-            break;
+      case BURIED:
+        ret = "Buried Index";
 
-        case BURIED:
-            ret = "Buried Index";
+        break;
 
-            break;
+      case NUCLEOTIDE:
+        ret = "Nucleotide";
 
-        case NUCLEOTIDE:
-            ret = "Nucleotide";
+        break;
 
-            break;
+      case USER_DEFINED:
+        ret = "User Defined";
 
-        case USER_DEFINED:
-            ret = "User Defined";
+        break;
 
-            break;
+      default:
+        ret = "None";
 
-        default:
-            ret = "None";
+        break;
+    }
 
-            break;
-        }
+    return ret;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param al DOCUMENT ME!
+   * @param name DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al,
+                                        String name)
+  {
+    return getColour(al.getSequences(), al.getWidth(), name);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param seqs DOCUMENT ME!
+   * @param width DOCUMENT ME!
+   * @param name DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public static ColourSchemeI getColour(java.util.Vector seqs, int width,
+                                        String name)
+  {
+    return getColour(seqs, width, getColourIndexFromName(name));
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param seqs DOCUMENT ME!
+   * @param width DOCUMENT ME!
+   * @param index DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public static ColourSchemeI getColour(java.util.Vector seqs, int width,
+                                        int index)
+  {
+    ColourSchemeI cs = null;
+
+    switch (index)
+    {
+      case CLUSTAL:
+        cs = new ClustalxColourScheme(seqs, width);
 
-        return ret;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param al DOCUMENT ME!
-     * @param name DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al,
-        String name)
-    {
-        return getColour(al.getSequences(), al.getWidth(), name);
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param seqs DOCUMENT ME!
-     * @param width DOCUMENT ME!
-     * @param name DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public static ColourSchemeI getColour(java.util.Vector seqs, int width,
-        String name)
-    {
-        return getColour(seqs, width, getColourIndexFromName(name));
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param seqs DOCUMENT ME!
-     * @param width DOCUMENT ME!
-     * @param index DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public static ColourSchemeI getColour(java.util.Vector seqs, int width,
-        int index)
-    {
-        ColourSchemeI cs = null;
-
-        switch (index)
-        {
-        case CLUSTAL:
-            cs = new ClustalxColourScheme(seqs, width);
+        break;
 
-            break;
+      case BLOSUM:
+        cs = new Blosum62ColourScheme();
 
-        case BLOSUM:
-            cs = new Blosum62ColourScheme();
+        break;
 
-            break;
+      case PID:
+        cs = new PIDColourScheme();
 
-        case PID:
-            cs = new PIDColourScheme();
+        break;
 
-            break;
+      case ZAPPO:
+        cs = new ZappoColourScheme();
 
-        case ZAPPO:
-            cs = new ZappoColourScheme();
+        break;
 
-            break;
+      case TAYLOR:
+        cs = new TaylorColourScheme();
+        break;
 
-        case TAYLOR:
-            cs = new TaylorColourScheme();
-            break;
+      case HYDROPHOBIC:
+        cs = new HydrophobicColourScheme();
 
-        case HYDROPHOBIC:
-            cs = new HydrophobicColourScheme();
+        break;
 
-            break;
+      case HELIX:
+        cs = new HelixColourScheme();
 
-        case HELIX:
-            cs = new HelixColourScheme();
+        break;
 
-            break;
+      case STRAND:
+        cs = new StrandColourScheme();
 
-        case STRAND:
-            cs = new StrandColourScheme();
+        break;
 
-            break;
+      case TURN:
+        cs = new TurnColourScheme();
 
-        case TURN:
-            cs = new TurnColourScheme();
+        break;
 
-            break;
+      case BURIED:
+        cs = new BuriedColourScheme();
 
-        case BURIED:
-            cs = new BuriedColourScheme();
+        break;
 
-            break;
+      case NUCLEOTIDE:
+        cs = new NucleotideColourScheme();
 
-        case NUCLEOTIDE:
-            cs = new NucleotideColourScheme();
+        break;
 
-            break;
+      case USER_DEFINED:
+        Color[] col = new Color[24];
+        for (int i = 0; i < 24; i++)
+        {
+          col[i] = Color.white;
+        }
+        cs = new UserColourScheme(col);
+        break;
 
-        case USER_DEFINED:
-          Color[] col = new Color[24];
-          for (int i = 0; i < 24; i++)
-            col[i] = Color.white;
-          cs = new UserColourScheme(col);
-            break;
+      default:
+        break;
+    }
 
-        default:
-            break;
-        }
+    return cs;
+  }
 
-        return cs;
-    }
-
-    public static Color getAWTColorFromName(String name)
-    {
-      Color col = null;
-      name = name.toLowerCase();
-      if(name.equals("black"))
-        col = Color.black;
-      else if(name.equals("blue"))
-        col = Color.blue;
-      else if(name.equals("cyan"))
-        col = Color.cyan;
-      else if(name.equals("darkGray"))
-        col = Color.darkGray;
-      else if(name.equals("gray"))
-        col = Color.gray;
-      else if(name.equals("green"))
-        col = Color.green;
-      else if(name.equals("lightGray"))
-        col = Color.lightGray;
-      else if(name.equals("magenta"))
-        col = Color.magenta;
-      else if(name.equals("orange"))
-        col = Color.orange;
-      else if(name.equals("pink"))
-        col = Color.pink;
-      else if(name.equals("red"))
-        col = Color.red;
-      else if(name.equals("white"))
-        col = Color.white;
-      else if(name.equals("yellow"))
-        col = Color.yellow;
-
-      return col;
+  public static Color getAWTColorFromName(String name)
+  {
+    Color col = null;
+    name = name.toLowerCase();
+    if (name.equals("black"))
+    {
+      col = Color.black;
+    }
+    else if (name.equals("blue"))
+    {
+      col = Color.blue;
+    }
+    else if (name.equals("cyan"))
+    {
+      col = Color.cyan;
+    }
+    else if (name.equals("darkGray"))
+    {
+      col = Color.darkGray;
+    }
+    else if (name.equals("gray"))
+    {
+      col = Color.gray;
     }
+    else if (name.equals("green"))
+    {
+      col = Color.green;
+    }
+    else if (name.equals("lightGray"))
+    {
+      col = Color.lightGray;
+    }
+    else if (name.equals("magenta"))
+    {
+      col = Color.magenta;
+    }
+    else if (name.equals("orange"))
+    {
+      col = Color.orange;
+    }
+    else if (name.equals("pink"))
+    {
+      col = Color.pink;
+    }
+    else if (name.equals("red"))
+    {
+      col = Color.red;
+    }
+    else if (name.equals("white"))
+    {
+      col = Color.white;
+    }
+    else if (name.equals("yellow"))
+    {
+      col = Color.yellow;
+    }
+
+    return col;
+  }
 }
diff --git a/src/jalview/schemes/Consensus.java b/src/jalview/schemes/Consensus.java
index 520196f..8aa59e3 100755
--- a/src/jalview/schemes/Consensus.java
+++ b/src/jalview/schemes/Consensus.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
diff --git a/src/jalview/schemes/HelixColourScheme.java b/src/jalview/schemes/HelixColourScheme.java
index 85bd529..7894965 100755
--- a/src/jalview/schemes/HelixColourScheme.java
+++ b/src/jalview/schemes/HelixColourScheme.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
diff --git a/src/jalview/schemes/HydrophobicColourScheme.java b/src/jalview/schemes/HydrophobicColourScheme.java
index 7302d20..9af174d 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) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 jalview.schemes;
 
 import java.awt.*;
 
-
 /**
  * DOCUMENT ME!
  *
  * @author $author$
  * @version $Revision$
  */
-public class HydrophobicColourScheme extends ScoreColourScheme
+public class HydrophobicColourScheme
+    extends ScoreColourScheme
 {
-    /**
-     * Creates a new HydrophobicColourScheme object.
-     */
-    public HydrophobicColourScheme()
-    {
-        super(ResidueProperties.hyd, ResidueProperties.hydmin,
-            ResidueProperties.hydmax);
-    }
+  /**
+   * 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);
-    }
+  /**
+   * 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 899fc60..4e14202 100755
--- a/src/jalview/schemes/NucleotideColourScheme.java
+++ b/src/jalview/schemes/NucleotideColourScheme.java
@@ -1,85 +1,87 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 jalview.schemes;
 
 import java.awt.*;
 
-
 /**
  * DOCUMENT ME!
  *
  * @author $author$
  * @version $Revision$
  */
-public class NucleotideColourScheme extends ResidueColourScheme
+public class NucleotideColourScheme
+    extends ResidueColourScheme
 {
-    /**
-     * Creates a new NucleotideColourScheme object.
-     */
-    public NucleotideColourScheme()
+  /**
+   * 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))
     {
-        super(ResidueProperties.nucleotide, 0);
+      try
+      {
+        currentColour = colors[ResidueProperties.nucleotideIndex[c]];
+      }
+      catch (Exception ex)
+      {
+        return Color.white;
+      }
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param n DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Color findColour(char c)
+    else
     {
-        // System.out.println("called"); log.debug
-        return colors[ResidueProperties.nucleotideIndex[c]];
+      return Color.white;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param n DOCUMENT ME!
-     * @param j DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Color findColour(char c, int j)
+    if (conservationColouring)
     {
-        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;
+      currentColour = applyConservation(currentColour, j);
     }
+
+    return currentColour;
+  }
 }
diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index 8686894..e1dbf46 100755
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -20,8 +20,8 @@ package jalview.schemes;
 
 import java.awt.*;
 
+import jalview.analysis.*;
 import jalview.datamodel.*;
-import jalview.analysis.AAFrequency;
 
 public class PIDColourScheme
     extends ResidueColourScheme
@@ -45,7 +45,7 @@ public class PIDColourScheme
 
     if (consensus == null
         || j >= consensus.length
-        || consensus[j]==null)
+        || consensus[j] == null)
     {
       return Color.white;
     }
@@ -59,30 +59,35 @@ public class PIDColourScheme
 
     double sc = 0;
 
-    if(consensus.length<=j)
+    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 ( (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))
+      if (!jalview.util.Comparison.isGap(c))
+      {
+        for (int i = 0; i < thresholds.length; i++)
         {
-          for (int i = 0; i < thresholds.length; i++)
+          if (sc > thresholds[i])
           {
-            if (sc > thresholds[i])
-            {
-              currentColour = pidColours[i];
+            currentColour = pidColours[i];
 
-              break;
-            }
+            break;
           }
         }
       }
+    }
 
-    if(conservationColouring)
+    if (conservationColouring)
+    {
       currentColour = applyConservation(currentColour, j);
+    }
 
     return currentColour;
   }
diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index 9800f82..67828ce 100755
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -1,29 +1,28 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 jalview.schemes;
 
-import jalview.analysis.*;
+import java.util.*;
 
 import java.awt.*;
 
-import java.util.*;
-
+import jalview.analysis.*;
 
 /**
  * DOCUMENT ME!
@@ -31,233 +30,240 @@ import java.util.*;
  * @author $author$
  * @version $Revision$
  */
-public class ResidueColourScheme implements ColourSchemeI
+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;
-
-   /** DOCUMENT ME!! */
-   int inc = 30;
-
-
-    /**
-     * Creates a new ResidueColourScheme object.
-     *
-     * @param colors DOCUMENT ME!
-     * @param threshold DOCUMENT ME!
-     */
-    public ResidueColourScheme(Color[] colours, int threshold)
+  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;
+
+  /** 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))
     {
-        this.colors = colours;
-        this.threshold = threshold;
+      currentColour = colors[ResidueProperties.aaIndex[c]];
     }
-
-    /**
-     * Creates a new ResidueColourScheme object.
-     */
-    public ResidueColourScheme()
+    else
     {
+      currentColour = Color.white;
     }
 
-    /**
-    * 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()
+    if (conservationColouring)
     {
-        return threshold;
+      currentColour = applyConservation(currentColour, j);
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param ct DOCUMENT ME!
-     */
-    public void setThreshold(int ct, boolean ignoreGaps)
+    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)
     {
-        threshold = ct;
-        if(ignoreGaps)
-          this.ignoreGaps = AAFrequency.PID_NOGAPS;
-        else
-          this.ignoreGaps = AAFrequency.PID_GAPS;
+      this.ignoreGaps = AAFrequency.PID_NOGAPS;
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param s DOCUMENT ME!
-     * @param j DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean aboveThreshold(char c, int j)
+    else
     {
-      if ('a' <= c && c <= 'z')
-        {
-          // TO UPPERCASE !!!
-          //Faster than toUpperCase
-          c -= ('a' - 'A');
-        }
-
-        if (consensus == null || 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;
+      this.ignoreGaps = AAFrequency.PID_GAPS;
     }
-
-
-    public boolean conservationApplied()
+  }
+
+  /**
+   * 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')
     {
-      return conservationColouring;
+      // TO UPPERCASE !!!
+      //Faster than toUpperCase
+      c -= ('a' - 'A');
     }
 
-    public void setConservationInc(int i)
+    if (consensus == null || consensus[j] == null)
     {
-      inc = i;
+      return false;
     }
 
-    public int getConservationInc()
+    if ( ( ( (Integer) consensus[j].get(AAFrequency.MAXCOUNT)).intValue() != -1) &&
+        consensus[j].contains(String.valueOf(c)))
     {
-      return inc;
+      if ( ( (Float) consensus[j].get(ignoreGaps)).floatValue() >= threshold)
+      {
+        return true;
+      }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param consensus DOCUMENT ME!
-     */
-    public void setConsensus(Hashtable [] consensus)
+    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)
     {
-      if(consensus==null)
-        return;
+      return;
+    }
 
-      this.consensus = consensus;
+    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);
+      }
+    }
+
+  }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param s DOCUMENT ME!
+   * @param i DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
 
+  Color applyConservation(Color currentColour, int i)
+  {
 
-    public void setConservation(Conservation cons)
+    if ( (conservation[i] != '*') && (conservation[i] != '+'))
     {
-      if(cons==null)
+      if (jalview.util.Comparison.isGap(conservation[i]))
       {
-        conservationColouring = false;
-        conservation = null;
+        currentColour = Color.white;
       }
       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);
-      }
+        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;
 
-    /**
-    * DOCUMENT ME!
-    *
-    * @param s DOCUMENT ME!
-    * @param i DOCUMENT ME!
-    *
-    * @return DOCUMENT ME!
-    */
-
-   Color applyConservation(Color currentColour, int i)
-   {
-
-     if ((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;
-   }
+        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 17f6a41..62d8d92 100755
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -24,20 +24,21 @@ import java.awt.*;
 
 public class ResidueProperties
 {
-  public static Hashtable scoreMatrices=new Hashtable();
+  public static Hashtable scoreMatrices = new Hashtable();
   //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 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
   {
     aaIndex = new int[255];
-    for(int i=0; i<255; i++)
+    for (int i = 0; i < 255; i++)
+    {
       aaIndex[i] = 23;
+    }
 
     aaIndex['A'] = 0;
     aaIndex['R'] = 1;
@@ -93,7 +94,9 @@ public class ResidueProperties
   {
     nucleotideIndex = new int[255];
     for (int i = 0; i < 255; i++)
+    {
       nucleotideIndex[i] = -1;
+    }
 
     nucleotideIndex['A'] = 0;
     nucleotideIndex['a'] = 0;
@@ -116,7 +119,6 @@ public class ResidueProperties
     nucleotideIndex['N'] = 9;
     nucleotideIndex['n'] = 9;
 
-
     nucleotideName.put("A", "Adenine");
     nucleotideName.put("a", "Adenine");
     nucleotideName.put("G", "Guanine");
@@ -139,7 +141,6 @@ public class ResidueProperties
     nucleotideName.put("n", "Unknown");
   }
 
-
   static
   {
     aa3Hash.put("ALA", new Integer(0));
@@ -165,7 +166,7 @@ public class ResidueProperties
     // IUB Nomenclature for ambiguous peptides
     aa3Hash.put("ASX", new Integer(20)); // "B";
     aa3Hash.put("GLX", new Integer(21)); // X
-    aa3Hash.put("XAA", new Integer(22));// X unknown
+    aa3Hash.put("XAA", new Integer(22)); // X unknown
     aa3Hash.put("-", new Integer(23));
     aa3Hash.put("*", new Integer(23));
     aa3Hash.put(".", new Integer(23));
@@ -605,11 +606,13 @@ public class ResidueProperties
   /**
    * register matrices in list
    */
-  static {
-    scoreMatrices.put("BLOSUM62", new ScoreMatrix("BLOSUM62",BLOSUM62, 0));
-    scoreMatrices.put("PAM250", new ScoreMatrix("PAM250",PAM250, 0));
+  static
+  {
+    scoreMatrices.put("BLOSUM62", new ScoreMatrix("BLOSUM62", BLOSUM62, 0));
+    scoreMatrices.put("PAM250", new ScoreMatrix("PAM250", PAM250, 0));
     scoreMatrices.put("DNA", new ScoreMatrix("DNA", DNA, 1));
   }
+
   public static final Color[] pidColours =
       {
       midBlue, new Color(153, 153, 255),
@@ -839,7 +842,6 @@ public class ResidueProperties
     Phe.addElement("TTT");
   }
 
-
   //Stores residue codes/names and colours and other things
   public static Hashtable propHash = new Hashtable();
   public static Hashtable hydrophobic = new Hashtable();
@@ -1220,10 +1222,13 @@ public class ResidueProperties
     return null;
   }
 
-  public static int[][] getDefaultPeptideMatrix() {
+  public static int[][] getDefaultPeptideMatrix()
+  {
     return ResidueProperties.getBLOSUM62();
   }
-  public static int[][] getDefaultDnaMatrix() {
+
+  public static int[][] getDefaultDnaMatrix()
+  {
     return ResidueProperties.getDNA();
   }
 
@@ -1232,10 +1237,13 @@ public class ResidueProperties
    * @param pwtype
    * @return matrix in scoreMatrices with key pwtype or null
    */
-  public static ScoreMatrix getScoreMatrix(String pwtype) {
-    Object val=scoreMatrices.get(pwtype);
-    if (val!=null)
+  public static ScoreMatrix getScoreMatrix(String pwtype)
+  {
+    Object val = scoreMatrices.get(pwtype);
+    if (val != null)
+    {
       return (ScoreMatrix) val;
+    }
     return null;
   }
 }
diff --git a/src/jalview/schemes/ScoreColourScheme.java b/src/jalview/schemes/ScoreColourScheme.java
index 1c9525c..134ed4c 100755
--- a/src/jalview/schemes/ScoreColourScheme.java
+++ b/src/jalview/schemes/ScoreColourScheme.java
@@ -1,119 +1,121 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 jalview.schemes;
 
 import java.awt.*;
 
-
 /**
  * DOCUMENT ME!
  *
  * @author $author$
  * @version $Revision$
  */
-public class ScoreColourScheme extends ResidueColourScheme
+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)
+  /** 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++)
     {
-        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);
-        }
+      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)
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param s DOCUMENT ME!
+   * @param j DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Color findColour(char c, int j)
+  {
+    if (threshold > 0)
     {
-        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);
+      if (!aboveThreshold(c, j))
+      {
+        return Color.white;
+      }
+    }
 
-        return currentColour;
+    if (jalview.util.Comparison.isGap(c))
+    {
+      return Color.white;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param c DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Color makeColour(float c)
+    Color currentColour = colors[ResidueProperties.aaIndex[c]];
+
+    if (conservationColouring)
     {
-        return new Color(c, (float) 0.0, (float) 1.0 - c);
+      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 03b6778..69a0922 100644
--- a/src/jalview/schemes/ScoreMatrix.java
+++ b/src/jalview/schemes/ScoreMatrix.java
@@ -1,6 +1,7 @@
 package jalview.schemes;
 
-public class ScoreMatrix {
+public class ScoreMatrix
+{
   String name;
   /**
    * reference to integer score matrix
@@ -10,36 +11,48 @@ public class ScoreMatrix {
    * 0 for Protein Score matrix. 1 for dna score matrix
    */
   int type;
-  ScoreMatrix(String name, int[][] matrix, int type) {
-    this.matrix=matrix;
-    this.type=type;
+  ScoreMatrix(String name, int[][] matrix, int type)
+  {
+    this.matrix = matrix;
+    this.type = type;
   }
-  public boolean isDNA() {
-    return type==1;
+
+  public boolean isDNA()
+  {
+    return type == 1;
   }
-  public boolean isProtein() {
-    return type==0;
+
+  public boolean isProtein()
+  {
+    return type == 0;
   }
-  public int[][] getMatrix() {
+
+  public int[][] getMatrix()
+  {
     return matrix;
   }
+
   /**
-   * 
+   *
    * @param A1
    * @param A2
    * @return score for substituting first char in A1 with first char in A2
    */
   public int getPairwiseScore(String A1, String A2)
   {
-    return getPairwiseScore(A1.charAt(0),A2.charAt(0));
+    return getPairwiseScore(A1.charAt(0), A2.charAt(0));
   }
-  public int getPairwiseScore(char c, char d) {
+
+  public int getPairwiseScore(char c, char d)
+  {
     int pog = 0;
 
     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];
     }
diff --git a/src/jalview/schemes/StrandColourScheme.java b/src/jalview/schemes/StrandColourScheme.java
index 4502449..ec57d50 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) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 jalview.schemes;
 
 import java.awt.*;
 
-
 /**
  * DOCUMENT ME!
  *
  * @author $author$
  * @version $Revision$
  */
-public class StrandColourScheme extends ScoreColourScheme
+public class StrandColourScheme
+    extends ScoreColourScheme
 {
-    /**
-     * Creates a new StrandColourScheme object.
-     */
-    public StrandColourScheme()
-    {
-        super(ResidueProperties.strand, ResidueProperties.strandmin,
-            ResidueProperties.strandmax);
-    }
+  /**
+   * 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);
-    }
+  /**
+   * 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 d8627bb..3a5c4da 100755
--- a/src/jalview/schemes/TaylorColourScheme.java
+++ b/src/jalview/schemes/TaylorColourScheme.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
diff --git a/src/jalview/schemes/TurnColourScheme.java b/src/jalview/schemes/TurnColourScheme.java
index a6473b0..2bd779b 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) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 jalview.schemes;
 
 import java.awt.*;
 
-
 /**
  * DOCUMENT ME!
  *
  * @author $author$
  * @version $Revision$
  */
-public class TurnColourScheme extends ScoreColourScheme
+public class TurnColourScheme
+    extends ScoreColourScheme
 {
-    /**
-     * Creates a new TurnColourScheme object.
-     */
-    public TurnColourScheme()
-    {
-        super(ResidueProperties.turn, ResidueProperties.turnmin,
-            ResidueProperties.turnmax);
-    }
+  /**
+   * 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);
-    }
+  /**
+   * 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 00f8f6f..81947b3 100755
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,18 +18,19 @@
  */
 package jalview.schemes;
 
+import java.util.*;
+
 import java.awt.*;
-import java.util.StringTokenizer;
 
 public class UserColourScheme
     extends ResidueColourScheme
 {
-  Color [] lowerCaseColours;
+  Color[] lowerCaseColours;
 
   protected String schemeName;
 
   public UserColourScheme()
-  {  }
+  {}
 
   public UserColourScheme(Color[] newColors)
   {
@@ -40,15 +41,17 @@ public class UserColourScheme
   {
     Color col = getColourFromString(colour);
 
-    if(col==null)
+    if (col == null)
     {
-      System.out.println("Unknown colour!! "+colour);
+      System.out.println("Unknown colour!! " + colour);
       col = createColourFromName(colour);
     }
 
     colors = new Color[24];
-    for(int i=0; i<24; i++)
+    for (int i = 0; i < 24; i++)
+    {
       colors[i] = col;
+    }
   }
 
   public Color[] getColours()
@@ -85,7 +88,9 @@ public class UserColourScheme
     {}
 
     if (col == null)
+    {
       col = ColourSchemeProperty.getAWTColorFromName(colour);
+    }
 
     if (col == null)
     {
@@ -119,7 +124,9 @@ public class UserColourScheme
     start = end;
     end += lsize / 3;
     if (end > lsize)
+    {
       end = lsize;
+    }
 
     g = Math.abs(name.substring(start, end).hashCode() + rgbOffset) % 210 + 20;
 
@@ -134,8 +141,9 @@ public class UserColourScheme
   {
     StringTokenizer st = new StringTokenizer(paramValue, ";");
     StringTokenizer st2;
-    String token=null, colour, residues;
-    try{
+    String token = null, colour, residues;
+    try
+    {
       while (st.hasMoreElements())
       {
         token = st.nextToken().trim();
@@ -147,72 +155,85 @@ public class UserColourScheme
         {
           token = st2.nextToken();
 
-          if (ResidueProperties.aaIndex[token.charAt(0)]==-1)
+          if (ResidueProperties.aaIndex[token.charAt(0)] == -1)
+          {
             continue;
+          }
 
           int colIndex = ResidueProperties.aaIndex[token.charAt(0)];
 
-          if(token.equalsIgnoreCase("lowerCase"))
+          if (token.equalsIgnoreCase("lowerCase"))
           {
             if (lowerCaseColours == null)
+            {
               lowerCaseColours = new Color[23];
+            }
             for (int i = 0; i < 23; i++)
+            {
               if (lowerCaseColours[i] == null)
+              {
                 lowerCaseColours[i] = getColourFromString(colour);
+              }
+            }
 
-              continue;
+            continue;
           }
 
-          if(token.equals(token.toLowerCase()))
+          if (token.equals(token.toLowerCase()))
           {
-            if(lowerCaseColours==null)
+            if (lowerCaseColours == null)
             {
               lowerCaseColours = new Color[23];
             }
             lowerCaseColours[colIndex] = getColourFromString(colour);
           }
           else
+          {
             colors[colIndex] = getColourFromString(colour);
+          }
         }
       }
     }
-    catch(Exception ex)
-  {
-    System.out.println("Error parsing userDefinedColours:\n"
-                       +token+"\n"+ex);
-  }
+    catch (Exception ex)
+    {
+      System.out.println("Error parsing userDefinedColours:\n"
+                         + token + "\n" + ex);
+    }
 
   }
 
-
-
   public Color findColour(char c, int j)
   {
-      Color currentColour;
-      int index = ResidueProperties.aaIndex[c];
+    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')
       {
-        if(lowerCaseColours!=null && 'a' <= c && c <= 'z')
-          currentColour = lowerCaseColours[index];
-        else
-          currentColour = colors[index];
+        currentColour = lowerCaseColours[index];
       }
       else
       {
-          currentColour = Color.white;
+        currentColour = colors[index];
       }
+    }
+    else
+    {
+      currentColour = Color.white;
+    }
 
-      if(conservationColouring)
-       currentColour =  applyConservation(currentColour, j);
-
+    if (conservationColouring)
+    {
+      currentColour = applyConservation(currentColour, j);
+    }
 
-      return currentColour;
-   }
+    return currentColour;
+  }
 
-   public void setLowerCaseColours(Color [] lcolours)
-   {
-     lowerCaseColours = lcolours;
-   }
+  public void setLowerCaseColours(Color[] lcolours)
+  {
+    lowerCaseColours = lcolours;
+  }
 
 }
diff --git a/src/jalview/schemes/ZappoColourScheme.java b/src/jalview/schemes/ZappoColourScheme.java
index 92a4dc1..0d1854c 100755
--- a/src/jalview/schemes/ZappoColourScheme.java
+++ b/src/jalview/schemes/ZappoColourScheme.java
@@ -1,37 +1,37 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 jalview.schemes;
 
-
 /**
  * DOCUMENT ME!
  *
  * @author $author$
  * @version $Revision$
  */
-public class ZappoColourScheme extends ResidueColourScheme
+public class ZappoColourScheme
+    extends ResidueColourScheme
 {
-    /**
-     * Creates a new ZappoColourScheme object.
-     */
-    public ZappoColourScheme()
-    {
-        super(ResidueProperties.color, 0);
-    }
+  /**
+   * Creates a new ZappoColourScheme object.
+   */
+  public ZappoColourScheme()
+  {
+    super(ResidueProperties.color, 0);
+  }
 }
diff --git a/src/jalview/util/BrowserLauncher.java b/src/jalview/util/BrowserLauncher.java
index 3c6e48a..2b8a4bd 100755
--- a/src/jalview/util/BrowserLauncher.java
+++ b/src/jalview/util/BrowserLauncher.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -695,13 +695,16 @@ public class BrowserLauncher
 
     return browser;
   }
+
   /**
    * used to ensure that browser is up-to-date after a configuration
    * change (Unix DEFAULT_BROWSER property change).
    */
-  public static void resetBrowser() {
+  public static void resetBrowser()
+  {
     browser = null;
   }
+
   /**
    * Attempts to open the default web browser to the given URL.
    * @param url The URL to open
diff --git a/src/jalview/util/Comparison.java b/src/jalview/util/Comparison.java
index 50472a5..67a668a 100755
--- a/src/jalview/util/Comparison.java
+++ b/src/jalview/util/Comparison.java
@@ -1,26 +1,25 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 jalview.util;
 
 import jalview.datamodel.*;
 
-
 /**
  * DOCUMENT ME!
  *
@@ -124,7 +123,7 @@ public class Comparison
   static final int caseShift = 'a' - 'A';
 
   // Another pid with region specification
-  public final static  float PID(String seq1, String seq2, int start, int end)
+  public final static float PID(String seq1, String seq2, int start, int end)
   {
 
     int s1len = seq1.length();
@@ -142,17 +141,15 @@ public class Comparison
       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) ;
+      chr1 = seq1.charAt(i);
 
-      chr2 =  seq2.charAt(i) ;
+      chr2 = seq2.charAt(i);
 
       if ('a' <= chr1 && chr1 <= 'z')
       {
@@ -167,10 +164,9 @@ public class Comparison
         chr2 -= caseShift;
       }
 
-
-      if (chr1!=chr2 && !isGap(chr1) && !isGap(chr2) )
+      if (chr1 != chr2 && !isGap(chr1) && !isGap(chr2))
       {
-          bad++;
+        bad++;
       }
     }
 
@@ -189,7 +185,7 @@ public class Comparison
     return (c == '-' || c == '.' || c == ' ') ? true : false;
   }
 
-  public static final boolean isNucleotide(SequenceI [] seqs)
+  public static final boolean isNucleotide(SequenceI[] seqs)
   {
     int i = 0, iSize = seqs.length, j, jSize;
     float nt = 0, aa = 0;
@@ -201,11 +197,15 @@ public class Comparison
       {
         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)))
+        }
+        else if (!jalview.util.Comparison.isGap(seqs[i].getCharAt(j)))
         {
           aa++;
         }
@@ -214,9 +214,13 @@ public class Comparison
     }
 
     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 5aed125..381ed70 100755
--- a/src/jalview/util/DBRefUtils.java
+++ b/src/jalview/util/DBRefUtils.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -22,45 +22,55 @@ import java.util.*;
 
 import jalview.datamodel.*;
 
-
 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
-     * @return Vector
-     */
-    public static DBRefEntry [] selectRefs(DBRefEntry [] dbrefs, String[] sources) {
-      if (dbrefs==null)
-        return null;
-      if (sources==null)
-        return dbrefs;
-      Hashtable srcs = new Hashtable();
-      Vector res=new Vector();
+  /**
+   * 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
+   * @return Vector
+   */
+  public static DBRefEntry[] selectRefs(DBRefEntry[] dbrefs, String[] sources)
+  {
+    if (dbrefs == null)
+    {
+      return null;
+    }
+    if (sources == null)
+    {
+      return dbrefs;
+    }
+    Hashtable srcs = new Hashtable();
+    Vector res = new Vector();
 
-      for (int i=0; i<sources.length; i++)
-        srcs.put(new String(sources[i]), new Integer(i));
-      for (int i = 0, j = dbrefs.length; i < j; i++)
-        {
-          if (srcs.containsKey(dbrefs[i].getSource()))
-            res.add(dbrefs[i]);
-        }
+    for (int i = 0; i < sources.length; i++)
+    {
+      srcs.put(new String(sources[i]), new Integer(i));
+    }
+    for (int i = 0, j = dbrefs.length; i < j; i++)
+    {
+      if (srcs.containsKey(dbrefs[i].getSource()))
+      {
+        res.add(dbrefs[i]);
+      }
+    }
 
-      if (res.size()>0)
+    if (res.size() > 0)
+    {
+      DBRefEntry[] reply = new DBRefEntry[res.size()];
+      for (int i = 0; i < res.size(); i++)
       {
-        DBRefEntry [] reply = new DBRefEntry[res.size()];
-        for(int i=0; i<res.size(); i++)
-          reply[i] = (DBRefEntry)res.elementAt(i);
-        return reply;
+        reply[i] = (DBRefEntry) res.elementAt(i);
       }
-      res = null;
-      // there are probable  memory leaks in the hashtable!
-      return null;
+      return reply;
     }
+    res = null;
+    // there are probable  memory leaks in the hashtable!
+    return null;
+  }
 
   /**
    * isDasCoordinateSystem
@@ -73,7 +83,7 @@ public class DBRefUtils
   public static boolean isDasCoordinateSystem(String string,
                                               DBRefEntry dBRefEntry)
   {
-    if (DasCoordinateSystemsLookup==null)
+    if (DasCoordinateSystemsLookup == null)
     { // Initialise
       DasCoordinateSystemsLookup = new Hashtable();
       DasCoordinateSystemsLookup.put("pdbresnum",
@@ -82,9 +92,12 @@ public class DBRefUtils
                                      jalview.datamodel.DBRefSource.UNIPROT);
     }
 
-    String coordsys = (String) DasCoordinateSystemsLookup.get(string.toLowerCase());
-    if (coordsys!=null)
+    String coordsys = (String) DasCoordinateSystemsLookup.get(string.
+        toLowerCase());
+    if (coordsys != null)
+    {
       return coordsys.equals(dBRefEntry.getSource());
+    }
     return false;
   }
 }
diff --git a/src/jalview/util/Format.java b/src/jalview/util/Format.java
index b564706..7c9b585 100755
--- a/src/jalview/util/Format.java
+++ b/src/jalview/util/Format.java
@@ -27,8 +27,6 @@
  */
 package jalview.util;
 
-
-
 /**
  * DOCUMENT ME!
  *
@@ -37,823 +35,833 @@ package jalview.util;
  */
 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--;
-            }
-
+  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;
+          }
         }
-
-        while (parse_state == 2)
+        else
         {
-            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;
-            }
+          throw new java.lang.IllegalArgumentException();
         }
+      }
+      else
+      {
+        pre = pre + s.charAt(i);
+      }
 
-        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;
-            }
-        }
+      i++;
+    }
 
-        if (parse_state == 4)
-        {
-            if (i >= length)
-            {
-                parse_state = 5;
-            }
-            else
-            {
-                fmt = s.charAt(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++;
+    }
 
-            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;
+      }
+    }
 
-        if (i < length)
-        {
-            post = s.substring(i, length);
-        }
+    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;
+      }
     }
 
-    /**
-     * 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;
-        }
+    if (parse_state == 4)
+    {
+      if (i >= length)
+      {
+        parse_state = 5;
+      }
+      else
+      {
+        fmt = s.charAt(i);
+      }
+
+      i++;
+    }
 
-        g = Integer.toHexString(color.getGreen());
+    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;
+    }
 
-        if (g.length() < 2)
-        {
-            g = "0" + g;
-        }
+    g = Integer.toHexString(color.getGreen());
 
-        b = Integer.toHexString(color.getBlue());
+    if (g.length() < 2)
+    {
+      g = "0" + g;
+    }
 
-        if (b.length() < 2)
-        {
-            b = "0" + b;
-        }
+    b = Integer.toHexString(color.getBlue());
 
-        return r + g + b;
+    if (b.length() < 2)
+    {
+      b = "0" + 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)
+    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)))
     {
-        s.print(new Format(fmt).form(x));
+      i++;
     }
 
-    /**
-    * 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)
+    if ( (i < s.length()) && (s.charAt(i) == '0'))
     {
-        s.print(new Format(fmt).form(x));
+      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);
+      }
     }
-
-    /**
-    * 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)
+    else
     {
-        s.print(new Format(fmt).form(x));
+      return parseLong(s, 10);
     }
-
-    /**
-    * 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)
+  }
+
+  /**
+   * 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)))
     {
-        s.print(new Format(fmt).form(x));
+      i++;
     }
 
-    /**
-    * 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)
+    if ( (i < s.length()) && (s.charAt(i) == '-'))
     {
-        return (int) atol(s);
+      sign = -1;
+      i++;
     }
-
-    /**
-    * 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)
+    else if ( (i < s.length()) && (s.charAt(i) == '+'))
     {
-        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);
-        }
+      i++;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param s DOCUMENT ME!
-     * @param base DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    private static long parseLong(String s, int base)
+    while (i < s.length())
     {
-        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++;
-        }
-
+      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++;
     }
 
-    /**
-    * Converts a string of digits to an double
-    * @param s a string
-    */
-    public static double atof(String s)
+    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)))
     {
-        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;
+      i++;
     }
 
-    /**
-    * 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)
+    if ( (i < s.length()) && (s.charAt(i) == '-'))
     {
-        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));
+      sign = -1;
+      i++;
+    }
+    else if ( (i < s.length()) && (s.charAt(i) == '+'))
+    {
+      i++;
     }
 
-    /**
-    * 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)
+    while (i < s.length())
     {
-        String r;
-        int s = 0;
+      char ch = s.charAt(i);
 
-        if ((fmt == 'd') || (fmt == 'i'))
-        {
-            if (x < 0)
-            {
-                r = ("" + x).substring(1);
-                s = -1;
-            }
-            else
-            {
-                r = "" + x;
-                s = 1;
-            }
-        }
-        else if (fmt == 'o')
+      if ( ('0' <= ch) && (ch <= '9'))
+      {
+        if (state == 0)
         {
-            r = convert(x, 3, 7, "01234567");
+          r = ( (r * 10) + ch) - '0';
         }
-        else if (fmt == 'x')
+        else if (state == 1)
         {
-            r = convert(x, 4, 15, "0123456789abcdef");
+          p = p / 10;
+          r = r + (p * (ch - '0'));
         }
-        else if (fmt == 'X')
+      }
+      else if (ch == '.')
+      {
+        if (state == 0)
         {
-            r = convert(x, 4, 15, "0123456789ABCDEF");
+          state = 1;
         }
         else
         {
-            throw new java.lang.IllegalArgumentException();
+          return sign * r;
         }
+      }
+      else if ( (ch == 'e') || (ch == 'E'))
+      {
+        long e = (int) parseLong(s.substring(i + 1), 10);
 
-        return pad(sign(s, r));
-    }
+        return sign * r * Math.pow(10, e);
+      }
+      else
+      {
+        return sign * 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();
-        }
+      i++;
+    }
 
-        String r = "" + c;
+    return sign * r;
+  }
 
-        return pad(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;
 
-    /**
-    * 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 (precision < 0)
     {
-        if (fmt != 's')
-        {
-            throw new java.lang.IllegalArgumentException();
-        }
+      precision = 6;
+    }
 
-        if (precision >= 0)
-        {
-            s = s.substring(0, precision);
-        }
+    int s = 1;
 
-        return pad(s);
+    if (x < 0)
+    {
+      x = -x;
+      s = -1;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param c DOCUMENT ME!
-     * @param n DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    private static String repeat(char c, int n)
+    if (fmt == 'f')
     {
-        if (n <= 0)
-        {
-            return "";
-        }
+      r = fixed_format(x);
+    }
+    else if ( (fmt == 'e') || (fmt == 'E') || (fmt == 'g') || (fmt == 'G'))
+    {
+      r = exp_format(x);
+    }
+    else
+    {
+      throw new java.lang.IllegalArgumentException();
+    }
 
-        StringBuffer s = new StringBuffer(n);
+    return pad(sign(s, r));
+  }
 
-        for (int i = 0; i < n; i++)
-            s.append(c);
+  /**
+   * 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;
 
-        return s.toString();
+    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();
     }
 
-    /**
-     * 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)
+    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')
     {
-        if (x == 0)
-        {
-            return "0";
-        }
+      throw new java.lang.IllegalArgumentException();
+    }
 
-        String r = "";
+    String r = "" + c;
 
-        while (x != 0)
-        {
-            r = d.charAt((int) (x & m)) + r;
-            x = x >>> n;
-        }
+    return pad(r);
+  }
 
-        return 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();
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param r DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    private String pad(String r)
+    if (precision >= 0)
     {
-        String p = repeat(' ', width - r.length());
-
-        if (left_align)
-        {
-            return pre + r + p + post;
-        }
-        else
-        {
-            return pre + p + r + post;
-        }
+      s = s.substring(0, precision);
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param s DOCUMENT ME!
-     * @param r DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    private String sign(int s, String r)
+    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)
     {
-        String p = "";
+      return "";
+    }
 
-        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";
-            }
-        }
+    StringBuffer s = new StringBuffer(n);
 
-        int w = 0;
+    for (int i = 0; i < n; i++)
+    {
+      s.append(c);
+    }
 
-        if (leading_zeroes)
-        {
-            w = width;
-        }
-        else if (((fmt == 'd') || (fmt == 'i') || (fmt == 'x') || (fmt == 'X') ||
-                (fmt == 'o')) && (precision > 0))
-        {
-            w = precision;
-        }
+    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";
+    }
 
-        return p + repeat('0', w - p.length() - r.length()) + r;
+    String r = "";
+
+    while (x != 0)
+    {
+      r = d.charAt( (int) (x & m)) + r;
+      x = x >>> n;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param d DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    private String fixed_format(double d)
+    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
     {
-        boolean removeTrailing = ((fmt == 'G') || (fmt == 'g')) && !alternate;
+      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";
+      }
+    }
 
-        // remove trailing zeroes and decimal point
-        if (d > 0x7FFFFFFFFFFFFFFFL)
-        {
-            return exp_format(d);
-        }
+    int w = 0;
 
-        if (precision == 0)
-        {
-            return (long) (d + 0.5) + (removeTrailing ? "" : ".");
-        }
+    if (leading_zeroes)
+    {
+      w = width;
+    }
+    else if ( ( (fmt == 'd') || (fmt == 'i') || (fmt == 'x') || (fmt == 'X') ||
+               (fmt == 'o')) && (precision > 0))
+    {
+      w = precision;
+    }
 
-        long whole = (long) d;
-        double fr = d - whole; // fractional part
+    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 ((fr >= 1) || (fr < 0))
-        {
-            return exp_format(d);
-        }
+    if (precision == 0)
+    {
+      return (long) (d + 0.5) + (removeTrailing ? "" : ".");
+    }
 
-        double factor = 1;
-        String leading_zeroes = "";
+    long whole = (long) d;
+    double fr = d - whole; // fractional part
 
-        for (int i = 1; (i <= precision) && (factor <= 0x7FFFFFFFFFFFFFFFL);
-                i++)
-        {
-            factor *= 10;
-            leading_zeroes = leading_zeroes + "0";
-        }
+    if ( (fr >= 1) || (fr < 0))
+    {
+      return exp_format(d);
+    }
 
-        long l = (long) ((factor * fr) + 0.5);
+    double factor = 1;
+    String leading_zeroes = "";
 
-        if (l >= factor)
-        {
-            l = 0;
-            whole++;
-        }
+    for (int i = 1; (i <= precision) && (factor <= 0x7FFFFFFFFFFFFFFFL);
+         i++)
+    {
+      factor *= 10;
+      leading_zeroes = leading_zeroes + "0";
+    }
 
-        // CSH 10-25-97
-        String z = leading_zeroes + l;
-        z = "." + z.substring(z.length() - precision, z.length());
+    long l = (long) ( (factor * fr) + 0.5);
 
-        if (removeTrailing)
-        {
-            int t = z.length() - 1;
+    if (l >= factor)
+    {
+      l = 0;
+      whole++;
+    }
 
-            while ((t >= 0) && (z.charAt(t) == '0'))
-                t--;
+    // CSH 10-25-97
+    String z = leading_zeroes + l;
+    z = "." + z.substring(z.length() - precision, z.length());
 
-            if ((t >= 0) && (z.charAt(t) == '.'))
-            {
-                t--;
-            }
+    if (removeTrailing)
+    {
+      int t = z.length() - 1;
 
-            z = z.substring(0, t + 1);
-        }
+      while ( (t >= 0) && (z.charAt(t) == '0'))
+      {
+        t--;
+      }
 
-        return whole + z;
+      if ( (t >= 0) && (z.charAt(t) == '.'))
+      {
+        t--;
+      }
+
+      z = z.substring(0, t + 1);
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param d DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    private String exp_format(double d)
+    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)
     {
-        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);
-        }
+      while (dd > 10)
+      {
+        e++;
+        factor /= 10;
+        dd = dd / 10;
+      }
+
+      while (dd < 1)
+      {
+        e--;
+        factor *= 10;
+        dd = dd * 10;
+      }
+    }
 
-        d = d * factor;
-        f = f + fixed_format(d);
+    if ( ( (fmt == 'g') || (fmt == 'G')) && (e >= -4) && (e < precision))
+    {
+      return fixed_format(d);
+    }
 
-        if ((fmt == 'e') || (fmt == 'g'))
-        {
-            f = f + "e";
-        }
-        else
-        {
-            f = f + "E";
-        }
+    d = d * factor;
+    f = f + fixed_format(d);
 
-        String p = "000";
+    if ( (fmt == 'e') || (fmt == 'g'))
+    {
+      f = f + "e";
+    }
+    else
+    {
+      f = f + "E";
+    }
 
-        if (e >= 0)
-        {
-            f = f + "+";
-            p = p + e;
-        }
-        else
-        {
-            f = f + "-";
-            p = p + (-e);
-        }
+    String p = "000";
 
-        return f + p.substring(p.length() - 3, p.length());
+    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 9323d0d..632c2ad 100755
--- a/src/jalview/util/ImageMaker.java
+++ b/src/jalview/util/ImageMaker.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,17 +18,15 @@
  */
 package jalview.util;
 
-import java.awt.RenderingHints;
-import javax.imageio.ImageIO;
-import org.jibble.epsgraphics.EpsGraphics2D;
-import jalview.gui.EPSOptions;
-import java.awt.Graphics2D;
 import java.io.*;
-import java.awt.image.BufferedImage;
-import java.awt.Graphics;
-import jalview.io.*;
+import javax.imageio.*;
+
 import java.awt.*;
+import java.awt.image.*;
 
+import org.jibble.epsgraphics.*;
+import jalview.gui.*;
+import jalview.io.*;
 
 public class ImageMaker
 {
@@ -42,7 +40,7 @@ public class ImageMaker
   BufferedImage bi;
 
   public ImageMaker(Component parent, int type, String title,
-                           int width, int height, File file, String EPStitle)
+                    int width, int height, File file, String EPStitle)
   {
     this.type = type;
 
@@ -66,16 +64,20 @@ public class ImageMaker
       }
     }
 
-    if(file!=null)
+    if (file != null)
     {
       try
       {
         out = new FileOutputStream(file);
 
         if (type == EPS)
+        {
           setupEPS(width, height, EPStitle);
+        }
         else
+        {
           setupPNG(width, height);
+        }
       }
       catch (Exception ex)
       {
@@ -90,21 +92,21 @@ public class ImageMaker
     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);
+    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)
+    try
+    {
+      switch (type)
       {
         case EPS:
           pg.flush();
@@ -118,7 +120,7 @@ public class ImageMaker
     }
     catch (Exception ex)
     {
-        ex.printStackTrace();
+      ex.printStackTrace();
     }
   }
 
@@ -140,7 +142,9 @@ public class ImageMaker
       renderStyle = eps.getValue();
 
       if (renderStyle == null || eps.cancelled)
+      {
         return;
+      }
     }
 
     if (renderStyle.equalsIgnoreCase("text"))
@@ -148,9 +152,10 @@ public class ImageMaker
       accurateText = false;
     }
 
-    try   {
+    try
+    {
       pg = new EpsGraphics2D(title, out, 0, 0, width,
-                                           height);
+                             height);
       Graphics2D ig2 = (Graphics2D) pg;
       ig2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
                            RenderingHints.VALUE_ANTIALIAS_ON);
@@ -159,10 +164,10 @@ public class ImageMaker
 
       graphics = pg;
     }
-    catch (Exception ex) {  }
+    catch (Exception ex)
+    {}
   }
 
-
   JalviewFileChooser getPNGChooser()
   {
     return new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
diff --git a/src/jalview/util/MapList.java b/src/jalview/util/MapList.java
index defa670..215ece9 100644
--- a/src/jalview/util/MapList.java
+++ b/src/jalview/util/MapList.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -30,110 +30,151 @@ import java.util.*;
  */
 public class MapList
 {
-    public Vector fromShifts;
-    public Vector toShifts;
-    int fromRatio; // number of steps in fromShifts to one toRatio unit
-    int toRatio; // number of steps in toShifts to one fromRatio
+  public Vector fromShifts;
+  public Vector toShifts;
+  int fromRatio; // number of steps in fromShifts to one toRatio unit
+  int toRatio; // number of steps in toShifts to one fromRatio
   public MapList(int from[], int to[], int fromRatio, int toRatio)
   {
     fromShifts = new Vector();
-    for (int i=0;i<from.length; i+=2)
-        fromShifts.add(new int[] { from[i], from[i+1]});
+    for (int i = 0; i < from.length; i += 2)
+    {
+      fromShifts.add(new int[]
+                     {from[i], from[i + 1]});
+    }
     toShifts = new Vector();
-    for (int i=0;i<to.length; i+=2)
-        toShifts.add(new int[] { to[i], to[i+1]});
-    this.fromRatio=fromRatio;
-    this.toRatio=toRatio;
+    for (int i = 0; i < to.length; i += 2)
+    {
+      toShifts.add(new int[]
+                   {to[i], to[i + 1]});
+    }
+    this.fromRatio = fromRatio;
+    this.toRatio = toRatio;
   }
+
   /**
    * get all mapped positions from 'from' to 'to'
    * @return int[][] { int[] { fromStart, fromFinish, toStart, toFinish }, int [fromFinish-fromStart+2] { toStart..toFinish mappings}}
    */
-  public int[][] makeFromMap() {
-      return posMap(fromShifts, fromRatio, toShifts, toRatio);
+  public int[][] makeFromMap()
+  {
+    return posMap(fromShifts, fromRatio, toShifts, toRatio);
   }
+
   /**
    * get all mapped positions from 'to' to 'from'
    * @return int[to position]=position mapped in from
    */
-  public int[][] makeToMap() {
-      return posMap(toShifts,toRatio, fromShifts, fromRatio);
+  public int[][] makeToMap()
+  {
+    return posMap(toShifts, toRatio, fromShifts, fromRatio);
   }
+
   /**
    * construct an int map for intervals in intVals
    * @param intVals
    * @return int[] { from, to pos in range }, int[range.to-range.from+1] returning mapped position
    */
-  private int[][] posMap(Vector intVals, int ratio, Vector toIntVals, int toRatio) {
-      Iterator iv = intVals.iterator();
-      if (!iv.hasNext())
-          return null;
-      int[] intv=(int[]) iv.next();
-      int from=intv[0],to=intv[1];
-      if (from>to) {
-          from = intv[1];
-          to=intv[0];
+  private int[][] posMap(Vector intVals, int ratio, Vector toIntVals,
+                         int toRatio)
+  {
+    Iterator iv = intVals.iterator();
+    if (!iv.hasNext())
+    {
+      return null;
+    }
+    int[] intv = (int[]) iv.next();
+    int from = intv[0], to = intv[1];
+    if (from > to)
+    {
+      from = intv[1];
+      to = intv[0];
+    }
+    while (iv.hasNext())
+    {
+      intv = (int[]) iv.next();
+      if (intv[0] < from)
+      {
+        from = intv[0];
+      }
+      if (intv[1] < from)
+      {
+        from = intv[1];
+      }
+      if (intv[0] > to)
+      {
+        to = intv[0];
       }
-      while (iv.hasNext()) {
-          intv = (int[]) iv.next();
-          if (intv[0]<from)
-              from=intv[0];
-          if (intv[1]<from)
-              from=intv[1];
-          if (intv[0]>to)
-              to=intv[0];
-          if (intv[1]>to)
-              to=intv[1];
+      if (intv[1] > to)
+      {
+        to = intv[1];
       }
-      int tF=0,tT=0;
-      int mp[][] = new int[to-from+2][];
-      for (int i=0;i<mp.length; i++) {
-          int[] m = shift(i+from,intVals,ratio,toIntVals, toRatio);
-          if (m!=null) {
-              if (i==0) {
-                  tF=tT=m[0];
-              } else {
-                  if (m[0]<tF) {
-                      tF=m[0];
-                  }
-                  if (m[0]>tT) {
-                      tT=m[0];
-                  }
-              }
+    }
+    int tF = 0, tT = 0;
+    int mp[][] = new int[to - from + 2][];
+    for (int i = 0; i < mp.length; i++)
+    {
+      int[] m = shift(i + from, intVals, ratio, toIntVals, toRatio);
+      if (m != null)
+      {
+        if (i == 0)
+        {
+          tF = tT = m[0];
+        }
+        else
+        {
+          if (m[0] < tF)
+          {
+            tF = m[0];
           }
-          mp[i] = m;
+          if (m[0] > tT)
+          {
+            tT = m[0];
+          }
+        }
       }
-      int[][] map=new int[][] { new int[]{from, to, tF, tT}, new int[to-from+2]};
+      mp[i] = m;
+    }
+    int[][] map = new int[][]
+        {
+        new int[]
+        {
+        from, to, tF, tT}, new int[to - from + 2]};
 
-      map[0][2] = tF;
-      map[0][3] = tT;
-      
-      for (int i=0;i<mp.length; i++) {
-          if (mp[i]!=null) {
-              map[1][i] = mp[i][0]-tF;
-          } else {
-              map[1][i] = -1; // indicates an out of range mapping
-          }
+    map[0][2] = tF;
+    map[0][3] = tT;
+
+    for (int i = 0; i < mp.length; i++)
+    {
+      if (mp[i] != null)
+      {
+        map[1][i] = mp[i][0] - tF;
+      }
+      else
+      {
+        map[1][i] = -1; // indicates an out of range mapping
       }
-      return map;
+    }
+    return map;
   }
+
   /**
    * addShift
    * @param pos start position for shift (in original reference frame)
    * @param shift length of shift
    *
-  public void addShift(int pos, int 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);
     else
       rshift[1]+=shift;
-  }
-*/
+     }
+   */
   /**
    * shift from pos to To(pos)
    *
@@ -142,7 +183,7 @@ public class MapList
    */
   public int[] shiftFrom(int pos)
   {
-      return shift(pos, fromShifts, fromRatio, toShifts, toRatio);
+    return shift(pos, fromShifts, fromRatio, toShifts, toRatio);
   }
 
   /**
@@ -150,131 +191,205 @@ public class MapList
    * @param pos (in To)
    * @return shifted position in From, frameshift in To
    */
-  public int[] shiftTo(int pos) {
-      return shift(pos, toShifts, toRatio, fromShifts, fromRatio);
+  public int[] shiftTo(int pos)
+  {
+    return shift(pos, toShifts, toRatio, fromShifts, fromRatio);
   }
+
   /**
-   * 
+   *
    * @param fromShifts
    * @param fromRatio
    * @param toShifts
    * @param toRatio
    * @return
    */
-  private int[] shift(int pos, Vector fromShifts, int fromRatio, Vector toShifts, int toRatio) {
-      int[] fromCount = countPos(fromShifts.iterator(), pos);
-      if (fromCount==null)
-          return null;
-      int fromRemainder=(fromCount[0]-1) % fromRatio;
-      int toCount = 1+(((fromCount[0]-1) / fromRatio) * toRatio);
-      int[] toPos = countToPos(toShifts.iterator(), toCount);
-      if (toPos==null)
-          return null; // throw new Error("Bad Mapping!");
-      //System.out.println(fromCount[0]+" "+fromCount[1]+" "+toCount);
-      return new int[] {toPos[0], fromRemainder};
+  private int[] shift(int pos, Vector fromShifts, int fromRatio,
+                      Vector toShifts, int toRatio)
+  {
+    int[] fromCount = countPos(fromShifts.iterator(), pos);
+    if (fromCount == null)
+    {
+      return null;
+    }
+    int fromRemainder = (fromCount[0] - 1) % fromRatio;
+    int toCount = 1 + ( ( (fromCount[0] - 1) / fromRatio) * toRatio);
+    int[] toPos = countToPos(toShifts.iterator(), toCount);
+    if (toPos == null)
+    {
+      return null; // throw new Error("Bad Mapping!");
+    }
+    //System.out.println(fromCount[0]+" "+fromCount[1]+" "+toCount);
+    return new int[]
+        {
+        toPos[0], fromRemainder};
   }
+
   /**
    * count how many positions pos is along the series of intervals.
    * @param intVals
    * @param pos
    * @return number of positions or null if pos is not within intervals
    */
-  private int[] countPos(Iterator intVals, int pos) {
-      int count=0,intv[];
-      while (intVals.hasNext()) {
-          intv = (int[])intVals.next();
-          if (intv[0] <= intv[1]) {
-              if (pos>=intv[0] && pos<=intv[1]) {
-                  return new int[] { count+pos-intv[0]+1, +1 };
-              } else {
-                  count+=intv[1]-intv[0]+1;
-              }
-          } else {
-              if (pos>=intv[1] && pos<=intv[0]) {
-                  return new int[] { count+intv[0]-pos+1, -1 };
-              } else {
-                  count+=intv[0]-intv[1]+1;
-              }
-          }
+  private int[] countPos(Iterator intVals, int pos)
+  {
+    int count = 0, intv[];
+    while (intVals.hasNext())
+    {
+      intv = (int[]) intVals.next();
+      if (intv[0] <= intv[1])
+      {
+        if (pos >= intv[0] && pos <= intv[1])
+        {
+          return new int[]
+              {
+              count + pos - intv[0] + 1, +1};
+        }
+        else
+        {
+          count += intv[1] - intv[0] + 1;
+        }
       }
-      return null;
+      else
+      {
+        if (pos >= intv[1] && pos <= intv[0])
+        {
+          return new int[]
+              {
+              count + intv[0] - pos + 1, -1};
+        }
+        else
+        {
+          count += intv[0] - intv[1] + 1;
+        }
+      }
+    }
+    return null;
   }
+
   /**
    * count out pos positions into a series of intervals and return the position
    * @param intVals
    * @param pos
    * @return position pos in interval set
    */
-  private int[] countToPos(Iterator intVals, int pos) {
-      int count=0,diff=0,intv[]={0,0};
-      while (intVals.hasNext()) {
-          intv = (int[])intVals.next();
-          diff = intv[1]-intv[0];
-          if (diff>=0) {
-              if (pos<=count+1+diff) {
-                  return new int[] { pos-count-1+intv[0],+1 };
-              } else {
-                  count+=1+diff;
-              }
-          } else {
-              if (pos<=count+1-diff) {
-                  return new int[] { intv[0]-(pos-count-1),-1 };
-              } else {
-                  count+=1-diff;
-              }
-          }
+  private int[] countToPos(Iterator intVals, int pos)
+  {
+    int count = 0, diff = 0, intv[] =
+        {
+        0, 0};
+    while (intVals.hasNext())
+    {
+      intv = (int[]) intVals.next();
+      diff = intv[1] - intv[0];
+      if (diff >= 0)
+      {
+        if (pos <= count + 1 + diff)
+        {
+          return new int[]
+              {
+              pos - count - 1 + intv[0], +1};
+        }
+        else
+        {
+          count += 1 + diff;
+        }
       }
-      return null;//(diff<0) ? (intv[1]-1) : (intv[0]+1);
+      else
+      {
+        if (pos <= count + 1 - diff)
+        {
+          return new int[]
+              {
+              intv[0] - (pos - count - 1), -1};
+        }
+        else
+        {
+          count += 1 - diff;
+        }
+      }
+    }
+    return null; //(diff<0) ? (intv[1]-1) : (intv[0]+1);
   }
-  public static void testMap(MapList ml, int fromS,int fromE) {
-      for (int from=1; from<=25; from++) {
-          int[] too=ml.shiftFrom(from);
-          System.out.print("ShiftFrom("+from+")==");
-          if (too==null)
-              System.out.print("NaN\n");
-          else {
-              System.out.print(too[0]+" % "+too[1]);
-              System.out.print("\t+--+\t");
-              int[] toofrom=ml.shiftTo(too[0]);
-              if (toofrom!=null) {
-                  if (toofrom[0]!=from)
-                      System.err.println("Mapping not reflexive:"+from+" "+too[0]+"->"+toofrom[0]);
-                  System.out.println("ShiftTo("+too[0]+")=="+toofrom[0]+" % "+toofrom[1]);
-              } else
-                  System.out.println("ShiftTo("+too[0]+")=="+"NaN! - not Bijective Mapping!");
-          }
+
+  public static void testMap(MapList ml, int fromS, int fromE)
+  {
+    for (int from = 1; from <= 25; from++)
+    {
+      int[] too = ml.shiftFrom(from);
+      System.out.print("ShiftFrom(" + from + ")==");
+      if (too == null)
+      {
+        System.out.print("NaN\n");
       }
-      int mmap[][] = ml.makeFromMap();
-      System.out.println("FromMap : ("+mmap[0][0]+" "+mmap[0][1]+" "+mmap[0][2]+" "+mmap[0][3]+" ");
-      for (int i=1;i<=mmap[1].length; i++) {
-          if (mmap[1][i-1]==-1) {
-              System.out.print(i+"=XXX");
-              
-          } else {
-              System.out.print(i+"="+(mmap[0][2]+mmap[1][i-1]));
+      else
+      {
+        System.out.print(too[0] + " % " + too[1]);
+        System.out.print("\t+--+\t");
+        int[] toofrom = ml.shiftTo(too[0]);
+        if (toofrom != null)
+        {
+          if (toofrom[0] != from)
+          {
+            System.err.println("Mapping not reflexive:" + from + " " + too[0] +
+                               "->" + toofrom[0]);
           }
-          if (i % 20==0)
-              System.out.print("\n");
-          else
-              System.out.print(",");
+          System.out.println("ShiftTo(" + too[0] + ")==" + toofrom[0] + " % " +
+                             toofrom[1]);
+        }
+        else
+        {
+          System.out.println("ShiftTo(" + too[0] + ")==" +
+                             "NaN! - not Bijective Mapping!");
+        }
+      }
+    }
+    int mmap[][] = ml.makeFromMap();
+    System.out.println("FromMap : (" + mmap[0][0] + " " + mmap[0][1] + " " +
+                       mmap[0][2] + " " + mmap[0][3] + " ");
+    for (int i = 1; i <= mmap[1].length; i++)
+    {
+      if (mmap[1][i - 1] == -1)
+      {
+        System.out.print(i + "=XXX");
+
+      }
+      else
+      {
+        System.out.print(i + "=" + (mmap[0][2] + mmap[1][i - 1]));
       }
-      System.out.print("\n");
+      if (i % 20 == 0)
+      {
+        System.out.print("\n");
+      }
+      else
+      {
+        System.out.print(",");
+      }
+    }
+    System.out.print("\n");
   }
-  public static void main(String argv[]) {
-      MapList ml=new MapList(new int[] { 1,5,10,15,25,20}, 
-              new int[] { 51,1}, 1, 3);
-      MapList ml1=new MapList(new int[] { 1,3,17,4}, 
-              new int[] { 51,1}, 1, 3);
-      
-      // test internal consistency
-      int to[] = new int[51];
-      MapList.testMap(ml, 1, 25);
-      /*
-      for (int from=1; from<=51; from++) {
-          int[] too=ml.shiftTo(from);
-          int[] toofrom=ml.shiftFrom(too[0]);
-          System.out.println("ShiftFrom("+from+")=="+too[0]+" % "+too[1]+"\t+-+\tShiftTo("+too[0]+")=="+toofrom[0]+" % "+toofrom[1]);
-      }*/
-      System.out.print("Success?\n"); // if we get here - something must be working!
+
+  public static void main(String argv[])
+  {
+    MapList ml = new MapList(new int[]
+                             {1, 5, 10, 15, 25, 20},
+                             new int[]
+                             {51, 1}, 1, 3);
+    MapList ml1 = new MapList(new int[]
+                              {1, 3, 17, 4},
+                              new int[]
+                              {51, 1}, 1, 3);
+
+    // test internal consistency
+    int to[] = new int[51];
+    MapList.testMap(ml, 1, 25);
+    /*
+           for (int from=1; from<=51; from++) {
+        int[] too=ml.shiftTo(from);
+        int[] toofrom=ml.shiftFrom(too[0]);
+        System.out.println("ShiftFrom("+from+")=="+too[0]+" % "+too[1]+"\t+-+\tShiftTo("+too[0]+")=="+toofrom[0]+" % "+toofrom[1]);
+           }*/
+    System.out.print("Success?\n"); // if we get here - something must be working!
   }
 }
diff --git a/src/jalview/util/QuickSort.java b/src/jalview/util/QuickSort.java
index f32ff7c..7836c5b 100755
--- a/src/jalview/util/QuickSort.java
+++ b/src/jalview/util/QuickSort.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
diff --git a/src/jalview/util/ShiftList.java b/src/jalview/util/ShiftList.java
index 325a681..8885e2c 100644
--- a/src/jalview/util/ShiftList.java
+++ b/src/jalview/util/ShiftList.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -28,7 +28,7 @@ import java.util.*;
  */
 public class ShiftList
 {
-    public Vector shifts;
+  public Vector shifts;
   public ShiftList()
   {
     shifts = new Vector();
@@ -42,13 +42,21 @@ public class ShiftList
   public void addShift(int pos, int shift)
   {
     int sidx = 0;
-    int[] rshift=null;
-    while (sidx<shifts.size() && (rshift=(int[]) shifts.elementAt(sidx))[0]<pos)
+    int[] rshift = null;
+    while (sidx < shifts.size() &&
+           (rshift = (int[]) shifts.elementAt(sidx))[0] < pos)
+    {
       sidx++;
-    if (sidx==shifts.size())
-      shifts.insertElementAt(new int[] { pos, shift}, sidx);
+    }
+    if (sidx == shifts.size())
+    {
+      shifts.insertElementAt(new int[]
+                             {pos, shift}, sidx);
+    }
     else
-      rshift[1]+=shift;
+    {
+      rshift[1] += shift;
+    }
   }
 
   /**
@@ -59,14 +67,17 @@ public class ShiftList
    */
   public int shift(int pos)
   {
-    if (shifts.size()==0)
+    if (shifts.size() == 0)
+    {
       return pos;
-    int shifted=pos;
-    int sidx=0;
+    }
+    int shifted = pos;
+    int sidx = 0;
     int rshift[];
-    while (sidx<shifts.size()
+    while (sidx < shifts.size()
            &&
-           (rshift=((int[]) shifts.elementAt(sidx++)))[0]<=pos) {
+           (rshift = ( (int[]) shifts.elementAt(sidx++)))[0] <= pos)
+    {
       shifted += rshift[1];
     }
     return shifted;
@@ -79,17 +90,24 @@ public class ShiftList
   {
     shifts.removeAllElements();
   }
+
   /**
    * invert the shifts
    * @return ShiftList with inverse shift operations
    */
-  public ShiftList getInverse() {
-    ShiftList inverse=new ShiftList();
-    if (shifts!=null) {
-      for (int i=0,j=shifts.size(); i<j; i++) {
-        int[] sh=(int[]) shifts.elementAt(i);
-        if (sh!=null)
-          inverse.shifts.addElement(new int[] {sh[0], -sh[1]});
+  public ShiftList getInverse()
+  {
+    ShiftList inverse = new ShiftList();
+    if (shifts != null)
+    {
+      for (int i = 0, j = shifts.size(); i < j; i++)
+      {
+        int[] sh = (int[]) shifts.elementAt(i);
+        if (sh != null)
+        {
+          inverse.shifts.addElement(new int[]
+                                    {sh[0], -sh[1]});
+        }
       }
     }
     return inverse;
@@ -101,14 +119,18 @@ public class ShiftList
    * @param gapMap
    * @return shifts from map index to mapped position
    */
-  public static ShiftList parseMap(int[] gapMap) {
+  public static ShiftList parseMap(int[] gapMap)
+  {
     ShiftList shiftList = null;
-    if (gapMap!=null && gapMap.length>0) {
-      shiftList=new ShiftList();
-      for (int i=0,p=0; i<gapMap.length; p++,i++) {
-        if (p!=gapMap[i]) {
-          shiftList.addShift(p, gapMap[i]-p);
-          p=gapMap[i];
+    if (gapMap != null && gapMap.length > 0)
+    {
+      shiftList = new ShiftList();
+      for (int i = 0, p = 0; i < gapMap.length; p++, i++)
+      {
+        if (p != gapMap[i])
+        {
+          shiftList.addShift(p, gapMap[i] - p);
+          p = gapMap[i];
         }
       }
     }
diff --git a/src/jalview/util/TableSorter.java b/src/jalview/util/TableSorter.java
index c03e804..469bd7f 100755
--- a/src/jalview/util/TableSorter.java
+++ b/src/jalview/util/TableSorter.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,14 +18,13 @@
  */
 package jalview.util;
 
-import java.awt.*;
-import java.awt.event.*;
 import java.util.*;
 import java.util.List;
 
+import java.awt.*;
+import java.awt.event.*;
 import javax.swing.*;
-import javax.swing.event.TableModelEvent;
-import javax.swing.event.TableModelListener;
+import javax.swing.event.*;
 import javax.swing.table.*;
 
 /**
@@ -80,422 +79,519 @@ import javax.swing.table.*;
  * @version 2.0 02/27/04
  */
 
-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);
-
-    public static final Comparator COMPARABLE_COMAPRATOR = new Comparator() {
-        public int compare(Object o1, Object o2) {
-            return ((Comparable) o1).compareTo(o2);
+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);
+
+  public static final Comparator COMPARABLE_COMAPRATOR = new Comparator()
+  {
+    public int compare(Object o1, Object o2)
+    {
+      return ( (Comparable) o1).compareTo(o2);
+    }
+  };
+  public static final Comparator LEXICAL_COMPARATOR = new Comparator()
+  {
+    public int compare(Object o1, Object o2)
+    {
+      return o1.toString().compareTo(o2.toString());
+    }
+  };
+
+  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()
+  {
+    this.mouseListener = new MouseHandler();
+    this.tableModelListener = new TableModelHandler();
+  }
+
+  public TableSorter(TableModel tableModel)
+  {
+    this();
+    setTableModel(tableModel);
+  }
+
+  public TableSorter(TableModel tableModel, JTableHeader tableHeader)
+  {
+    this();
+    setTableHeader(tableHeader);
+    setTableModel(tableModel);
+  }
+
+  private void clearSortingState()
+  {
+    viewToModel = null;
+    modelToView = null;
+  }
+
+  public TableModel getTableModel()
+  {
+    return tableModel;
+  }
+
+  public void setTableModel(TableModel tableModel)
+  {
+    if (this.tableModel != null)
+    {
+      this.tableModel.removeTableModelListener(tableModelListener);
+    }
+
+    this.tableModel = tableModel;
+    if (this.tableModel != null)
+    {
+      this.tableModel.addTableModelListener(tableModelListener);
+    }
+
+    clearSortingState();
+    fireTableStructureChanged();
+  }
+
+  public JTableHeader getTableHeader()
+  {
+    return tableHeader;
+  }
+
+  public void setTableHeader(JTableHeader tableHeader)
+  {
+    if (this.tableHeader != null)
+    {
+      this.tableHeader.removeMouseListener(mouseListener);
+      TableCellRenderer defaultRenderer = this.tableHeader.getDefaultRenderer();
+      if (defaultRenderer instanceof SortableHeaderRenderer)
+      {
+        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()));
+    }
+  }
+
+  public boolean isSorting()
+  {
+    return sortingColumns.size() != 0;
+  }
+
+  private Directive getDirective(int column)
+  {
+    for (int i = 0; i < sortingColumns.size(); i++)
+    {
+      Directive directive = (Directive) sortingColumns.get(i);
+      if (directive.column == column)
+      {
+        return directive;
+      }
+    }
+    return EMPTY_DIRECTIVE;
+  }
+
+  public int getSortingStatus(int column)
+  {
+    return getDirective(column).direction;
+  }
+
+  private void sortingStatusChanged()
+  {
+    clearSortingState();
+    fireTableDataChanged();
+    if (tableHeader != null)
+    {
+      tableHeader.repaint();
+    }
+  }
+
+  public void setSortingStatus(int column, int status)
+  {
+    Directive directive = getDirective(column);
+    if (directive != EMPTY_DIRECTIVE)
+    {
+      sortingColumns.remove(directive);
+    }
+    if (status != NOT_SORTED)
+    {
+      sortingColumns.add(new Directive(column, status));
+    }
+    sortingStatusChanged();
+  }
+
+  protected Icon getHeaderRendererIcon(int column, int size)
+  {
+    Directive directive = getDirective(column);
+    if (directive == EMPTY_DIRECTIVE)
+    {
+      return null;
+    }
+    return new Arrow(directive.direction == DESCENDING, size,
+                     sortingColumns.indexOf(directive));
+  }
+
+  private void cancelSorting()
+  {
+    sortingColumns.clear();
+    sortingStatusChanged();
+  }
+
+  public void setColumnComparator(Class type, Comparator comparator)
+  {
+    if (comparator == null)
+    {
+      columnComparators.remove(type);
+    }
+    else
+    {
+      columnComparators.put(type, comparator);
+    }
+  }
+
+  protected Comparator getComparator(int column)
+  {
+    Class columnType = tableModel.getColumnClass(column);
+    Comparator comparator = (Comparator) columnComparators.get(columnType);
+    if (comparator != null)
+    {
+      return comparator;
+    }
+    if (Comparable.class.isAssignableFrom(columnType))
+    {
+      return COMPARABLE_COMAPRATOR;
+    }
+    return LEXICAL_COMPARATOR;
+  }
+
+  private Row[] getViewToModel()
+  {
+    if (viewToModel == null)
+    {
+      int tableModelRowCount = tableModel.getRowCount();
+      viewToModel = new Row[tableModelRowCount];
+      for (int row = 0; row < tableModelRowCount; row++)
+      {
+        viewToModel[row] = new Row(row);
+      }
+
+      if (isSorting())
+      {
+        Arrays.sort(viewToModel);
+      }
+    }
+    return viewToModel;
+  }
+
+  public int modelIndex(int viewIndex)
+  {
+    return getViewToModel()[viewIndex].modelIndex;
+  }
+
+  private int[] getModelToView()
+  {
+    if (modelToView == null)
+    {
+      int n = getViewToModel().length;
+      modelToView = new int[n];
+      for (int i = 0; i < n; i++)
+      {
+        modelToView[modelIndex(i)] = i;
+      }
+    }
+    return modelToView;
+  }
+
+  // TableModel interface methods
+
+  public int getRowCount()
+  {
+    return (tableModel == null) ? 0 : tableModel.getRowCount();
+  }
+
+  public int getColumnCount()
+  {
+    return (tableModel == null) ? 0 : tableModel.getColumnCount();
+  }
+
+  public String getColumnName(int column)
+  {
+    return tableModel.getColumnName(column);
+  }
+
+  public Class getColumnClass(int column)
+  {
+    return tableModel.getColumnClass(column);
+  }
+
+  public boolean isCellEditable(int row, int column)
+  {
+    return tableModel.isCellEditable(modelIndex(row), column);
+  }
+
+  public Object getValueAt(int row, int column)
+  {
+    return tableModel.getValueAt(modelIndex(row), column);
+  }
+
+  public void setValueAt(Object aValue, int row, int column)
+  {
+    tableModel.setValueAt(aValue, modelIndex(row), column);
+  }
+
+  // Helper classes
+
+  private class Row
+      implements Comparable
+  {
+    private int modelIndex;
+
+    public Row(int index)
+    {
+      this.modelIndex = index;
+    }
+
+    public int compareTo(Object o)
+    {
+      int row1 = modelIndex;
+      int row2 = ( (Row) o).modelIndex;
+
+      for (Iterator it = sortingColumns.iterator(); it.hasNext(); )
+      {
+        Directive directive = (Directive) it.next();
+        int column = directive.column;
+        Object o1 = tableModel.getValueAt(row1, column);
+        Object o2 = tableModel.getValueAt(row2, column);
+
+        int comparison = 0;
+        // Define null less than everything, except null.
+        if (o1 == null && o2 == null)
+        {
+          comparison = 0;
         }
-    };
-    public static final Comparator LEXICAL_COMPARATOR = new Comparator() {
-        public int compare(Object o1, Object o2) {
-            return o1.toString().compareTo(o2.toString());
-        }
-    };
-
-    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() {
-        this.mouseListener = new MouseHandler();
-        this.tableModelListener = new TableModelHandler();
-    }
-
-    public TableSorter(TableModel tableModel) {
-        this();
-        setTableModel(tableModel);
-    }
-
-    public TableSorter(TableModel tableModel, JTableHeader tableHeader) {
-        this();
-        setTableHeader(tableHeader);
-        setTableModel(tableModel);
-    }
-
-    private void clearSortingState() {
-        viewToModel = null;
-        modelToView = null;
-    }
-
-    public TableModel getTableModel() {
-        return tableModel;
-    }
-
-    public void setTableModel(TableModel tableModel) {
-        if (this.tableModel != null) {
-            this.tableModel.removeTableModelListener(tableModelListener);
+        else if (o1 == null)
+        {
+          comparison = -1;
         }
-
-        this.tableModel = tableModel;
-        if (this.tableModel != null) {
-            this.tableModel.addTableModelListener(tableModelListener);
+        else if (o2 == null)
+        {
+          comparison = 1;
         }
-
-        clearSortingState();
-        fireTableStructureChanged();
-    }
-
-    public JTableHeader getTableHeader() {
-        return tableHeader;
-    }
-
-    public void setTableHeader(JTableHeader tableHeader) {
-        if (this.tableHeader != null) {
-            this.tableHeader.removeMouseListener(mouseListener);
-            TableCellRenderer defaultRenderer = this.tableHeader.getDefaultRenderer();
-            if (defaultRenderer instanceof SortableHeaderRenderer) {
-                this.tableHeader.setDefaultRenderer(((SortableHeaderRenderer) defaultRenderer).tableCellRenderer);
-            }
+        else
+        {
+          comparison = getComparator(column).compare(o1, o2);
         }
-        this.tableHeader = tableHeader;
-        if (this.tableHeader != null) {
-            this.tableHeader.addMouseListener(mouseListener);
-            this.tableHeader.setDefaultRenderer(
-                    new SortableHeaderRenderer(this.tableHeader.getDefaultRenderer()));
+        if (comparison != 0)
+        {
+          return directive.direction == DESCENDING ? -comparison : comparison;
         }
-    }
-
-    public boolean isSorting() {
-        return sortingColumns.size() != 0;
-    }
-
-    private Directive getDirective(int column) {
-        for (int i = 0; i < sortingColumns.size(); i++) {
-            Directive directive = (Directive)sortingColumns.get(i);
-            if (directive.column == column) {
-                return directive;
-            }
-        }
-        return EMPTY_DIRECTIVE;
-    }
-
-    public int getSortingStatus(int column) {
-        return getDirective(column).direction;
-    }
-
-    private void sortingStatusChanged() {
+      }
+      return 0;
+    }
+  }
+
+  private class TableModelHandler
+      implements TableModelListener
+  {
+    public void tableChanged(TableModelEvent e)
+    {
+      // If we're not sorting by anything, just pass the event along.
+      if (!isSorting())
+      {
         clearSortingState();
-        fireTableDataChanged();
-        if (tableHeader != null) {
-            tableHeader.repaint();
-        }
-    }
-
-    public void setSortingStatus(int column, int status) {
-        Directive directive = getDirective(column);
-        if (directive != EMPTY_DIRECTIVE) {
-            sortingColumns.remove(directive);
-        }
-        if (status != NOT_SORTED) {
-            sortingColumns.add(new Directive(column, status));
-        }
-        sortingStatusChanged();
-    }
-
-    protected Icon getHeaderRendererIcon(int column, int size) {
-        Directive directive = getDirective(column);
-        if (directive == EMPTY_DIRECTIVE) {
-            return null;
-        }
-        return new Arrow(directive.direction == DESCENDING, size, sortingColumns.indexOf(directive));
-    }
-
-    private void cancelSorting() {
-        sortingColumns.clear();
-        sortingStatusChanged();
-    }
-
-    public void setColumnComparator(Class type, Comparator comparator) {
-        if (comparator == null) {
-            columnComparators.remove(type);
-        } else {
-            columnComparators.put(type, comparator);
-        }
-    }
-
-    protected Comparator getComparator(int column) {
-        Class columnType = tableModel.getColumnClass(column);
-        Comparator comparator = (Comparator) columnComparators.get(columnType);
-        if (comparator != null) {
-            return comparator;
-        }
-        if (Comparable.class.isAssignableFrom(columnType)) {
-            return COMPARABLE_COMAPRATOR;
-        }
-        return LEXICAL_COMPARATOR;
-    }
-
-    private Row[] getViewToModel() {
-        if (viewToModel == null) {
-            int tableModelRowCount = tableModel.getRowCount();
-            viewToModel = new Row[tableModelRowCount];
-            for (int row = 0; row < tableModelRowCount; row++) {
-                viewToModel[row] = new Row(row);
-            }
-
-            if (isSorting()) {
-                Arrays.sort(viewToModel);
-            }
-        }
-        return viewToModel;
-    }
-
-    public int modelIndex(int viewIndex) {
-        return getViewToModel()[viewIndex].modelIndex;
-    }
-
-    private int[] getModelToView() {
-        if (modelToView == null) {
-            int n = getViewToModel().length;
-            modelToView = new int[n];
-            for (int i = 0; i < n; i++) {
-                modelToView[modelIndex(i)] = i;
-            }
-        }
-        return modelToView;
-    }
-
-    // TableModel interface methods
-
-    public int getRowCount() {
-        return (tableModel == null) ? 0 : tableModel.getRowCount();
-    }
-
-    public int getColumnCount() {
-        return (tableModel == null) ? 0 : tableModel.getColumnCount();
-    }
-
-    public String getColumnName(int column) {
-        return tableModel.getColumnName(column);
-    }
-
-    public Class getColumnClass(int column) {
-        return tableModel.getColumnClass(column);
-    }
-
-    public boolean isCellEditable(int row, int column) {
-        return tableModel.isCellEditable(modelIndex(row), column);
-    }
-
-    public Object getValueAt(int row, int column) {
-        return tableModel.getValueAt(modelIndex(row), column);
-    }
-
-    public void setValueAt(Object aValue, int row, int column) {
-        tableModel.setValueAt(aValue, modelIndex(row), column);
-    }
-
-    // Helper classes
-
-    private class Row implements Comparable {
-        private int modelIndex;
-
-        public Row(int index) {
-            this.modelIndex = index;
-        }
-
-        public int compareTo(Object o) {
-            int row1 = modelIndex;
-            int row2 = ((Row) o).modelIndex;
-
-            for (Iterator it = sortingColumns.iterator(); it.hasNext();) {
-                Directive directive = (Directive) it.next();
-                int column = directive.column;
-                Object o1 = tableModel.getValueAt(row1, column);
-                Object o2 = tableModel.getValueAt(row2, column);
-
-                int comparison = 0;
-                // Define null less than everything, except null.
-                if (o1 == null && o2 == null) {
-                    comparison = 0;
-                } else if (o1 == null) {
-                    comparison = -1;
-                } else if (o2 == null) {
-                    comparison = 1;
-                } else {
-                    comparison = getComparator(column).compare(o1, o2);
-                }
-                if (comparison != 0) {
-                    return directive.direction == DESCENDING ? -comparison : comparison;
-                }
-            }
-            return 0;
+        fireTableChanged(e);
+        return;
+      }
+
+      // If the table structure has changed, cancel the sorting; the
+      // sorting columns may have been either moved or deleted from
+      // the model.
+      if (e.getFirstRow() == TableModelEvent.HEADER_ROW)
+      {
+        cancelSorting();
+        fireTableChanged(e);
+        return;
+      }
+
+      // 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,
+      // 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.
+      //
+      // The last check, for (modelToView != null) is to see if modelToView
+      // is already allocated. If we don't do this check; sorting can become
+      // a performance bottleneck for applications where cells
+      // change rapidly in different parts of the table. If cells
+      // change alternately in the sorting column and then outside of
+      // it this class can end up re-sorting on alternate cell updates -
+      // which can be a performance problem for large tables. The last
+      // clause avoids this problem.
+      int column = e.getColumn();
+      if (e.getFirstRow() == e.getLastRow()
+          && 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()));
+        return;
+      }
+
+      // Something has happened to the data that may have invalidated the row order.
+      clearSortingState();
+      fireTableDataChanged();
+      return;
+    }
+  }
+
+  private class MouseHandler
+      extends MouseAdapter
+  {
+    public void mouseClicked(MouseEvent e)
+    {
+      JTableHeader h = (JTableHeader) e.getSource();
+      TableColumnModel columnModel = h.getColumnModel();
+      int viewColumn = columnModel.getColumnIndexAtX(e.getX());
+      int column = columnModel.getColumn(viewColumn).getModelIndex();
+      if (column != -1)
+      {
+        int status = getSortingStatus(column);
+        if (!e.isControlDown())
+        {
+          cancelSorting();
         }
-    }
-
-    private class TableModelHandler implements TableModelListener {
-        public void tableChanged(TableModelEvent e) {
-            // If we're not sorting by anything, just pass the event along.
-            if (!isSorting()) {
-                clearSortingState();
-                fireTableChanged(e);
-                return;
-            }
-
-            // If the table structure has changed, cancel the sorting; the
-            // sorting columns may have been either moved or deleted from
-            // the model.
-            if (e.getFirstRow() == TableModelEvent.HEADER_ROW) {
-                cancelSorting();
-                fireTableChanged(e);
-                return;
-            }
-
-            // 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,
-            // 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.
-            //
-            // The last check, for (modelToView != null) is to see if modelToView
-            // is already allocated. If we don't do this check; sorting can become
-            // a performance bottleneck for applications where cells
-            // change rapidly in different parts of the table. If cells
-            // change alternately in the sorting column and then outside of
-            // it this class can end up re-sorting on alternate cell updates -
-            // which can be a performance problem for large tables. The last
-            // clause avoids this problem.
-            int column = e.getColumn();
-            if (e.getFirstRow() == e.getLastRow()
-                    && 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()));
-                return;
-            }
-
-            // Something has happened to the data that may have invalidated the row order.
-            clearSortingState();
-            fireTableDataChanged();
-            return;
-        }
-    }
-
-    private class MouseHandler extends MouseAdapter {
-        public void mouseClicked(MouseEvent e) {
-            JTableHeader h = (JTableHeader) e.getSource();
-            TableColumnModel columnModel = h.getColumnModel();
-            int viewColumn = columnModel.getColumnIndexAtX(e.getX());
-            int column = columnModel.getColumn(viewColumn).getModelIndex();
-            if (column != -1) {
-                int status = getSortingStatus(column);
-                if (!e.isControlDown()) {
-                    cancelSorting();
-                }
-                // 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);
-            }
-        }
-    }
-
-    private static class Arrow implements Icon {
-        private boolean descending;
-        private int size;
-        private int priority;
-
-        public Arrow(boolean descending, int size, int priority) {
-            this.descending = descending;
-            this.size = size;
-            this.priority = priority;
-        }
-
-        public void paintIcon(Component c, Graphics g, int x, int y) {
-            Color color = c == null ? Color.GRAY : c.getBackground();
-            // In a compound sort, make each succesive triangle 20%
-            // smaller than the previous one.
-            int dx = (int)(size/2*Math.pow(0.8, priority));
-            int dy = descending ? dx : -dx;
-            // Align icon (roughly) with font baseline.
-            y = y + 5*size/6 + (descending ? -dy : 0);
-            int shift = descending ? 1 : -1;
-            g.translate(x, y);
-
-            // Right diagonal.
-            g.setColor(color.darker());
-            g.drawLine(dx / 2, dy, 0, 0);
-            g.drawLine(dx / 2, dy + shift, 0, shift);
-
-            // Left diagonal.
-            g.setColor(color.brighter());
-            g.drawLine(dx / 2, dy, dx, 0);
-            g.drawLine(dx / 2, dy + shift, dx, shift);
-
-            // Horizontal line.
-            if (descending) {
-                g.setColor(color.darker().darker());
-            } else {
-                g.setColor(color.brighter().brighter());
-            }
-            g.drawLine(dx, 0, 0, 0);
-
-            g.setColor(color);
-            g.translate(-x, -y);
-        }
-
-        public int getIconWidth() {
-            return size;
-        }
-
-        public int getIconHeight() {
-            return size;
-        }
-    }
-
-    private class SortableHeaderRenderer implements TableCellRenderer {
-        private TableCellRenderer tableCellRenderer;
-
-        public SortableHeaderRenderer(TableCellRenderer tableCellRenderer) {
-            this.tableCellRenderer = tableCellRenderer;
-        }
-
-        public Component getTableCellRendererComponent(JTable table,
-                                                       Object value,
-                                                       boolean isSelected,
-                                                       boolean hasFocus,
-                                                       int row,
-                                                       int column) {
-            Component c = tableCellRenderer.getTableCellRendererComponent(table,
-                    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()));
-            }
-            return c;
-        }
-    }
-
-    private static class Directive {
-        private int column;
-        private int direction;
-
-        public Directive(int column, int direction) {
-            this.column = column;
-            this.direction = direction;
-        }
-    }
+        // 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);
+      }
+    }
+  }
+
+  private static class Arrow
+      implements Icon
+  {
+    private boolean descending;
+    private int size;
+    private int priority;
+
+    public Arrow(boolean descending, int size, int priority)
+    {
+      this.descending = descending;
+      this.size = size;
+      this.priority = priority;
+    }
+
+    public void paintIcon(Component c, Graphics g, int x, int y)
+    {
+      Color color = c == null ? Color.GRAY : c.getBackground();
+      // In a compound sort, make each succesive triangle 20%
+      // smaller than the previous one.
+      int dx = (int) (size / 2 * Math.pow(0.8, priority));
+      int dy = descending ? dx : -dx;
+      // Align icon (roughly) with font baseline.
+      y = y + 5 * size / 6 + (descending ? -dy : 0);
+      int shift = descending ? 1 : -1;
+      g.translate(x, y);
+
+      // Right diagonal.
+      g.setColor(color.darker());
+      g.drawLine(dx / 2, dy, 0, 0);
+      g.drawLine(dx / 2, dy + shift, 0, shift);
+
+      // Left diagonal.
+      g.setColor(color.brighter());
+      g.drawLine(dx / 2, dy, dx, 0);
+      g.drawLine(dx / 2, dy + shift, dx, shift);
+
+      // Horizontal line.
+      if (descending)
+      {
+        g.setColor(color.darker().darker());
+      }
+      else
+      {
+        g.setColor(color.brighter().brighter());
+      }
+      g.drawLine(dx, 0, 0, 0);
+
+      g.setColor(color);
+      g.translate( -x, -y);
+    }
+
+    public int getIconWidth()
+    {
+      return size;
+    }
+
+    public int getIconHeight()
+    {
+      return size;
+    }
+  }
+
+  private class SortableHeaderRenderer
+      implements TableCellRenderer
+  {
+    private TableCellRenderer tableCellRenderer;
+
+    public SortableHeaderRenderer(TableCellRenderer tableCellRenderer)
+    {
+      this.tableCellRenderer = tableCellRenderer;
+    }
+
+    public Component getTableCellRendererComponent(JTable table,
+        Object value,
+        boolean isSelected,
+        boolean hasFocus,
+        int row,
+        int column)
+    {
+      Component c = tableCellRenderer.getTableCellRendererComponent(table,
+          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()));
+      }
+      return c;
+    }
+  }
+
+  private static class Directive
+  {
+    private int column;
+    private int direction;
+
+    public Directive(int column, int direction)
+    {
+      this.column = column;
+      this.direction = direction;
+    }
+  }
 }
diff --git a/src/jalview/ws/Discoverer.java b/src/jalview/ws/Discoverer.java
index 4a83ba7..02028b4 100755
--- a/src/jalview/ws/Discoverer.java
+++ b/src/jalview/ws/Discoverer.java
@@ -1,21 +1,21 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 jalview.ws;
 
 /**
@@ -30,11 +30,11 @@ package jalview.ws;
  * @author not attributable
  * @version 1.0
  */
+import java.util.*;
+
+import javax.swing.*;
+
 import ext.vamsas.*;
-import java.util.Vector;
-import java.util.Hashtable;
-import java.util.StringTokenizer;
-import javax.swing.JOptionPane;
 
 public class Discoverer
     extends Thread implements Runnable
@@ -111,12 +111,14 @@ public class Discoverer
 
   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() {
+  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");
 
-    try{
+    try
+    {
       StringTokenizer st = new StringTokenizer(RootServiceURLs, ",");
       while (st.hasMoreElements())
       {
@@ -125,24 +127,36 @@ public class Discoverer
         {
           java.net.URL u = new java.net.URL(url = st.nextToken());
           if (!urls.contains(u))
+          {
             urls.add(u);
+          }
           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)
         {
           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);
+              ( (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)
-    {jalview.bin.Cache.log.warn("Error parsing comma separated list of urls in DISCOVERY_URLS.",ex);}
-    if (urls.size()>0)
+    }
+    catch (Exception ex)
+    {
+      jalview.bin.Cache.log.warn(
+          "Error parsing comma separated list of urls in DISCOVERY_URLS.", ex);
+    }
+    if (urls.size() > 0)
+    {
       return urls;
+    }
     return null;
   }
 
@@ -164,19 +178,20 @@ public class Discoverer
         jalview.bin.Cache.log.debug("Setting default services");
         services = new Hashtable();
         // Muscle, Clustal and JPred.
-        ServiceHandle[] defServices = {
+        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"
-),
+            ),
             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",
+                "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(
@@ -191,8 +206,9 @@ public class Discoverer
                 "Cuff J. A and Barton G.J (2000) Application of " +
                 "multiple sequence alignment profiles to improve protein secondary structure prediction, " +
                 "Proteins 40:502-511",
-                "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred","JNet Secondary Structure Prediction"
-                )};
+                "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred",
+                "JNet Secondary Structure Prediction"
+            )};
         services = new Hashtable();
         serviceList = new Vector();
         buildServiceLists(defServices, serviceList, services);
@@ -207,6 +223,7 @@ public class Discoverer
     }
 
   }
+
   // TODO: JBPNote : make this discover more services based on list of
   // discovery service urls, break cyclic references to the same url and
   // duplicate service entries (same endpoint *and* same interface)
@@ -218,20 +235,27 @@ 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)
+      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);
-      } else {
+                                        "Proxy Authorization Failed",
+                                        JOptionPane.WARNING_MESSAGE);
+        }
+      }
+      else
+      {
         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.debug("Discovery Service General Exception", e);
@@ -252,7 +276,7 @@ public class Discoverer
    * @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++)
@@ -260,9 +284,9 @@ public class Discoverer
       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");
+                                    " 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());
@@ -307,9 +331,10 @@ public class Discoverer
     Vector cat = new Vector();
     ServiceHandle sh[] = null;
     int s_url = 0;
-    if (ServiceURLList==null)
+    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())
@@ -318,11 +343,13 @@ public class Discoverer
       {
 
         buildServiceLists(sh, cat, sscat);
-      } else {
+      }
+      else
+      {
         jalview.bin.Cache.log.warn(
             "No services at "
-            +((java.net.URL) ServiceURLList.get(s_url))
-            +" - check DISCOVERY_URLS property in .jalview_properties");
+            + ( (java.net.URL) ServiceURLList.get(s_url))
+            + " - check DISCOVERY_URLS property in .jalview_properties");
       }
       s_url++;
     }
@@ -343,8 +370,10 @@ public class Discoverer
   public void run()
   {
     final Discoverer discoverer = this;
-    Thread discoverThread = new Thread() {
-      public void run() {
+    Thread discoverThread = new Thread()
+    {
+      public void run()
+      {
         discoverer.doDiscovery();
         discoverer.discoverServices();
       }
diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java
index aee3418..2475fb1 100755
--- a/src/jalview/ws/JPredClient.java
+++ b/src/jalview/ws/JPredClient.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -26,26 +26,29 @@ import ext.vamsas.*;
 import jalview.analysis.*;
 import jalview.bin.*;
 import jalview.datamodel.*;
-import jalview.datamodel.AlignmentView;
 import jalview.gui.*;
 
 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
-     */
-    public JPredClient(ext.vamsas.ServiceHandle sh, String title, boolean msa, AlignmentView alview, AlignFrame parentFrame, boolean viewonly) {
+  /**
+   * 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
+   */
+  public JPredClient(ext.vamsas.ServiceHandle sh, String title, boolean msa,
+                     AlignmentView alview, AlignFrame parentFrame,
+                     boolean viewonly)
+  {
     super();
-    wsInfo=setWebService(sh);
+    wsInfo = setWebService(sh);
     startJPredClient(title, msa, alview, parentFrame, viewonly);
 
   }
+
   /**
    * startJPredClient
    * TODO: refine submission to cope with local prediction of visible regions or multiple single sequence jobs
@@ -58,7 +61,8 @@ public class JPredClient
    * @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)
@@ -71,42 +75,47 @@ public class JPredClient
       Cache.log.warn("Couldn't find a Jpred webservice to invoke!");
       return;
     }
-    SeqCigar[] msf=null;
-    SequenceI seq=null;
-    int[] delMap=null;
+    SeqCigar[] msf = null;
+    SequenceI seq = null;
+    int[] delMap = null;
     // original JNetClient behaviour - submit full length of sequence or profile
     // and mask result.
     msf = input.getSequences();
     seq = msf[0].getSeq('-');
 
-    if (viewonly) {
+    if (viewonly)
+    {
       int[] viscontigs = alview.getVisibleContigs();
-      int spos=0;
-      int i=0;
-      if (viscontigs!=null) {
+      int spos = 0;
+      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
 
-        delMap = new int[seq.getEnd()-seq.getStart()+1];
+        delMap = new int[seq.getEnd() - seq.getStart() + 1];
         int gapMap[] = seq.gapMap();
-        for (int contig = 0; contig<viscontigs.length; contig += 2)
+        for (int contig = 0; contig < viscontigs.length; contig += 2)
         {
 
-          while (spos<gapMap.length && gapMap[spos]<viscontigs[contig]) {
+          while (spos < gapMap.length && gapMap[spos] < viscontigs[contig])
+          {
             spos++;
           }
-          while (spos<gapMap.length && gapMap[spos]<=viscontigs[contig+1]) {
+          while (spos < gapMap.length && gapMap[spos] <= viscontigs[contig + 1])
+          {
             delMap[i++] = spos++;
           }
         }
         int tmap[] = new int[i];
         System.arraycopy(delMap, 0, tmap, 0, i);
-        delMap=tmap;
+        delMap = tmap;
       }
     }
     if (msa && msf.length > 1)
     {
 
-      String altitle = "JNet prediction on "+(viewonly?"visible ":"") + seq.getName() +
+      String altitle = "JNet prediction on " + (viewonly ? "visible " : "") +
+          seq.getName() +
           " using alignment from " + title;
 
       SequenceI aln[] = new SequenceI[msf.length];
@@ -115,9 +124,9 @@ public class JPredClient
         aln[i] = msf[i].getSeq('-');
       }
 
-
       Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln, true);
-      if (viewonly) {
+      if (viewonly)
+      {
         // Remove hidden regions from sequence objects.
         String seqs[] = alview.getSequenceStrings('-');
         for (int i = 0, j = msf.length; i < j; i++)
@@ -126,49 +135,62 @@ 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();
     }
     else
     {
-      if (!msa && msf.length>1)
+      if (!msa && msf.length > 1)
+      {
         throw new Error("Implementation Error! Multiple single sequence prediction jobs are not yet supported.");
-      String altitle = "JNet prediction for "+(viewonly?"visible ":"")+"sequence " + seq.getName() +
+      }
+      String altitle = "JNet prediction for " + (viewonly ? "visible " : "") +
+          "sequence " + seq.getName() +
           " from " +
           title;
       String seqname = seq.getName();
       Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(
           seq);
-      if (viewonly) {
+      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();
     }
   }
-  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);
@@ -184,7 +206,8 @@ public class JPredClient
     startJPredClient(title, seq, null);
   }
 
-  private void startJPredClient(String title, SequenceI[] msf, AlignFrame parentFrame)
+  private void startJPredClient(String title, SequenceI[] msf,
+                                AlignFrame parentFrame)
   {
     if (wsInfo == null)
     {
@@ -209,17 +232,19 @@ public class JPredClient
     Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln, true);
 
     Jpred server = locateWebService();
-    if (server==null)
+    if (server == null)
     {
       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)
+  public void startJPredClient(String title, SequenceI seq,
+                               AlignFrame parentFrame)
   {
     if (wsInfo == null)
     {
@@ -235,12 +260,14 @@ public class JPredClient
     Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq);
 
     Jpred server = locateWebService();
-    if (server==null)
+    if (server == null)
     {
       return;
     }
 
-    JPredThread jthread = new JPredThread(wsInfo, altitle, server, WsURL, SequenceInfo, seq,null, null, parentFrame);
+    JPredThread jthread = new JPredThread(wsInfo, altitle, server, WsURL,
+                                          SequenceInfo, seq, null, null,
+                                          parentFrame);
     wsInfo.setthisService(jthread);
     jthread.start();
   }
@@ -264,11 +291,11 @@ public class JPredClient
   private ext.vamsas.Jpred locateWebService()
   {
     ext.vamsas.JpredServiceLocator loc = new JpredServiceLocator(); // Default
-    ext.vamsas.Jpred server=null;
+    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) server).setTimeout(60000); // one minute stub
       //((JpredSoapBindingStub)this.server)._setProperty(org.apache.axis.encoding.C, Boolean.TRUE);
 
     }
@@ -291,4 +318,3 @@ public class JPredClient
     return server;
   }
 }
-
diff --git a/src/jalview/ws/JPredThread.java b/src/jalview/ws/JPredThread.java
index b4833b1..0cac709 100644
--- a/src/jalview/ws/JPredThread.java
+++ b/src/jalview/ws/JPredThread.java
@@ -2,31 +2,28 @@ package jalview.ws;
 
 import java.util.*;
 
-import javax.swing.*;
-
-import vamsas.objects.simple.JpredResult;
-
 import jalview.analysis.*;
 import jalview.bin.*;
 import jalview.datamodel.*;
+import jalview.datamodel.Alignment;
 import jalview.gui.*;
 import jalview.io.*;
 import jalview.util.*;
+import vamsas.objects.simple.JpredResult;
 
 class JPredThread
-extends WSThread
-implements WSClientI
+    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
+      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
+    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.
@@ -50,20 +47,21 @@ implements WSClientI
       }
       return false;
     }
+
     /**
      *
      * @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
+        throws Exception
     {
       if (result == null || !result.isFinished())
       {
         return null;
       }
       Alignment al = null;
-      ColumnSelection alcsel=null;
+      ColumnSelection alcsel = null;
       int FirstSeq = -1; // the position of the query sequence in Alignment al
 
       JpredResult result = (JpredResult)this.result;
@@ -72,7 +70,7 @@ implements WSClientI
       // JPredFile prediction = new JPredFile("C:/JalviewX/files/jpred.txt", "File");
       jalview.io.JPredFile prediction = new jalview.io.JPredFile(result.
           getPredfile(),
-      "Paste");
+          "Paste");
       SequenceI[] preds = prediction.getSeqsAsArray();
       jalview.bin.Cache.log.debug("Got prediction profile.");
 
@@ -82,19 +80,23 @@ implements WSClientI
         // we ignore the returned alignment if we only predicted on a single sequence
         String format = new jalview.io.IdentifyFile().Identify(result.
             getAligfile(),
-        "Paste");
+            "Paste");
 
         if (jalview.io.FormatAdapter.isValidFormat(format))
         {
           SequenceI sqs[];
-          if (predMap!=null) {
-            Object[] alandcolsel = input.getAlignmentAndColumnSelection(alignFrame.getViewport().getGapCharacter());
+          if (predMap != null)
+          {
+            Object[] alandcolsel = input.getAlignmentAndColumnSelection(
+                alignFrame.getViewport().getGapCharacter());
             sqs = (SequenceI[]) alandcolsel[0];
             al = new Alignment(sqs);
-            alcsel=(ColumnSelection) alandcolsel[1];
-          } else {
+            alcsel = (ColumnSelection) alandcolsel[1];
+          }
+          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++)
@@ -105,20 +107,21 @@ implements WSClientI
                 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);
+          jalview.io.JnetAnnotationMaker.add_annotation(prediction, al,
+              FirstSeq,
+              false, predMap);
 
         }
         else
         {
           throw (new Exception(
-              "Unknown format "+format+" for file : \n" +
+              "Unknown format " + format + " for file : \n" +
               result.getAligfile()));
         }
       }
@@ -126,20 +129,27 @@ implements WSClientI
       {
         al = new Alignment(preds);
         FirstSeq = prediction.getQuerySeqPosition();
-        if (predMap!=null) {
+        if (predMap != null)
+        {
           char gc = alignFrame.getViewport().getGapCharacter();
-          SequenceI[] sqs = (SequenceI[]) ((java.lang.Object[]) input.getAlignmentAndColumnSelection(gc))[0];
-          if (this.msaIndex>=sqs.length)
+          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!");
+          }
 
           /////
           //Uses RemoveGapsCommand
           /////
           new jalview.commands.RemoveGapsCommand("Remove Gaps",
-                                                 new SequenceI[] {sqs[msaIndex]},
-                                                 alignFrame.getCurrentView().getAlignment());
+                                                 new SequenceI[]
+                                                 {sqs[msaIndex]},
+                                                 alignFrame.getCurrentView().
+                                                 getAlignment());
 
-          SequenceI profileseq=al.getSequenceAt(FirstSeq);
+          SequenceI profileseq = al.getSequenceAt(FirstSeq);
           profileseq.setSequence(sqs[msaIndex].getSequenceAsString());
         }
 
@@ -147,53 +157,73 @@ implements WSClientI
             al.getSequenceAt(FirstSeq), SequenceInfo))
         {
           throw (new Exception(
-          "Couldn't recover sequence properties for JNet Query sequence!"));
-        } else {
+              "Couldn't recover sequence properties for JNet Query sequence!"));
+        }
+        else
+        {
           al.setDataset(null);
-          jalview.io.JnetAnnotationMaker.add_annotation(prediction, al, FirstSeq,
+          jalview.io.JnetAnnotationMaker.add_annotation(prediction, al,
+              FirstSeq,
               true, predMap);
-          SequenceI profileseq=al.getSequenceAt(0); // this includes any gaps.
+          SequenceI profileseq = al.getSequenceAt(0); // this includes any gaps.
           alignToProfileSeq(al, profileseq);
-          if (predMap!=null) {
+          if (predMap != null)
+          {
             // Adjust input view for gaps
             // propagate insertions into profile
-            alcsel=propagateInsertions(profileseq, al, input);
+            alcsel = propagateInsertions(profileseq, al, input);
           }
         }
       }
-      return new Object[] { al, alcsel}; // , FirstSeq, noMsa};
+      return new Object[]
+          {
+          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
      * @param al
      * @param profileseq
      */
-    private void alignToProfileSeq(Alignment al, SequenceI profileseq) {
+    private void alignToProfileSeq(Alignment al, SequenceI profileseq)
+    {
       char gc = al.getGapCharacter();
       int[] gapMap = profileseq.gapMap();
       // insert gaps into profile
-      for (int lp=0,r=0; r<gapMap.length; r++) {
-        if (gapMap[r]-lp>1) {
-          StringBuffer sb=new StringBuffer();
-          for (int s=0, ns=gapMap[r]-lp; s<ns; s++) {
+      for (int lp = 0, r = 0; r < gapMap.length; r++)
+      {
+        if (gapMap[r] - lp > 1)
+        {
+          StringBuffer sb = new StringBuffer();
+          for (int s = 0, ns = gapMap[r] - lp; s < ns; s++)
+          {
             sb.append(gc);
           }
-          for (int s=1,ns=al.getHeight(); s<ns; s++) {
+          for (int s = 1, ns = al.getHeight(); s < ns; s++)
+          {
             String sq = al.getSequenceAt(s).getSequenceAsString();
-            int diff=gapMap[r]-sq.length();
-            if (diff>0) {
+            int diff = gapMap[r] - sq.length();
+            if (diff > 0)
+            {
               // pad gaps
-              sq=sq+sb;
-              while ((diff=gapMap[r]-sq.length())>0) {
-                sq=sq+((diff>=sb.length()) ? sb.toString() : sb.substring(0, diff));
+              sq = sq + sb;
+              while ( (diff = gapMap[r] - sq.length()) > 0)
+              {
+                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]));
+            }
+            else
+            {
+              al.getSequenceAt(s).setSequence(sq.substring(0, gapMap[r]) +
+                                              sb.toString() +
+                                              sq.substring(gapMap[r]));
             }
           }
         }
-        lp=gapMap[r];
+        lp = gapMap[r];
       }
     }
 
@@ -203,59 +233,82 @@ implements WSClientI
      * @param al
      * @param input
      */
-    private ColumnSelection propagateInsertions(SequenceI profileseq, Alignment al, AlignmentView input) {
+    private ColumnSelection propagateInsertions(SequenceI profileseq,
+                                                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.
-      int[] viscontigs=nview.getVisibleContigs(0, profileseq.getLength());
-      int spos=0;
-      int offset=0;
+      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()))
       // add profile to visible contigs
-      for (int v=0; v<viscontigs.length; v+=2) {
-        if (viscontigs[v]>spos) {
-          StringBuffer sb=new StringBuffer();
-          for (int s=0, ns=viscontigs[v]-spos; s<ns; s++) {
+      for (int v = 0; v < viscontigs.length; v += 2)
+      {
+        if (viscontigs[v] > spos)
+        {
+          StringBuffer sb = new StringBuffer();
+          for (int s = 0, ns = viscontigs[v] - spos; s < ns; s++)
+          {
             sb.append(gc);
           }
-          for (int s=0,ns=al.getHeight(); s<ns; s++) {
+          for (int s = 0, ns = al.getHeight(); s < ns; s++)
+          {
             SequenceI sqobj = al.getSequenceAt(s);
-            if (sqobj!=profileseq) {
+            if (sqobj != profileseq)
+            {
               String sq = al.getSequenceAt(s).getSequenceAsString();
-              if (sq.length()<=spos+offset) {
+              if (sq.length() <= spos + offset)
+              {
                 // pad sequence
-                int diff=spos+offset-sq.length()-1;
-                if (diff>0) {
+                int diff = spos + offset - sq.length() - 1;
+                if (diff > 0)
+                {
                   // pad gaps
-                  sq=sq+sb;
-                  while ((diff=spos+offset-sq.length()-1)>0) {
-                    sq=sq+((diff>=sb.length()) ? sb.toString() : sb.substring(0, diff));
+                  sq = sq + sb;
+                  while ( (diff = spos + offset - sq.length() - 1) > 0)
+                  {
+                    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));
+                sq += sb.toString();
+              }
+              else
+              {
+                al.getSequenceAt(s).setSequence(sq.substring(0, spos + offset) +
+                                                sb.toString() +
+                                                sq.substring(spos + offset));
               }
             }
           }
           //offset+=sb.length();
         }
-        spos = viscontigs[v+1]+1;
+        spos = viscontigs[v + 1] + 1;
       }
-      if ((offset+spos)<profileseq.getLength()) {
-        StringBuffer sb=new StringBuffer();
-        for (int s=0, ns=profileseq.getLength()-spos-offset; s<ns; s++) {
+      if ( (offset + spos) < profileseq.getLength())
+      {
+        StringBuffer sb = new StringBuffer();
+        for (int s = 0, ns = profileseq.getLength() - spos - offset; s < ns; s++)
+        {
           sb.append(gc);
         }
-        for (int s=1,ns=al.getHeight(); s<ns; s++) {
+        for (int s = 1, ns = al.getHeight(); s < ns; s++)
+        {
           String sq = al.getSequenceAt(s).getSequenceAsString();
           // pad sequence
-          int diff=origseq.getLength()-sq.length();
-          while (diff>0) {
-            sq=sq+((diff>=sb.length()) ? sb.toString() : sb.substring(0, diff));
-            diff=origseq.getLength()-sq.length();
+          int diff = origseq.getLength() - sq.length();
+          while (diff > 0)
+          {
+            sq = sq +
+                ( (diff >= sb.length()) ? sb.toString() : sb.substring(0, diff));
+            diff = origseq.getLength() - sq.length();
           }
         }
       }
@@ -291,9 +344,12 @@ implements WSClientI
       }
     }
   }
+
   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();
     this.altitle = altitle;
     this.server = server;
@@ -303,40 +359,44 @@ implements WSClientI
     WsUrl = wsurl;
   }
 
-
-  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);
+    this(wsinfo, altitle, server, wsurl, alview, alframe);
     JPredJob job = new JPredJob(SequenceInfo, seq, delMap);
     if (job.hasValidInput())
     {
       OutputHeader = wsInfo.getProgressText();
       jobs = new WSJob[]
-                       {
+          {
           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);
+    this(wsinfo, altitle, server, wsurl, alview, alframe);
     JPredJob job = new JPredJob(SequenceInfo, msf, delMap);
     if (job.hasValidInput())
     {
       jobs = new WSJob[]
-                       {
+          {
           job};
       OutputHeader = wsInfo.getProgressText();
       job.jobnum = 0;
     }
   }
+
   void StartJob(WSJob j)
   {
     if (! (j instanceof JPredJob))
     {
       throw new Error("Implementation error - StartJob(JpredJob) called on " +
-          j.getClass());
+                      j.getClass());
     }
     try
     {
@@ -346,10 +406,10 @@ implements WSClientI
         job.jobId = server.predictOnMsa(job.msa);
       }
       else
-        if (job.sequence!=null)
-        {
-          job.jobId = server.predict(job.sequence); // debug like : job.jobId = "/jobs/www-jpred/jp_Yatat29";//
-        }
+      if (job.sequence != null)
+      {
+        job.jobId = server.predict(job.sequence); // debug like : job.jobId = "/jobs/www-jpred/jp_Yatat29";//
+      }
 
       if (job.jobId != null)
       {
@@ -377,9 +437,9 @@ implements WSClientI
       {
         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");
+                               "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");
@@ -391,9 +451,9 @@ implements WSClientI
         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);
 
@@ -422,13 +482,13 @@ implements WSClientI
     {
 
       Cache.log.error("Unexpected exception when processing results for " +
-          altitle, ex);
+                      altitle, ex);
       wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
     }
     if (results > 0)
     {
       wsInfo.showResultsNewFrame
-      .addActionListener(new java.awt.event.ActionListener()
+          .addActionListener(new java.awt.event.ActionListener()
       {
         public void actionPerformed(
             java.awt.event.ActionEvent evt)
@@ -437,7 +497,7 @@ implements WSClientI
         }
       });
       wsInfo.mergeResults
-      .addActionListener(new java.awt.event.ActionListener()
+          .addActionListener(new java.awt.event.ActionListener()
       {
         public void actionPerformed(
             java.awt.event.ActionEvent evt)
@@ -459,7 +519,7 @@ implements WSClientI
     if (jobs != null)
     {
       Object[] res = null;
-      boolean msa=false;
+      boolean msa = false;
       for (int jn = 0; jn < jobs.length; jn++)
       {
         Object[] jobres = null;
@@ -468,17 +528,21 @@ implements WSClientI
         if (j.hasResults())
         {
           // hack - we only deal with all single seuqence predictions or all profile predictions
-          msa = (j.msa!=null) ? true : msa;
+          msa = (j.msa != null) ? true : msa;
           try
           {
             jalview.bin.Cache.log.debug("Parsing output of job " + jn);
             jobres = j.getResultSet();
             jalview.bin.Cache.log.debug("Finished parsing output.");
-            if (jobs.length==1)
+            if (jobs.length == 1)
+            {
               res = jobres;
-            else {
+            }
+            else
+            {
               // do merge with other job results
-              throw new Error("Multiple JNet subjob merging not yet implemented.");
+              throw new Error(
+                  "Multiple JNet subjob merging not yet implemented.");
             }
           }
           catch (Exception e)
@@ -488,10 +552,10 @@ implements WSClientI
                 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());
+                                      OutputHeader + "\n" +
+                                      j.result.getStatus() +
+                                      "\nInvalid JNet job result data!\n" +
+                                      e.getMessage());
             j.result.setBroken(true);
           }
         }
@@ -502,30 +566,41 @@ implements WSClientI
         if (newWindow)
         {
           AlignFrame af;
-          if (input==null) {
-            if (res[1]!=null) {
-              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);
+          if (input == null)
+          {
+            if (res[1] != null)
+            {
+              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);
             }
-          } else {
+          }
+          else
+          {
             /*java.lang.Object[] alandcolsel = input.getAlignmentAndColumnSelection(alignFrame.getViewport().getGapCharacter());
-
-            if (((SequenceI[])alandcolsel[0])[0].getLength()!=res.getWidth()) {
+             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) {
+                         }
+                         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);
+            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);
+                                   AlignFrame.DEFAULT_WIDTH,
+                                   AlignFrame.DEFAULT_HEIGHT);
         }
         else
         {
@@ -534,11 +609,13 @@ implements WSClientI
       }
     }
   }
+
   void pollJob(WSJob job)
-  throws Exception
+      throws Exception
   {
     job.result = server.getresult(job.jobId);
   }
+
   public boolean isCancellable()
   {
     return false;
@@ -555,5 +632,3 @@ implements WSClientI
   }
 
 }
-
-
diff --git a/src/jalview/ws/MsaWSClient.java b/src/jalview/ws/MsaWSClient.java
index c159a94..03a801e 100755
--- a/src/jalview/ws/MsaWSClient.java
+++ b/src/jalview/ws/MsaWSClient.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,14 +18,12 @@
  */
 package jalview.ws;
 
-import ext.vamsas.*;
+import javax.swing.*;
 
+import ext.vamsas.*;
 import jalview.datamodel.*;
-
 import jalview.gui.*;
 
-import javax.swing.*;
-
 /**
  * DOCUMENT ME!
  *
@@ -41,7 +39,6 @@ public class MsaWSClient
   ext.vamsas.MuscleWS server;
   AlignFrame alignFrame;
 
-
   /**
    * Creates a new MsaWSClient object that uses a service
    * given by an externally retrieved ServiceHandle
@@ -65,30 +62,30 @@ public class MsaWSClient
     {
       JOptionPane.showMessageDialog(Desktop.desktop,
                                     "The Service called \n" + sh.getName() +
-          "\nis not a \nMultiple Sequence Alignment Service !",
+                                    "\nis not a \nMultiple Sequence Alignment Service !",
                                     "Internal Jalview Error",
                                     JOptionPane.WARNING_MESSAGE);
 
       return;
     }
 
-    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);
+    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);
 
-       return;
-     }
+      return;
+    }
     startMsaWSClient(altitle, msa, submitGaps, preserveOrder, seqdataset);
 
   }
 
-
   private void startMsaWSClient(String altitle, AlignmentView msa,
-                     boolean submitGaps, boolean preserveOrder, Alignment seqdataset)
+                                boolean submitGaps, boolean preserveOrder,
+                                Alignment seqdataset)
   {
     if (!locateWebService())
     {
@@ -98,24 +95,33 @@ public class MsaWSClient
     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)) {
-            int pos=jobtitle.indexOf("alignment");
-            jobtitle = WebServiceName.substring(0, pos) + "re-alignment of "+altitle;
-        } else {
-            jobtitle = WebServiceName+" of "+altitle;
-        }
-    } else {
-        jobtitle = WebServiceName+(submitGaps? " re" : " ") +"alignment of "+altitle;
+    if (jobtitle.endsWith("alignment"))
+    {
+      if (submitGaps
+          && (!jobtitle.endsWith("realignment")
+              || jobtitle.indexOf("profile") == -1))
+      {
+        int pos = jobtitle.indexOf("alignment");
+        jobtitle = WebServiceName.substring(0, pos) + "re-alignment of " +
+            altitle;
+      }
+      else
+      {
+        jobtitle = WebServiceName + " of " + altitle;
+      }
+    }
+    else
+    {
+      jobtitle = WebServiceName + (submitGaps ? " re" : " ") + "alignment of " +
+          altitle;
     }
 
     MsaWSThread msathread = new MsaWSThread(server, WsURL, wsInfo, alignFrame,
-                                               WebServiceName,
-                                               jobtitle,
-                                               msa,
-                                               submitGaps, preserveOrder, seqdataset);
+                                            WebServiceName,
+                                            jobtitle,
+                                            msa,
+                                            submitGaps, preserveOrder,
+                                            seqdataset);
     wsInfo.setthisService(msathread);
     msathread.start();
   }
diff --git a/src/jalview/ws/MsaWSThread.java b/src/jalview/ws/MsaWSThread.java
index c123b7e..c40c23b 100644
--- a/src/jalview/ws/MsaWSThread.java
+++ b/src/jalview/ws/MsaWSThread.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -58,7 +58,8 @@ class MsaWSThread
 
   // order
 
-  class MsaWSJob extends WSThread.WSJob
+  class MsaWSJob
+      extends WSThread.WSJob
   {
     // hold special input for this
     vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.
@@ -157,7 +158,8 @@ class MsaWSThread
     public boolean hasResults()
     {
       if (subjobComplete && result != null && result.isFinished()
-          && ((MsaResult) result).getMsa() != null && ((MsaResult) result).getMsa().getSeqs() != null)
+          && ( (MsaResult) result).getMsa() != null &&
+          ( (MsaResult) result).getMsa().getSeqs() != null)
       {
         return true;
       }
@@ -172,10 +174,10 @@ class MsaWSThread
         SequenceI[] alseqs = null;
         char alseq_gapchar = '-';
         int alseq_l = 0;
-        if (((MsaResult) result).getMsa() != null)
+        if ( ( (MsaResult) result).getMsa() != null)
         {
-          alseqs = getVamsasAlignment(((MsaResult) result).getMsa());
-          alseq_gapchar = ((MsaResult) result).getMsa().getGapchar().charAt(0);
+          alseqs = getVamsasAlignment( ( (MsaResult) result).getMsa());
+          alseq_gapchar = ( (MsaResult) result).getMsa().getGapchar().charAt(0);
           alseq_l = alseqs.length;
         }
         if (emptySeqs.size() > 0)
@@ -266,26 +268,31 @@ class MsaWSThread
       }
       return null;
     }
+
     /**
      * mark subjob as cancelled and set result object appropriatly
      */
-    void cancel() {
-      cancelled=true;
+    void cancel()
+    {
+      cancelled = true;
       subjobComplete = true;
       result = null;
     }
+
     /**
      *
      * @return boolean true if job can be submitted.
      */
-    boolean hasValidInput() {
-      if (seqs.getSeqs()!=null)
+    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
 
@@ -355,11 +362,14 @@ class MsaWSThread
           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;
@@ -383,7 +393,7 @@ class MsaWSThread
             {
               // CANCELLED_JOB
               cancelledMessage = "Job cancelled.";
-              ((MsaWSJob) jobs[job]).cancel();
+              ( (MsaWSJob) jobs[job]).cancel();
               wsInfo.setStatus(jobs[job].jobnum,
                                WebserviceInfo.STATE_CANCELLED_OK);
             }
@@ -409,7 +419,8 @@ class MsaWSThread
             cancelledMessage +=
                 ("\nProblems cancelling the job : Exception received...\n"
                  + exc + "\n");
-            Cache.log.warn("Exception whilst cancelling "+jobs[job].jobId,exc);
+            Cache.log.warn("Exception whilst cancelling " + jobs[job].jobId,
+                           exc);
           }
           wsInfo.setProgressText(jobs[job].jobnum, OutputHeader
                                  + cancelledMessage + "\n");
@@ -432,13 +443,19 @@ class MsaWSThread
       }
     }
   }
-  void pollJob(WSJob job) throws Exception {
-    ((MsaWSJob) job).result = server.getResult(((MsaWSJob) job).jobId);
+
+  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());
+    if (! (job instanceof MsaWSJob))
+    {
+      throw new Error("StartJob(MsaWSJob) called on a WSJobInstance " +
+                      job.getClass());
     }
     MsaWSJob j = (MsaWSJob) job;
     if (j.submitted)
@@ -456,7 +473,7 @@ class MsaWSThread
       j.result = new MsaResult();
       j.result.setFinished(true);
       j.result.setStatus("Empty Alignment Job");
-      ((MsaResult) j.result).setMsa(null);
+      ( (MsaResult) j.result).setMsa(null);
     }
     try
     {
@@ -534,7 +551,8 @@ class MsaWSThread
         if (jobs[j].submitted && jobs[j].subjobComplete && jobs[j].hasResults())
         {
           results++;
-          vamsas.objects.simple.Alignment valign = ((MsaResult) jobs[j].result).getMsa();
+          vamsas.objects.simple.Alignment valign = ( (MsaResult) jobs[j].result).
+              getMsa();
           if (valign != null)
           {
             wsInfo.appendProgressText(jobs[j].jobnum,
@@ -579,31 +597,39 @@ class MsaWSThread
         }
       });
       wsInfo.setResultsReady();
-    } else
+    }
+    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][];
+    SequenceI[][] results = new SequenceI[jobs.length][];
     AlignmentOrder[] orders = new AlignmentOrder[jobs.length];
 
-    for (int j=0; j<jobs.length; j++) {
-      if (jobs[j].hasResults()) {
+    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;
+      }
+      else
+      {
+        results[j] = null;
       }
     }
     Object[] newview = input.getUpdatedView(results, orders, '-');
     // trash references to original result data
-    for (int j=0; j<jobs.length; j++) {
+    for (int j = 0; j < jobs.length; j++)
+    {
       results[j] = null;
       orders[j] = null;
     }
@@ -620,8 +646,8 @@ class MsaWSThread
     if (newFrame)
     {
       AlignFrame af = new AlignFrame(al, columnselection,
-                                           AlignFrame.DEFAULT_WIDTH,
-                                           AlignFrame.DEFAULT_HEIGHT);
+                                     AlignFrame.DEFAULT_WIDTH,
+                                     AlignFrame.DEFAULT_HEIGHT);
 
       // >>>This is a fix for the moment, until a better solution is
       // found!!<<<
@@ -671,7 +697,7 @@ class MsaWSThread
           for (int i = 0, l = alorders.size(); i < l; i++)
           {
             af.addSortByOrderMenuItem(WebServiceName
-                                      +( (String) names.get(i)) +
+                                      + ( (String) names.get(i)) +
                                       " Ordering",
                                       (AlignmentOrder) alorders.get(i));
           }
diff --git a/src/jalview/ws/WSClient.java b/src/jalview/ws/WSClient.java
index 17f51c0..8c9acb5 100755
--- a/src/jalview/ws/WSClient.java
+++ b/src/jalview/ws/WSClient.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,8 +18,8 @@
  */
 package jalview.ws;
 
+import ext.vamsas.*;
 import jalview.gui.*;
-import ext.vamsas.ServiceHandle;
 
 public class WSClient
 {
@@ -39,9 +39,9 @@ public class WSClient
    */
   protected java.util.Hashtable ServiceActions;
   {
-      ServiceActions = new java.util.Hashtable();
-      ServiceActions.put("MsaWS", "Multiple Sequence Alignment");
-      ServiceActions.put("SecStrPred", "Secondary Structure Prediction");
+    ServiceActions = new java.util.Hashtable();
+    ServiceActions.put("MsaWS", "Multiple Sequence Alignment");
+    ServiceActions.put("SecStrPred", "Secondary Structure Prediction");
   };
   public WSClient()
   {
@@ -57,7 +57,7 @@ public class WSClient
     }
     else
     {
-      WebServiceJobTitle = sh.getAbstractName()+" using "+sh.getName();
+      WebServiceJobTitle = sh.getAbstractName() + " using " + sh.getName();
 
     }
     WebServiceReference = sh.getDescription();
diff --git a/src/jalview/ws/WSClientI.java b/src/jalview/ws/WSClientI.java
index 452072e..d3f473f 100755
--- a/src/jalview/ws/WSClientI.java
+++ b/src/jalview/ws/WSClientI.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -20,15 +20,17 @@ package jalview.ws;
 
 public interface WSClientI
 {
-    /**
-     *
-     * @return boolean true if job is cancellable
-     */
-    boolean isCancellable();
-    /**
-     *
-     * @return boolean true if results can be merged into the source of input data
-     */
+  /**
+   *
+   * @return boolean true if job is cancellable
+   */
+  boolean isCancellable();
+
+  /**
+   *
+   * @return boolean true if results can be merged into the source of input data
+   */
   boolean canMergeResults();
+
   void cancelJob();
 }
diff --git a/src/jalview/ws/WSThread.java b/src/jalview/ws/WSThread.java
index 86ee49a..6b6c483 100644
--- a/src/jalview/ws/WSThread.java
+++ b/src/jalview/ws/WSThread.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -16,28 +16,29 @@
  * along 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;
+package jalview.ws;
 
-import jalview.gui.AlignFrame;
-import jalview.gui.WebserviceInfo;
-import jalview.datamodel.AlignmentView;
-import jalview.gui.Desktop;
-import javax.swing.JOptionPane;
-import jalview.bin.Cache;
+import javax.swing.*;
 
-public abstract class WSThread extends Thread
+import jalview.bin.*;
+import jalview.datamodel.*;
+import jalview.gui.*;
+
+public abstract class WSThread
+    extends Thread
 {
-    /**
-     * Generic properties for Web Service Client threads.
-     */
-    AlignFrame alignFrame=null;
+  /**
+   * Generic properties for Web Service Client threads.
+   */
+  AlignFrame alignFrame = null;
   WebserviceInfo wsInfo = null;
-  AlignmentView input=null;
+  AlignmentView input = null;
   boolean jobComplete = false;
-  abstract class WSJob {
-      /**
-       * Generic properties for an individual job within a Web Service Client thread
-       */
+  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
     boolean cancelled = false;
@@ -49,14 +50,18 @@ public abstract class WSThread extends Thread
      * @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();
+
     vamsas.objects.simple.Result result;
   }
-  class JobStateSummary {
+
+  class JobStateSummary
+  {
     int running = 0;
     int queuing = 0;
     int finished = 0;
@@ -86,7 +91,9 @@ public abstract class WSThread extends Thread
           finished++;
           j.subjobComplete = true;
           if (j.hasResults())
+          {
             results++;
+          }
           wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_OK);
         }
         else if (j.result.isFailed())
@@ -138,132 +145,140 @@ public abstract class WSThread extends Thread
   String WebServiceName = null;
   String OutputHeader;
   String WsUrl = null;
-  abstract void pollJob(WSJob job) throws Exception;
+  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++)
+    JobStateSummary jstate = null;
+    if (jobs == null)
     {
-
-      if (!jobs[j].submitted && jobs[j].hasValidInput())
+      jobComplete = true;
+    }
+    while (!jobComplete)
+    {
+      jstate = new JobStateSummary();
+      for (int j = 0; j < jobs.length; j++)
       {
-        StartJob(jobs[j]);
-      }
 
-      if (jobs[j].submitted && !jobs[j].subjobComplete)
-      {
-        try
+        if (!jobs[j].submitted && jobs[j].hasValidInput())
         {
-          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() + ")");
+          StartJob(jobs[j]);
         }
-        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)
+        if (jobs[j].submitted && !jobs[j].subjobComplete)
+        {
+          try
           {
-            jobs[j].allowedServerExceptions--;
-            Cache.log.debug("Sleeping after a server exception.");
-            try
+            pollJob(jobs[j]);
+            if (jobs[j].result == null)
             {
-              Thread.sleep(5000);
+              throw (new Exception(
+                  "Timed out when communicating with server\nTry again later.\n"));
             }
-            catch (InterruptedException ex1)
+            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);
             }
           }
-          else
+          catch (OutOfMemoryError er)
           {
-            Cache.log.warn("Dropping job " + j + " " + jobs[j].jobId);
+            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_SERVERERROR);
+                             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();
           }
         }
-        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);
+        jstate.updateJobPanelState(wsInfo, OutputHeader, jobs[j]);
       }
-      else if (jstate.error > 0)
+      // Decide on overall state based on collected jobs[] states
+      if (jstate.running > 0)
       {
-        wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+        wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
       }
-      else if (jstate.serror > 0)
+      else if (jstate.queuing > 0)
       {
-        wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
+        wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
       }
-    }
-    if (!jobComplete)
-    {
-      try
+      else
       {
-        Thread.sleep(5000);
+        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);
+        }
       }
-      catch (InterruptedException e)
+      if (!jobComplete)
       {
-        Cache.log.debug("Interrupted sleep waiting for next job poll.", e);
+        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);
       }
-      // 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.");
     }
   }
-  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.");
-  }
-}
-abstract void StartJob(WSJob job);
-abstract void parseResult();
+
+  abstract void StartJob(WSJob job);
+
+  abstract void parseResult();
 }
diff --git a/src/org/biojava/dasobert/das/DAS_FeatureRetrieve.java b/src/org/biojava/dasobert/das/DAS_FeatureRetrieve.java
index 99ded7d..051df9f 100755
--- a/src/org/biojava/dasobert/das/DAS_FeatureRetrieve.java
+++ b/src/org/biojava/dasobert/das/DAS_FeatureRetrieve.java
@@ -23,23 +23,14 @@
  */
 package org.biojava.dasobert.das;
 
+import java.io.*;
+import java.lang.reflect.*;
+import java.net.*;
+import java.util.*;
+import java.util.logging.*;
+import javax.xml.parsers.*;
 
-import java.net.URL                         ;
-import java.io.InputStream                  ;
-import org.xml.sax.InputSource              ;
-import org.xml.sax.XMLReader                ;
-import javax.xml.parsers.*                  ;
-import org.xml.sax.*                        ;
-import java.util.ArrayList                  ;
-import java.util.List;
-import java.util.logging.*                  ;
-import java.net.HttpURLConnection           ;
-import java.io.IOException;
-import java.net.ConnectException;
-import java.lang.reflect.Method;
-
-
-
+import org.xml.sax.*;
 
 /**
  * A class to perform a DAS features request
@@ -47,196 +38,222 @@ import java.lang.reflect.Method;
  * @author Andreas Prlic
  *
  */
-public class DAS_FeatureRetrieve {
-
-    List features ;
-    Logger logger     ;
-    int comeBackLater;
-    URL url;
-    /**
-     * @param url the URL the features should be downloaded from
-     *
-     */
-    public DAS_FeatureRetrieve(URL url) {
-        super();
-
-        logger = Logger.getLogger("org.biojava.spice");
-        features = new ArrayList() ;
-        comeBackLater = -1;
-        this.url=url;
-        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.
-     *
-     */
-    public void reload(){
-
-        try {
-
-            InputStream dasInStream = null;
-            try {
-                dasInStream	= open(url);
-            } catch (Exception e ){
-                comeBackLater = -1;
-                System.out.println("NO RESPONSE FROM "+url);
-                logger.log(Level.FINE,"could not open connection to " + url,e);
-                return ;
-            }
-
-
-            SAXParserFactory spfactory =
-                SAXParserFactory.newInstance();
-
-            spfactory.setValidating(false);
-
-            SAXParser saxParser = null ;
-
-            try{
-                saxParser =
-                    spfactory.newSAXParser();
-            } catch (ParserConfigurationException e) {
-                e.printStackTrace();
-            }
-
-
-
-            String vali = System.getProperty("XMLVALIDATION");
-
-            boolean validation = false ;
-            if ( vali != null )
-                if ( vali.equals("true") )
-                    validation = true ;
-
-
-            XMLReader xmlreader = saxParser.getXMLReader();
-
-            //XMLReader xmlreader = XMLReaderFactory.createXMLReader();
-            try {
-                xmlreader.setFeature("http://xml.org/sax/features/validation", 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){
-                e.printStackTrace();
-                logger.log(Level.FINE,"Cannot set load-external-dtd "+validation);
-
-            }
-
-            DAS_Feature_Handler cont_handle = new DAS_Feature_Handler() ;
-            cont_handle.setDASCommand(url.toString());
-            xmlreader.setContentHandler(cont_handle);
-            xmlreader.setErrorHandler(new org.xml.sax.helpers.DefaultHandler());
-            InputSource insource = new InputSource() ;
-            insource.setByteStream(dasInStream);
+public class DAS_FeatureRetrieve
+{
+
+  List features;
+  Logger logger;
+  int comeBackLater;
+  URL url;
+  /**
+   * @param url the URL the features should be downloaded from
+   *
+   */
+  public DAS_FeatureRetrieve(URL url)
+  {
+    super();
+
+    logger = Logger.getLogger("org.biojava.spice");
+    features = new ArrayList();
+    comeBackLater = -1;
+    this.url = url;
+    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.
+   *
+   */
+  public void reload()
+  {
+
+    try
+    {
 
-            try {
-                xmlreader.parse(insource);
-                features = cont_handle.get_features();
-                comeBackLater = cont_handle.getComBackLater();
-            }
-            catch ( Exception 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)
+      InputStream dasInStream = null;
+      try
+      {
+        dasInStream = open(url);
+      }
+      catch (Exception e)
+      {
+        comeBackLater = -1;
+        System.out.println("NO RESPONSE FROM " + url);
+        logger.log(Level.FINE, "could not open connection to " + url, e);
+        return;
+      }
+
+      SAXParserFactory spfactory =
+          SAXParserFactory.newInstance();
+
+      spfactory.setValidating(false);
+
+      SAXParser saxParser = null;
+
+      try
+      {
+        saxParser =
+            spfactory.newSAXParser();
+      }
+      catch (ParserConfigurationException e)
+      {
+        e.printStackTrace();
+      }
+
+      String vali = System.getProperty("XMLVALIDATION");
+
+      boolean validation = false;
+      if (vali != null)
+      {
+        if (vali.equals("true"))
         {
-            ex.printStackTrace();
-            comeBackLater = -1;
+          validation = true;
         }
+      }
+
+      XMLReader xmlreader = saxParser.getXMLReader();
+
+      //XMLReader xmlreader = XMLReaderFactory.createXMLReader();
+      try
+      {
+        xmlreader.setFeature("http://xml.org/sax/features/validation",
+                             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)
+      {
+        e.printStackTrace();
+        logger.log(Level.FINE, "Cannot set load-external-dtd " + validation);
+
+      }
+
+      DAS_Feature_Handler cont_handle = new DAS_Feature_Handler();
+      cont_handle.setDASCommand(url.toString());
+      xmlreader.setContentHandler(cont_handle);
+      xmlreader.setErrorHandler(new org.xml.sax.helpers.DefaultHandler());
+      InputSource insource = new InputSource();
+      insource.setByteStream(dasInStream);
+
+      try
+      {
+        xmlreader.parse(insource);
+        features = cont_handle.get_features();
+        comeBackLater = cont_handle.getComBackLater();
+      }
+      catch (Exception 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();
+      }
     }
-
-
-    /** 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 {
+    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*/
+  public static HttpURLConnection openHttpURLConnection(URL url)
+      throws IOException, ConnectException
+  {
     HttpURLConnection huc = null;
     huc = (HttpURLConnection) url.openConnection();
 
-    String os_name    = java.lang.System.getProperty("os.name");
+    String os_name = java.lang.System.getProperty("os.name");
     String os_version = java.lang.System.getProperty("os.version");
-    String os_arch    = java.lang.System.getProperty("os.arch");
+    String os_arch = java.lang.System.getProperty("os.arch");
     String VERSION = "1.0";
 
-    String userAgent = "Jalview " + VERSION + "("+os_name+"; "+os_arch + " ; "+ os_version+")";
+    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);
+    huc.addRequestProperty("User-Agent", userAgent);
     //logger.finest("opening "+url);
 
 
     int timeout = 10000;
-    System.setProperty("sun.net.client.defaultConnectTimeout", timeout+"");
-    System.setProperty("sun.net.client.defaultReadTimeout", 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
-        // seems java 1.5 does not watch the System properties any longer...
-        // and java 1.4 did not provide these...
+    // 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
 
-    try {
-        // try to use reflection to set timeout property
-        Class urlconnectionClass = Class.forName("java.net.HttpURLConnection");
-
-        Method setconnecttimeout = urlconnectionClass.getMethod (
-                                     "setConnectTimeout", new Class [] {int.class}
-                                     );
-        setconnecttimeout.invoke(huc,new Object[] {new Integer(timeout)});
-
-        Method setreadtimeout = urlconnectionClass.getMethod (
-                                  "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) {
-        //e.printStackTrace();
-        // most likely it was a NoSuchMEthodException and we are running java 1.4.
-    }
-    return huc;
+    try
+    {
+      // try to use reflection to set timeout property
+      Class urlconnectionClass = Class.forName("java.net.HttpURLConnection");
+
+      Method setconnecttimeout = urlconnectionClass.getMethod(
+          "setConnectTimeout", new Class[]
+          {int.class}
+          );
+      setconnecttimeout.invoke(huc, new Object[]
+                               {new Integer(timeout)});
+
+      Method setreadtimeout = urlconnectionClass.getMethod(
+          "setReadTimeout", new Class[]
+          {int.class}
+          );
+      setreadtimeout.invoke(huc, new Object[]
+                            {new Integer(timeout)});
+      //System.out.println("successfully set java 1.5 timeout");
     }
-
-
-    private InputStream open(URL url)
-    throws java.io.IOException, java.net.ConnectException
+    catch (Exception e)
     {
-        InputStream inStream = null;
-
+      //e.printStackTrace();
+      // most likely it was a NoSuchMEthodException and we are running java 1.4.
+    }
+    return huc;
+  }
 
-        HttpURLConnection huc = openHttpURLConnection(url);
+  private InputStream open(URL url)
+      throws java.io.IOException, java.net.ConnectException
+  {
+    InputStream inStream = null;
 
-        inStream = huc.getInputStream();
+    HttpURLConnection huc = openHttpURLConnection(url);
 
-        return inStream;
+    inStream = huc.getInputStream();
 
-    }
+    return inStream;
 
-    /** returns a List of Features
-     * @return a List of Maps containing the features*/
-    public List get_features() {
+  }
 
-        return features;
-    }
+  /** returns a List of Features
+   * @return a List of Maps containing the features*/
+  public List get_features()
+  {
 
-    /** returns the comeBackLater value - if a server returned suchh -
-     *
-     * @return comeBackLater in seconds, or -1 if not provided by server
-     */
-    public int getComeBackLater(){
+    return features;
+  }
 
-        return comeBackLater;
+  /** returns the comeBackLater value - if a server returned suchh -
+   *
+   * @return comeBackLater in seconds, or -1 if not provided by server
+   */
+  public int getComeBackLater()
+  {
 
-    }
+    return comeBackLater;
 
+  }
 
 }
diff --git a/src/org/biojava/dasobert/das/DAS_Feature_Handler.java b/src/org/biojava/dasobert/das/DAS_Feature_Handler.java
index 105388e..b506c51 100755
--- a/src/org/biojava/dasobert/das/DAS_Feature_Handler.java
+++ b/src/org/biojava/dasobert/das/DAS_Feature_Handler.java
@@ -23,168 +23,204 @@
  */
 package org.biojava.dasobert.das;
 
-import org.xml.sax.helpers.DefaultHandler;
-import org.xml.sax.Attributes;
+import java.util.*;
 
-import java.util.ArrayList ;
-import java.util.HashMap ;
-import java.util.List;
+import org.xml.sax.*;
+import org.xml.sax.helpers.*;
 
 /**
  * a class to parse the response of a DAS - Feature request
  * @author Andreas Prlic
  *
  */
-public class DAS_Feature_Handler  extends DefaultHandler{
-    
-    /**
-     * 
-     */
-    List features ;
-    boolean first_flag ;
-    HashMap feature ;
-    String featurefield ;
-    String characterdata ;
-    String dasCommand ;
-    
-    int comeBackLater ;
-
-    int maxFeatures ;
-
-    public DAS_Feature_Handler() {
-        super();
-        
-        features= new ArrayList() ;
-        first_flag = true ;
-        featurefield = "" ;
-        characterdata = "";
-        dasCommand = "" ;
-        comeBackLater = -1; 
-	maxFeatures = -1;
-    }
+public class DAS_Feature_Handler
+    extends DefaultHandler
+{
 
-    /** 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
-    */
+  /**
+   *
+   */
+  List features;
+  boolean first_flag;
+  HashMap feature;
+  String featurefield;
+  String characterdata;
+  String dasCommand;
 
-    public void setMaxFeatures(int max) {
-	maxFeatures = max;
-    }
+  int comeBackLater;
 
-    public int getMaxFeatures() {
-	return maxFeatures;
-    }
-    
-    public void setDASCommand(String cmd) { dasCommand = cmd ;}
-    public String getDASCommand() { return dasCommand; }
-    
-    public List get_features() {
-        return features ;
-    }
-    
-    public int getComBackLater(){
-        return comeBackLater;
+  int maxFeatures;
+
+  public DAS_Feature_Handler()
+  {
+    super();
+
+    features = new ArrayList();
+    first_flag = true;
+    featurefield = "";
+    characterdata = "";
+    dasCommand = "";
+    comeBackLater = -1;
+    maxFeatures = -1;
+  }
+
+  /** 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)
+  {
+    maxFeatures = max;
+  }
+
+  public int getMaxFeatures()
+  {
+    return maxFeatures;
+  }
+
+  public void setDASCommand(String cmd)
+  {
+    dasCommand = cmd;
+  }
+
+  public String getDASCommand()
+  {
+    return dasCommand;
+  }
+
+  public List get_features()
+  {
+    return features;
+  }
+
+  public int getComBackLater()
+  {
+    return comeBackLater;
+  }
+
+  void start_feature(String uri, String name, String qName, Attributes atts)
+  {
+
+    if ( (maxFeatures > 0) && (features.size() > maxFeatures))
+    {
+      characterdata = "";
+      return;
     }
-    
-    void start_feature(String uri, String name, String qName, Attributes atts) {
-
-	if (( maxFeatures > 0 ) && ( features.size() > maxFeatures ) ) {
-	    characterdata = "";
-	    return;
-	}
-        feature = new HashMap() ;
-        String id 	= atts.getValue("id");
-        feature.put("id",id);
-        feature.put("dassource",dasCommand);
-        characterdata = "";
+    feature = new HashMap();
+    String id = atts.getValue("id");
+    feature.put("id", id);
+    feature.put("dassource", dasCommand);
+    characterdata = "";
+  }
+
+  void add_featuredata(String uri, String name, String qName)
+  {
+    //System.out.println("featurefield "+featurefield+ " data "+characterdata);
+    // NOTE can have multiple lines ..
+
+    if ( (maxFeatures > 0) && (features.size() > maxFeatures))
+    {
+      return;
     }
-    
-    void add_featuredata(String uri, String name, String qName) {
-        //System.out.println("featurefield "+featurefield+ " data "+characterdata);
-        // NOTE can have multiple lines ..
-        
-	if (( maxFeatures > 0 ) && ( features.size() > maxFeatures ) ) {
-	    return;
-	}
-
-
-        String data = (String)feature.get(featurefield);
-        if (data != null){
-            characterdata = data + " " + characterdata;
-        }
-        
-        feature.put(featurefield,characterdata);
-        featurefield = "";
-        characterdata = "";
+
+    String data = (String) feature.get(featurefield);
+    if (data != null)
+    {
+      characterdata = data + " " + characterdata;
     }
-    
-    private void addLink(String uri, String name, String qName, Attributes atts) {
-        String href = atts.getValue("href");
-        feature.put("LINK",href);
-        characterdata="";
-        featurefield = "LINK-TEXT";
-                
+
+    feature.put(featurefield, characterdata);
+    featurefield = "";
+    characterdata = "";
+  }
+
+  private void addLink(String uri, String name, String qName, Attributes atts)
+  {
+    String href = atts.getValue("href");
+    feature.put("LINK", href);
+    characterdata = "";
+    featurefield = "LINK-TEXT";
+
+  }
+
+  public void startElement(String uri, String name, String qName,
+                           Attributes atts)
+  {
+    //System.out.println("new element "+qName);
+
+    if (qName.equals("FEATURE"))
+    {
+      start_feature(uri, name, qName, atts);
     }
-    
-    public void startElement (String uri, String name, String qName, Attributes atts){
-        //System.out.println("new element "+qName);
-        
-        if (qName.equals("FEATURE")) 
-            start_feature(uri,  name,  qName,  atts);
-        else if ( qName.equals("LINK"))
-            addLink(uri,name,qName, atts);
-        else if ( qName.equals("METHOD") || 
-                qName.equals("TYPE") ||
-                qName.equals("START") ||
-                qName.equals("END") ||
-                qName.equals("NOTE") ||                
-                qName.equals("SCORE")
-        ){
-            characterdata ="";
-            featurefield = qName ;
-        }
-        
+    else if (qName.equals("LINK"))
+    {
+      addLink(uri, name, qName, atts);
     }
-    
-    public void startDocument() {
+    else if (qName.equals("METHOD") ||
+             qName.equals("TYPE") ||
+             qName.equals("START") ||
+             qName.equals("END") ||
+             qName.equals("NOTE") ||
+             qName.equals("SCORE")
+        )
+    {
+      characterdata = "";
+      featurefield = qName;
     }
-    
-    public void endDocument ()	{        
+
+  }
+
+  public void startDocument()
+  {
+  }
+
+  public void endDocument()
+  {
+  }
+
+  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")
+        )
+    {
+      add_featuredata(uri, name, qName);
     }
-    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")
-        ) {
-            add_featuredata(uri,name,qName);
-        }
-        else if ( qName.equals("FEATURE")) {
-
-	    if ( maxFeatures > 0 ) {
-		if ( features.size() < maxFeatures ) {
-		     features.add(feature);
-		} 
-	    } else {
-		// no restriction
-		features.add(feature);
-	    }
+    else if (qName.equals("FEATURE"))
+    {
+
+      if (maxFeatures > 0)
+      {
+        if (features.size() < maxFeatures)
+        {
+          features.add(feature);
         }
+      }
+      else
+      {
+        // no restriction
+        features.add(feature);
+      }
     }
-    
-    public void characters (char ch[], int start, int length){
+  }
 
-        for (int i = start; i < start + length; i++) {
-            
-            characterdata += ch[i];
-        }
-        
+  public void characters(char ch[], int start, int length)
+  {
+
+    for (int i = start; i < start + length; i++)
+    {
+
+      characterdata += ch[i];
     }
-    
+
+  }
+
 }
diff --git a/src/org/biojava/dasobert/das/FeatureThread.java b/src/org/biojava/dasobert/das/FeatureThread.java
index 8c8923e..83219df 100755
--- a/src/org/biojava/dasobert/das/FeatureThread.java
+++ b/src/org/biojava/dasobert/das/FeatureThread.java
@@ -22,159 +22,173 @@
  *
  */
 
-package org.biojava.dasobert.das ;
+package org.biojava.dasobert.das;
 
-import java.util.*;
 import java.net.*;
-import java.util.logging.* ;
-import org.biojava.dasobert.eventmodel.FeatureListener;
-import org.biojava.dasobert.eventmodel.FeatureEvent;
-import org.biojava.dasobert.dasregistry.Das1Source;
+import java.util.*;
+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
- * 
+ *
  * @author Andreas Prlic
  */
 
 
 
 public class FeatureThread
-    implements Runnable 
+    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.
-     */
-    public static int MAX_COME_BACK_ITERATIONS = 5;
-
-    public static int MAX_NR_FEATURES = 300;
-
-    static Logger logger = Logger.getLogger("org.biojava.spice");
-
-    Das1Source dasSource;
-    String ac ;
-    List featureListeners;
-    Thread thread;
-    
-    public FeatureThread (String accessionCode, Das1Source dasSource) {
-	this.dasSource = dasSource;
-	this.ac = accessionCode;
-	featureListeners = new ArrayList();
-    }
 
-    public void addFeatureListener(FeatureListener li) {
-	featureListeners.add(li);
-    }
-    
-    public void clearFeatureListeners() {
-	featureListeners.clear();
-    }
+  /** 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;
+
+  public static int MAX_NR_FEATURES = 300;
+
+  static Logger logger = Logger.getLogger("org.biojava.spice");
+
+  Das1Source dasSource;
+  String ac;
+  List featureListeners;
+  Thread thread;
+
+  public FeatureThread(String accessionCode, Das1Source dasSource)
+  {
+    this.dasSource = dasSource;
+    this.ac = accessionCode;
+    featureListeners = new ArrayList();
+  }
+
+  public void addFeatureListener(FeatureListener li)
+  {
+    featureListeners.add(li);
+  }
+
+  public void clearFeatureListeners()
+  {
+    featureListeners.clear();
+  }
+
+  public synchronized void stop()
+  {
+    thread = null;
+    notify();
+  }
+
+  public void run()
+  {
+    Thread me = Thread.currentThread();
+    while (thread == me)
+    {
+      String url = dasSource.getUrl();
+      String queryString = url + "features?segment=" + ac;
+      URL cmd = null;
+      try
+      {
+        cmd = new URL(queryString);
+      }
+      catch (MalformedURLException e)
+      {
+        logger.warning("got MalformedURL from das source " + dasSource);
+        e.printStackTrace();
+
+      }
+
+      logger.info("requesting features from " + cmd);
+      DAS_FeatureRetrieve ftmp = new DAS_FeatureRetrieve(cmd);
+
+      int comeBackLater = ftmp.getComeBackLater();
+      int securityCounter = 0;
+      while ( (thread == me) && (comeBackLater > 0))
+      {
+        securityCounter++;
+        if (securityCounter >= MAX_COME_BACK_ITERATIONS)
+        {
+          comeBackLater = -1;
+          break;
 
-    public synchronized void stop(){
-	thread = null;
-	notify();
-    }
+        }
+        notifyComeBackLater(comeBackLater);
+        // server is still calculating - asks us to come back later
+        try
+        {
+          wait(comeBackLater);
+        }
+        catch (InterruptedException e)
+        {
+          comeBackLater = -1;
+          break;
+        }
 
-    
-
-
-    public void run() {
-	Thread me = Thread.currentThread();
-	while ( thread == me) {
-	    String url = dasSource.getUrl();
-	    String queryString = url + "features?segment="+ ac ;
-	    URL cmd = null ;
-	    try {
-		cmd = new URL(queryString);
-	    } catch (MalformedURLException e ) {
-		logger.warning("got MalformedURL from das source " +dasSource);
-		e.printStackTrace();
-		
-	    }
-
-	    logger.info("requesting features from " + cmd);
-	    DAS_FeatureRetrieve ftmp = new DAS_FeatureRetrieve(cmd);
-        
-	    
-	    int comeBackLater = ftmp.getComeBackLater();
-	    int securityCounter = 0;
-	    while ( (thread == me) && ( comeBackLater > 0 )) {
-		securityCounter++;
-		if ( securityCounter >= MAX_COME_BACK_ITERATIONS){
-		    comeBackLater = -1; 
-		    break;
-                
-		}
-		notifyComeBackLater(comeBackLater);
-		// server is still calculating - asks us to come back later
-		try {
-		    wait (comeBackLater);
-		} catch (InterruptedException e){
-		    comeBackLater = -1;
-		    break;
-		}
-                
-		ftmp.reload();
-		comeBackLater = ftmp.getComeBackLater(); 
-	    }
-
-	    if ( ! (thread == me ) ) {
-		break;
-	    }
-
-	    List features = ftmp.get_features();
-        
-	    // 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);
-		features = features.subList(0,MAX_NR_FEATURES);
-	    }
-      
-              
-	    // notify FeatureListeners
-	    Map[] feats = (Map[])features.toArray(new Map[features.size()]);
-	    notifyFeatureListeners(feats);
-
-	    break;
-
-
-	}
-	thread = null;
+        ftmp.reload();
+        comeBackLater = ftmp.getComeBackLater();
+      }
 
-    }
+      if (! (thread == me))
+      {
+        break;
+      }
 
-    public void start() {
-	thread = new Thread(this);
-	thread.start();
-    }
+      List features = ftmp.get_features();
+
+      // 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);
+        features = features.subList(0, MAX_NR_FEATURES);
+      }
+
+      // notify FeatureListeners
+      Map[] feats = (Map[]) features.toArray(new Map[features.size()]);
+      notifyFeatureListeners(feats);
+
+      break;
 
-    private void notifyFeatureListeners(Map[] feats){
-        logger.finest("FeatureThread found " + feats.length + " features");
-        FeatureEvent fevent = new FeatureEvent(feats,dasSource);
-        Iterator fiter = featureListeners.iterator();
-        while (fiter.hasNext()){
-            FeatureListener fi = (FeatureListener)fiter.next();
-            fi.newFeatures(fevent);
-        }
     }
-    
- /** the Annotation server requested to be queried again in a while
-     * 
-     * @param comeBackLater
-     */
-    private void notifyComeBackLater(int comeBackLater){
-        FeatureEvent event = new FeatureEvent(new HashMap[0],dasSource);
-        event.setComeBackLater(comeBackLater);
-        Iterator fiter = featureListeners.iterator();
-        while (fiter.hasNext()){
-            FeatureListener fi = (FeatureListener)fiter.next();
-            fi.comeBackLater(event);
-        }
-        
+    thread = null;
+
+  }
+
+  public void start()
+  {
+    thread = new Thread(this);
+    thread.start();
+  }
+
+  private void notifyFeatureListeners(Map[] feats)
+  {
+    logger.finest("FeatureThread found " + feats.length + " features");
+    FeatureEvent fevent = new FeatureEvent(feats, dasSource);
+    Iterator fiter = featureListeners.iterator();
+    while (fiter.hasNext())
+    {
+      FeatureListener fi = (FeatureListener) fiter.next();
+      fi.newFeatures(fevent);
+    }
+  }
+
+  /** the Annotation server requested to be queried again in a while
+   *
+   * @param comeBackLater
+   */
+  private void notifyComeBackLater(int comeBackLater)
+  {
+    FeatureEvent event = new FeatureEvent(new HashMap[0], dasSource);
+    event.setComeBackLater(comeBackLater);
+    Iterator fiter = featureListeners.iterator();
+    while (fiter.hasNext())
+    {
+      FeatureListener fi = (FeatureListener) fiter.next();
+      fi.comeBackLater(event);
     }
 
+  }
 
 }
-
diff --git a/src/org/biojava/dasobert/das2/Das2Capability.java b/src/org/biojava/dasobert/das2/Das2Capability.java
index 5b5c17c..43fad73 100755
--- a/src/org/biojava/dasobert/das2/Das2Capability.java
+++ b/src/org/biojava/dasobert/das2/Das2Capability.java
@@ -16,30 +16,35 @@
  * at:
  *
  *      http://www.biojava.org/
- * 
+ *
  * Created on Feb 9, 2006
  *
  */
 package org.biojava.dasobert.das2;
 
-public interface Das2Capability {
-
-    public boolean equals(Das2Capability other);
-    public int hashCode();
-    
-    public void setCapability(String type);
-    public String getCapability();
-    
-    public void setQueryUri(String id);
-    public String getQueryUri();
-    
-    public void setFormats(String[] formats);
-    public String[] getFormats();
-    
-    /** checks if this capability is actually of das1 style
-     * 
-     * @return boolean true if the capability is in DAS1 style
-     */
-    public boolean isDas1Style();
-    
+public interface Das2Capability
+{
+
+  public boolean equals(Das2Capability other);
+
+  public int hashCode();
+
+  public void setCapability(String type);
+
+  public String getCapability();
+
+  public void setQueryUri(String id);
+
+  public String getQueryUri();
+
+  public void setFormats(String[] formats);
+
+  public String[] getFormats();
+
+  /** 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 273defa..5a061c7 100755
--- a/src/org/biojava/dasobert/das2/Das2CapabilityImpl.java
+++ b/src/org/biojava/dasobert/das2/Das2CapabilityImpl.java
@@ -16,94 +16,115 @@
  * at:
  *
  *      http://www.biojava.org/
- * 
+ *
  * Created on Feb 9, 2006
  *
  */
 package org.biojava.dasobert.das2;
 
-public class Das2CapabilityImpl 
-implements Das2Capability{
-
-    String capability;
-    String[] formats;
-    String queryId;
-    
-    public static String DAS1_CAPABILITY_PREFIX = "das1:";
-    
-    public Das2CapabilityImpl() {
-        super();
-        capability = "undef";
-        queryId = "";
-        formats = new String[0];
+public class Das2CapabilityImpl
+    implements Das2Capability
+{
+
+  String capability;
+  String[] formats;
+  String queryId;
+
+  public static String DAS1_CAPABILITY_PREFIX = "das1:";
+
+  public Das2CapabilityImpl()
+  {
+    super();
+    capability = "undef";
+    queryId = "";
+    formats = new String[0];
+
+  }
+
+  public boolean isDas1Style()
+  {
 
+    if (capability == null)
+    {
+      return false;
     }
-    
-    public boolean isDas1Style(){
-        
-        if ( capability == null)
-            return false;
-        if ( capability.length() < DAS1_CAPABILITY_PREFIX.length())
-            return false;
-        if ( capability.substring(0,DAS1_CAPABILITY_PREFIX.length()).equals(DAS1_CAPABILITY_PREFIX))
-            return true;
-        return false;
-    
+    if (capability.length() < DAS1_CAPABILITY_PREFIX.length())
+    {
+      return false;
     }
-    
-    public boolean equals(Das2Capability other){
-        
-        boolean status = true;
-        
-        if (!  capability.equals(other.getCapability()))
-            status = false;
-        if ( ! queryId.equals(other.getQueryUri()))
-            status = false;
-        
-        return status;
+    if (capability.substring(0,
+        DAS1_CAPABILITY_PREFIX.length()).equals(DAS1_CAPABILITY_PREFIX))
+    {
+      return true;
     }
-    
-    public int hashCode(){
-        int h = 7;
-        h = 31 * h + ( null == capability ? 0 : capability.hashCode()) ;
-        h = 31 * h + ( null == queryId    ? 0 : queryId.hashCode()) ;
-        
-        return h;
+    return false;
+
+  }
+
+  public boolean equals(Das2Capability other)
+  {
+
+    boolean status = true;
+
+    if (!capability.equals(other.getCapability()))
+    {
+      status = false;
     }
-    
-    public String toString(){
-        String txt ="capability " + capability + " queryId " + queryId;
-        return txt;
+    if (!queryId.equals(other.getQueryUri()))
+    {
+      status = false;
     }
 
-    public String getCapability() {
-        
-        return capability;
-    }
+    return status;
+  }
 
-    public String[] getFormats() {      
-        return formats;
-    }
+  public int hashCode()
+  {
+    int h = 7;
+    h = 31 * h + (null == capability ? 0 : capability.hashCode());
+    h = 31 * h + (null == queryId ? 0 : queryId.hashCode());
 
-    public String getQueryUri() {      
-        return queryId;
-    }
+    return h;
+  }
 
-    public void setCapability(String type) {
-       capability = type;
-        
-    }
+  public String toString()
+  {
+    String txt = "capability " + capability + " queryId " + queryId;
+    return txt;
+  }
 
-    public void setFormats(String[] formats) {
-       
-        this.formats = formats; 
-    }
+  public String getCapability()
+  {
 
-    public void setQueryUri(String id) {
-       queryId = id;
-        
-    }
-    
-    
+    return capability;
+  }
+
+  public String[] getFormats()
+  {
+    return formats;
+  }
+
+  public String getQueryUri()
+  {
+    return queryId;
+  }
+
+  public void setCapability(String type)
+  {
+    capability = type;
+
+  }
+
+  public void setFormats(String[] formats)
+  {
+
+    this.formats = formats;
+  }
+
+  public void setQueryUri(String id)
+  {
+    queryId = id;
+
+  }
 
 }
diff --git a/src/org/biojava/dasobert/das2/Das2Source.java b/src/org/biojava/dasobert/das2/Das2Source.java
index 21a008a..1d96298 100755
--- a/src/org/biojava/dasobert/das2/Das2Source.java
+++ b/src/org/biojava/dasobert/das2/Das2Source.java
@@ -16,25 +16,27 @@
  * at:
  *
  *      http://www.biojava.org/
- * 
+ *
  * Created on Feb 9, 2006
  *
  */
 package org.biojava.dasobert.das2;
 
-import org.biojava.dasobert.dasregistry.DasSource;
+import org.biojava.dasobert.dasregistry.*;
 
 public interface Das2Source
-extends DasSource {
+    extends DasSource
+{
+
+  public Das2Capability[] getDas2Capabilities();
+
+  public void setDas2Capabilities(Das2Capability[] capabilities);
 
-   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);
-    *
-    * @return true if the DasSource has DAS1 capabilties
-    */
-   public boolean hasDas1Capabilities();
+  /** 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 aca49b2..efdf40d 100755
--- a/src/org/biojava/dasobert/das2/Das2SourceImpl.java
+++ b/src/org/biojava/dasobert/das2/Das2SourceImpl.java
@@ -16,129 +16,142 @@
  * at:
  *
  *      http://www.biojava.org/
- * 
+ *
  * Created on Feb 9, 2006
  *
  */
 package org.biojava.dasobert.das2;
 
-import org.biojava.dasobert.dasregistry.Das1Source;
-import org.biojava.dasobert.dasregistry.DasSource;
+import org.biojava.dasobert.dasregistry.*;
 
-public class Das2SourceImpl 
-extends Das1Source
-implements Das2Source 
+public class Das2SourceImpl
+    extends Das1Source implements Das2Source
 
 {
 
-    Das2Capability[] capabilities;
-    
-    public Das2SourceImpl() {
-        super();
+  Das2Capability[] capabilities;
+
+  public Das2SourceImpl()
+  {
+    super();
+
+    capabilities = new Das2Capability[0];
+  }
+
+  /**  compare if two DasSources are identical
+   *
+   */
+  public boolean equals(DasSource other)
+  {
 
-        capabilities = new Das2Capability[0];
+    if (this == other)
+    {
+      return true;
     }
-    
-    
-    /**  compare if two DasSources are identical
-     * 
-     */
-    public boolean equals(DasSource other){
-        
-        if ( this == other)
-            return true;
-        
-        if ( ( other == null) || (other.getClass() != this.getClass()))    
-            return false;
-       
-        // to compare if two Das2Sources are identical we do the following:
-        //  we check the capabilities
-        
-        Das2SourceImpl d2o = (Das2SourceImpl)other;
-        
-        if ( nickname.equals(d2o.getNickname()))
-            return true;
-        
-        Das2Capability[] othercaps = d2o.getDas2Capabilities();
-        
-        if ( ! (capabilities.length == othercaps.length))
-            return false;
-        
-        for ( int x=0;x<capabilities.length;x++){
-            Das2Capability tmpcap = capabilities[x];
-            boolean foundCap = false;
-            for (int y=0; y< othercaps.length;y++){
-                Das2Capability tmpcapo = othercaps[y];
-                if ( tmpcap.equals(tmpcapo))
-                    foundCap = true;
-            }
-            if ( ! foundCap)
-                return false;
-        }
-        
-        
-        //TODO?
-        // should we add a check for coordinate systems?
-        // but we already check for the endpoints, that should be enough...
-        
-        return true;
-        
+
+    if ( (other == null) || (other.getClass() != this.getClass()))
+    {
+      return false;
     }
-    
-    public int hashCode(){
-        int h = 7 ;
-        
-        h = 31 * h + (null == nickname ? 0 :  nickname.hashCode());
-        
-        for ( int x=0;x<capabilities.length;x++){
-            Das2Capability cap = capabilities[x];
-            h = 31 * h + cap.hashCode();
-        }
-        
-        return h;
+
+    // to compare if two Das2Sources are identical we do the following:
+    //  we check the capabilities
+
+    Das2SourceImpl d2o = (Das2SourceImpl) other;
+
+    if (nickname.equals(d2o.getNickname()))
+    {
+      return true;
+    }
+
+    Das2Capability[] othercaps = d2o.getDas2Capabilities();
+
+    if (! (capabilities.length == othercaps.length))
+    {
+      return false;
     }
-    
-    
-    public boolean hasDas1Capabilities(){
-        
-        // test if any of the capabilities is a das1 capabilitiy
-        
-        for (int i = 0 ; i < capabilities.length; i++) {
-            Das2Capability cap = capabilities[i];
-            if ( cap.isDas1Style())
-                return true;            
+
+    for (int x = 0; x < capabilities.length; x++)
+    {
+      Das2Capability tmpcap = capabilities[x];
+      boolean foundCap = false;
+      for (int y = 0; y < othercaps.length; y++)
+      {
+        Das2Capability tmpcapo = othercaps[y];
+        if (tmpcap.equals(tmpcapo))
+        {
+          foundCap = true;
         }
+      }
+      if (!foundCap)
+      {
         return false;
-        
-        
-    }
-    
-    public String[] getCapabilities() {
-        //todo mark as not needed / not appropriate ...
-        return super.getCapabilities();
+      }
     }
 
+    //TODO?
+    // should we add a check for coordinate systems?
+    // but we already check for the endpoints, that should be enough...
 
+    return true;
 
-    public void setCapabilities(String[] u) {
-        // TODO Auto-generated method stub
-        super.setCapabilities(u);
-    }
+  }
 
+  public int hashCode()
+  {
+    int h = 7;
 
+    h = 31 * h + (null == nickname ? 0 : nickname.hashCode());
 
-    public Das2Capability[] getDas2Capabilities() {
-        // TODO Auto-generated method stub
-        return capabilities;
+    for (int x = 0; x < capabilities.length; x++)
+    {
+      Das2Capability cap = capabilities[x];
+      h = 31 * h + cap.hashCode();
     }
 
-    public void setDas2Capabilities(Das2Capability[] capabilities) {
-        // TODO Auto-generated method stub
-        this.capabilities = capabilities;
-        
+    return h;
+  }
+
+  public boolean hasDas1Capabilities()
+  {
+
+    // test if any of the capabilities is a das1 capabilitiy
+
+    for (int i = 0; i < capabilities.length; i++)
+    {
+      Das2Capability cap = capabilities[i];
+      if (cap.isDas1Style())
+      {
+        return true;
+      }
     }
-    
-    
-    
+    return false;
+
+  }
+
+  public String[] getCapabilities()
+  {
+    //todo mark as not needed / not appropriate ...
+    return super.getCapabilities();
+  }
+
+  public void setCapabilities(String[] u)
+  {
+    // TODO Auto-generated method stub
+    super.setCapabilities(u);
+  }
+
+  public Das2Capability[] getDas2Capabilities()
+  {
+    // TODO Auto-generated method stub
+    return capabilities;
+  }
+
+  public void setDas2Capabilities(Das2Capability[] capabilities)
+  {
+    // TODO Auto-generated method stub
+    this.capabilities = capabilities;
+
+  }
 
 }
diff --git a/src/org/biojava/dasobert/das2/DasSourceConverter.java b/src/org/biojava/dasobert/das2/DasSourceConverter.java
index 513ba3f..77cda0f 100755
--- a/src/org/biojava/dasobert/das2/DasSourceConverter.java
+++ b/src/org/biojava/dasobert/das2/DasSourceConverter.java
@@ -23,60 +23,67 @@
 package org.biojava.dasobert.das2;
 
 //import org.biojava.bio.program.das.dasalignment.DASException;
-import org.biojava.dasobert.dasregistry.Das1Source;
+import org.biojava.dasobert.dasregistry.*;
 
-public class DasSourceConverter {
+public class DasSourceConverter
+{
 
-    public DasSourceConverter() {
-        super();
+  public DasSourceConverter()
+  {
+    super();
 
-    }
-
-
-    /** 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{
-        if ( ! das2source.hasDas1Capabilities())
-            throw new Exception("this das source does not have das1 capabilitites");
+  }
 
-        Das1Source ds = new Das1Source();
-        ds.setAdminemail(das2source.getAdminemail());
-        ds.setDescription(das2source.getDescription());
-        ds.setHelperurl(das2source.getHelperurl());
-        ds.setRegisterDate(das2source.getRegisterDate());
-        ds.setLeaseDate(das2source.getLeaseDate());
-        ds.setLabels(das2source.getLabels());
-        ds.setCoordinateSystem(das2source.getCoordinateSystem());
-        ds.setNickname(das2source.getNickname());
-        ds.setId(das2source.getId());
-        ds.setLabels(das2source.getLabels());
+  /** 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
+  {
+    if (!das2source.hasDas1Capabilities())
+    {
+      throw new Exception("this das source does not have das1 capabilitites");
+    }
 
-        // 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();
+    Das1Source ds = new Das1Source();
+    ds.setAdminemail(das2source.getAdminemail());
+    ds.setDescription(das2source.getDescription());
+    ds.setHelperurl(das2source.getHelperurl());
+    ds.setRegisterDate(das2source.getRegisterDate());
+    ds.setLeaseDate(das2source.getLeaseDate());
+    ds.setLabels(das2source.getLabels());
+    ds.setCoordinateSystem(das2source.getCoordinateSystem());
+    ds.setNickname(das2source.getNickname());
+    ds.setId(das2source.getId());
+    ds.setLabels(das2source.getLabels());
 
-        for ( int i = 0 ; i< caps.length;i++){
-            Das2Capability cap = caps[i];
+    // 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();
 
-            String c = cap.getCapability();
+    for (int i = 0; i < caps.length; i++)
+    {
+      Das2Capability cap = caps[i];
 
-            das1capabilitites[i] = c.substring(DASPREFIXLENGTH,c.length());
+      String c = cap.getCapability();
 
-            String query_uri = cap.getQueryUri();
+      das1capabilitites[i] = c.substring(DASPREFIXLENGTH, c.length());
 
-            String url = query_uri.substring(0,(query_uri.length() - c.length() + DASPREFIXLENGTH));
-            ds.setUrl(url);
-        }
-        ds.setCapabilities(das1capabilitites);
+      String query_uri = cap.getQueryUri();
 
-        return ds ;
+      String url = query_uri.substring(0,
+                                       (query_uri.length() - c.length() + DASPREFIXLENGTH));
+      ds.setUrl(url);
     }
+    ds.setCapabilities(das1capabilitites);
+
+    return ds;
+  }
 
 }
diff --git a/src/org/biojava/dasobert/das2/io/DAS2SourceHandler.java b/src/org/biojava/dasobert/das2/io/DAS2SourceHandler.java
index caf6798..d8c61fa 100755
--- a/src/org/biojava/dasobert/das2/io/DAS2SourceHandler.java
+++ b/src/org/biojava/dasobert/das2/io/DAS2SourceHandler.java
@@ -16,166 +16,195 @@
  * at:
  *
  *      http://www.biojava.org/
- * 
+ *
  * Created on Mar 15, 2006
  *
  */
 package org.biojava.dasobert.das2.io;
 
-import java.util.ArrayList;
-import java.util.List;
+import java.util.*;
 
-import org.biojava.dasobert.das2.Das2Capability;
-import org.biojava.dasobert.das2.Das2CapabilityImpl;
-import org.biojava.dasobert.das2.Das2Source;
-import org.biojava.dasobert.das2.Das2SourceImpl;
-import org.biojava.dasobert.dasregistry.DasCoordinateSystem;
-import org.biojava.dasobert.dasregistry.DasSource;
-import org.xml.sax.Attributes;
-import org.xml.sax.helpers.DefaultHandler;
+import org.biojava.dasobert.das2.*;
+import org.biojava.dasobert.dasregistry.*;
+import org.xml.sax.*;
+import org.xml.sax.helpers.*;
 
 /** a parser for the DAS2 sources response
- * 
+ *
  * @author Andreas Prlic
  * @since 6:53:45 PM
  * @version %I% %G%
  */
-public class DAS2SourceHandler extends DefaultHandler{
-
-    List sources;
-    Das2Source currentSource;
-    List coordinates;
-    List capabilities;
-    List labels;
-
-    public static final String LABELPROPERTY = "label";
-
-    public DAS2SourceHandler() {
-        super();
-        
-        sources       = new ArrayList();
-        currentSource = new Das2SourceImpl();
-        coordinates   = new ArrayList();
-        capabilities  = new ArrayList();
-	labels        = new ArrayList();
+public class DAS2SourceHandler
+    extends DefaultHandler
+{
+
+  List sources;
+  Das2Source currentSource;
+  List coordinates;
+  List capabilities;
+  List labels;
+
+  public static final String LABELPROPERTY = "label";
+
+  public DAS2SourceHandler()
+  {
+    super();
+
+    sources = new ArrayList();
+    currentSource = new Das2SourceImpl();
+    coordinates = new ArrayList();
+    capabilities = new ArrayList();
+    labels = new ArrayList();
+  }
+
+  private void startSource(String uri, String name, String qName,
+                           Attributes atts)
+  {
+
+    String id = atts.getValue("uri");
+    String title = atts.getValue("title");
+    String doc_ref = atts.getValue("doc_href");
+    String description = atts.getValue("description");
+
+    currentSource.setId(id);
+    currentSource.setNickname(title);
+    currentSource.setHelperurl(doc_ref);
+    currentSource.setDescription(description);
+
+  }
+
+  private DasCoordinateSystem getCoordinateSystem(String uri, String name,
+                                                  String qname, Attributes atts)
+  {
+    // e.g. uri="http://das.sanger.ac.uk/dasregistry/coordsys/CS_LOCAL6"
+    // source="Protein Sequence" authority="UniProt" test_range="P06213" />
+    DasCoordinateSystem dcs = new DasCoordinateSystem();
+    String id = atts.getValue("uri");
+    dcs.setUniqueId(id);
+
+    String source = atts.getValue("source");
+    dcs.setCategory(source);
+
+    String authority = atts.getValue("authority");
+    dcs.setName(authority);
+
+    String test_range = atts.getValue("test_range");
+    dcs.setTestCode(test_range);
+
+    try
+    {
+      String taxidstr = atts.getValue("taxid");
+      int taxid = Integer.parseInt(taxidstr);
+      dcs.setNCBITaxId(taxid);
     }
-    
-    private void startSource (String uri, String name, String qName, Attributes atts){
-        
-        String id = atts.getValue("uri");
-        String title = atts.getValue("title");
-        String doc_ref = atts.getValue("doc_href");
-        String description = atts.getValue("description");
-
-           
-        currentSource.setId(id);
-        currentSource.setNickname(title);
-        currentSource.setHelperurl(doc_ref);
-        currentSource.setDescription(description);
-        
+    catch (Exception e)
+    {}
+
+    String version = atts.getValue("version");
+    if (version != null)
+    {
+      dcs.setVersion(version);
     }
-    
-    private DasCoordinateSystem getCoordinateSystem(String uri, String name, String qname, Attributes atts){
-        // e.g. uri="http://das.sanger.ac.uk/dasregistry/coordsys/CS_LOCAL6" 
-        // source="Protein Sequence" authority="UniProt" test_range="P06213" />
-        DasCoordinateSystem dcs = new DasCoordinateSystem();
-        String id = atts.getValue("uri");
-        dcs.setUniqueId(id);
-        
-        String source = atts.getValue("source");
-        dcs.setCategory(source);
-        
-        String authority = atts.getValue("authority");
-        dcs.setName(authority);
-        
-        String test_range = atts.getValue("test_range");
-        dcs.setTestCode(test_range);
-        
-        try {
-            String taxidstr = atts.getValue("taxid");
-            int taxid = Integer.parseInt(taxidstr);
-            dcs.setNCBITaxId(taxid);
-        } catch (Exception e){}
-        
-        String version = atts.getValue("version");
-        if ( version != null)
-            dcs.setVersion(version);
-        
-        return dcs;
+
+    return dcs;
+  }
+
+  public void startElement(String uri, String name, String qName,
+                           Attributes atts)
+  {
+    //System.out.println("new element "+qName);
+
+    if (qName.equals("SOURCE"))
+    {
+      //System.out.println("new Source " + atts.getValue(uri));
+      currentSource = new Das2SourceImpl();
+      coordinates = new ArrayList();
+      capabilities = new ArrayList();
+
+      startSource(uri, name, qName, atts);
+
     }
-    
-    public void startElement (String uri, String name, String qName, Attributes atts){
-        //System.out.println("new element "+qName);
-        
-        if (qName.equals("SOURCE")) {
-            //System.out.println("new Source " + atts.getValue(uri));
-            currentSource = new Das2SourceImpl();
-            coordinates = new ArrayList();
-            capabilities = new ArrayList();
-            
-            startSource(uri,name, qName, atts);
-            
-        } else if ( qName.equals("MAINTAINER")){
-            String email = atts.getValue("email");
-            currentSource.setAdminemail(email);
-        } else if ( qName.equals("COORDINATES")){
-            DasCoordinateSystem dcs = getCoordinateSystem(uri,name,qName,atts);
-            coordinates.add(dcs);
-            
-        } else if ( qName.equals("CAPABILITY")){
-            Das2Capability cap = getCapability(uri,name,qName,atts);
-            capabilities.add(cap);
-        } else if (qName.equals("PROPERTY")) {
-	    addProperty(uri,name,qName,atts);
-	}                
+    else if (qName.equals("MAINTAINER"))
+    {
+      String email = atts.getValue("email");
+      currentSource.setAdminemail(email);
     }
-    
-    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" />
-        Das2Capability cap = new Das2CapabilityImpl();
-        
-        String type = atts.getValue("type");
-        cap.setCapability(type);
-        String query_uri = atts.getValue("query_uri");
-        cap.setQueryUri(query_uri);
-        return cap;
-        
+    else if (qName.equals("COORDINATES"))
+    {
+      DasCoordinateSystem dcs = getCoordinateSystem(uri, name, qName, atts);
+      coordinates.add(dcs);
+
     }
-    
-    private void addProperty(String uri, String name, String qName, Attributes atts){
-	String pname = atts.getValue("name");
-	String label = atts.getValue("value");
-	if ( pname.equals(LABELPROPERTY) )
-	    labels.add(label);
+    else if (qName.equals("CAPABILITY"))
+    {
+      Das2Capability cap = getCapability(uri, name, qName, atts);
+      capabilities.add(cap);
     }
-    
-    public void startDocument(){
-        sources = new ArrayList();
-        coordinates = new ArrayList();
-        capabilities = new ArrayList();
+    else if (qName.equals("PROPERTY"))
+    {
+      addProperty(uri, name, qName, atts);
     }
-    
-    public void endElement(String uri, String name, String qName) {
-        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()]));
-	    labels.clear();
-
-            //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();
-        } 		
+  }
+
+  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" />
+    Das2Capability cap = new Das2CapabilityImpl();
+
+    String type = atts.getValue("type");
+    cap.setCapability(type);
+    String query_uri = atts.getValue("query_uri");
+    cap.setQueryUri(query_uri);
+    return cap;
+
+  }
+
+  private void addProperty(String uri, String name, String qName,
+                           Attributes atts)
+  {
+    String pname = atts.getValue("name");
+    String label = atts.getValue("value");
+    if (pname.equals(LABELPROPERTY))
+    {
+      labels.add(label);
     }
-    
-    public DasSource[] getSources(){    
-        //System.out.println("Das2SourceHandler: source size: " + sources.size());
-        return (DasSource[])sources.toArray(new DasSource[sources.size()]);
+  }
+
+  public void startDocument()
+  {
+    sources = new ArrayList();
+    coordinates = new ArrayList();
+    capabilities = new ArrayList();
+  }
+
+  public void endElement(String uri, String name, String qName)
+  {
+    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()]));
+      labels.clear();
+
+      //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();
     }
-    
-    
+  }
+
+  public DasSource[] getSources()
+  {
+    //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/DasSourceReader.java b/src/org/biojava/dasobert/das2/io/DasSourceReader.java
index 0b05df8..62a28f6 100755
--- a/src/org/biojava/dasobert/das2/io/DasSourceReader.java
+++ b/src/org/biojava/dasobert/das2/io/DasSourceReader.java
@@ -16,17 +16,18 @@
  * at:
  *
  *      http://www.biojava.org/
- * 
+ *
  * Created on Feb 24, 2006
  *
  */
 package org.biojava.dasobert.das2.io;
 
-import java.io.InputStream;
+import java.io.*;
 
-import org.biojava.dasobert.dasregistry.DasSource;
+import org.biojava.dasobert.dasregistry.*;
 
-public interface DasSourceReader {
+public interface DasSourceReader
+{
 
-    public DasSource[] readDasSource(InputStream stream);
+  public DasSource[] readDasSource(InputStream stream);
 }
diff --git a/src/org/biojava/dasobert/das2/io/DasSourceReaderImpl.java b/src/org/biojava/dasobert/das2/io/DasSourceReaderImpl.java
index 3f0a07a..af403ed 100755
--- a/src/org/biojava/dasobert/das2/io/DasSourceReaderImpl.java
+++ b/src/org/biojava/dasobert/das2/io/DasSourceReaderImpl.java
@@ -22,152 +22,168 @@
  */
 package org.biojava.dasobert.das2.io;
 
-import java.io.InputStream;
-import java.net.HttpURLConnection;
-import java.net.URL;
+import java.io.*;
+import java.net.*;
+import javax.xml.parsers.*;
 
+import org.biojava.dasobert.das.*;
+import org.biojava.dasobert.dasregistry.*;
+import org.xml.sax.*;
 
-import javax.xml.parsers.ParserConfigurationException;
-import javax.xml.parsers.SAXParser;
-import javax.xml.parsers.SAXParserFactory;
+public class DasSourceReaderImpl
+    implements DasSourceReader
+{
 
-//import org.biojava.dasobert.das.AlignmentThread;
-import org.biojava.dasobert.das.DAS_FeatureRetrieve;
-import org.biojava.dasobert.dasregistry.DasSource;
-import org.xml.sax.InputSource;
-import org.xml.sax.SAXException;
-import org.xml.sax.SAXNotRecognizedException;
-import org.xml.sax.XMLReader;
+  Exception loggedException;
 
-public class DasSourceReaderImpl implements DasSourceReader {
+  public DasSourceReaderImpl()
+  {
+    super();
+    loggedException = null;
 
-    Exception loggedException;
+    // open the stream to a server and then parse the result ...
+  }
 
-    public DasSourceReaderImpl() {
-        super();
-        loggedException = null;
+  private InputStream open(URL url)
+      throws java.io.IOException, java.net.ConnectException
+  {
+    InputStream inStream = null;
 
-        // open the stream to a server and then parse the result ...
-    }
+    HttpURLConnection huc = DAS_FeatureRetrieve.openHttpURLConnection(url);
 
-    private InputStream open(URL url)
-    throws java.io.IOException, java.net.ConnectException
-    {
-        InputStream inStream = null;
+    inStream = huc.getInputStream();
 
+    return inStream;
 
-        HttpURLConnection huc = DAS_FeatureRetrieve.openHttpURLConnection(url);
+  }
 
-        inStream = huc.getInputStream();
+  public DasSource[] readDasSource(URL url)
+  {
+    DasSource[] sources = new DasSource[0];
 
-        return inStream;
+    try
+    {
+      InputStream stream = open(url);
 
+      sources = readDasSource(stream);
     }
-
-
-    public DasSource[] readDasSource(URL url){
-        DasSource[] sources = new DasSource[0];
-
-        try {
-            InputStream stream = open(url);
-
-            sources = readDasSource(stream);
-        } catch (Exception e){
-            e.printStackTrace();
-            loggedException = e;
-        }
-        return sources;
+    catch (Exception e)
+    {
+      e.printStackTrace();
+      loggedException = e;
     }
+    return sources;
+  }
 
-    /** read a DAS2 sources response and return a list of DAS sources.
-     *
-     */
-    public DasSource[] readDasSource(InputStream stream)  {
-
-        DasSource[] sources = new DasSource[0];
+  /** read a DAS2 sources response and return a list of DAS sources.
+   *
+   */
+  public DasSource[] readDasSource(InputStream stream)
+  {
 
-        try {
-        SAXParserFactory spfactory =
-            SAXParserFactory.newInstance();
-
-        spfactory.setValidating(false);
-
-        SAXParser saxParser = null ;
-
-        try{
-            saxParser =
-                spfactory.newSAXParser();
-        } catch (ParserConfigurationException e) {
-            e.printStackTrace();
-            loggedException = e;
-        }
-
-        String vali = System.getProperty("XMLVALIDATION");
-
-        boolean validation = false ;
-        if ( vali != null )
-            if ( vali.equals("true") )
-                validation = true ;
-
-
-        XMLReader xmlreader = saxParser.getXMLReader();
-
-        //XMLReader xmlreader = XMLReaderFactory.createXMLReader();
-        try {
-            xmlreader.setFeature("http://xml.org/sax/features/validation", 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){
-            e.printStackTrace();
-            //logger.log(Level.FINE,"Cannot set load-external-dtd "+validation);
+    DasSource[] sources = new DasSource[0];
 
+    try
+    {
+      SAXParserFactory spfactory =
+          SAXParserFactory.newInstance();
+
+      spfactory.setValidating(false);
+
+      SAXParser saxParser = null;
+
+      try
+      {
+        saxParser =
+            spfactory.newSAXParser();
+      }
+      catch (ParserConfigurationException e)
+      {
+        e.printStackTrace();
+        loggedException = e;
+      }
+
+      String vali = System.getProperty("XMLVALIDATION");
+
+      boolean validation = false;
+      if (vali != null)
+      {
+        if (vali.equals("true"))
+        {
+          validation = true;
         }
+      }
+
+      XMLReader xmlreader = saxParser.getXMLReader();
+
+      //XMLReader xmlreader = XMLReaderFactory.createXMLReader();
+      try
+      {
+        xmlreader.setFeature("http://xml.org/sax/features/validation",
+                             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)
+      {
+        e.printStackTrace();
+        //logger.log(Level.FINE,"Cannot set load-external-dtd "+validation);
+
+      }
+
+      DAS2SourceHandler cont_handle = new DAS2SourceHandler();
+
+      xmlreader.setContentHandler(cont_handle);
+      xmlreader.setErrorHandler(new org.xml.sax.helpers.DefaultHandler());
+      InputSource insource = new InputSource();
+      insource.setByteStream(stream);
+
+      xmlreader.parse(insource);
+      sources = cont_handle.getSources();
 
-        DAS2SourceHandler cont_handle = new DAS2SourceHandler() ;
-
-        xmlreader.setContentHandler(cont_handle);
-        xmlreader.setErrorHandler(new org.xml.sax.helpers.DefaultHandler());
-        InputSource insource = new InputSource() ;
-        insource.setByteStream(stream);
-
-
-        xmlreader.parse(insource);
-        sources = cont_handle.getSources();
-
-
-
-        } catch (Exception e) {
-            e.printStackTrace();
-            loggedException = e;
-        }
-        return sources;
     }
-
-    public Exception getLoggedException(){
-        return loggedException;
+    catch (Exception e)
+    {
+      e.printStackTrace();
+      loggedException = e;
     }
-
-    public static void main (String[] args){
-        String url = "http://www.spice-3d.org/dasregistry/das2/sources/";
-        DasSourceReaderImpl reader = new DasSourceReaderImpl();
-        try {
-            URL u = new URL(url);
-            DasSource[] sources = reader.readDasSource(u);
-            for (int i=0; i< sources.length;i++){
-                DasSource ds = sources[i];
-                System.out.println(ds.toString());
-            }
-
-        } catch (Exception e){
-            e.printStackTrace();
-        }
+    return sources;
+  }
+
+  public Exception getLoggedException()
+  {
+    return loggedException;
+  }
+
+  public static void main(String[] args)
+  {
+    String url = "http://www.spice-3d.org/dasregistry/das2/sources/";
+    DasSourceReaderImpl reader = new DasSourceReaderImpl();
+    try
+    {
+      URL u = new URL(url);
+      DasSource[] sources = reader.readDasSource(u);
+      for (int i = 0; i < sources.length; i++)
+      {
+        DasSource ds = sources[i];
+        System.out.println(ds.toString());
+      }
 
     }
+    catch (Exception e)
+    {
+      e.printStackTrace();
+    }
 
-
+  }
 
 }
diff --git a/src/org/biojava/dasobert/dasregistry/Das1Source.java b/src/org/biojava/dasobert/dasregistry/Das1Source.java
index de007d6..4b8ae2a 100755
--- a/src/org/biojava/dasobert/dasregistry/Das1Source.java
+++ b/src/org/biojava/dasobert/dasregistry/Das1Source.java
@@ -23,11 +23,7 @@
  */
 package org.biojava.dasobert.dasregistry;
 
-import java.util.Date ;
-import java.io.IOException;
-import java.io.PrintWriter;
-import java.io.StringWriter;
-
+import java.util.*;
 
 //import org.biojava.dasobert.das2.io.DasSourceWriter;
 //import org.biojava.dasobert.das2.io.DasSourceWriterImpl;
@@ -38,169 +34,235 @@ import java.io.StringWriter;
  * @author Andreas Prlic
  */
 
-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;
-
-    boolean alertAdmin;
-
-    public static String EMPTY_ID = "UNK:-1" ;
-
-    public Das1Source () {
-        id               = EMPTY_ID;
-        url              = "";
-        adminemail       = "" ;
-        description      = "" ;
-        //String empty     = "" ;
-        nickname         = "" ;
-        coordinateSystem = new DasCoordinateSystem[0];
-        //coordinateSystem[0] = new DasCoordinateSystem();
-        capabilities     =  new String[0];
-        labels 	         = new String[0];
-        //capabilities[0]  = empty ;
-        registerDate     = new Date() ;
-        leaseDate        = new Date() ;
-        helperurl        = "";
-        local=true;
-    }
-
-
-    public boolean equals(DasSource other){
-        System.out.println("Das1Source equals, comparing with other DasSource");
-        if (! (other instanceof Das1Source))
-            return false;
-
-        Das1Source ods = (Das1Source) other;
-
-        if ( ods.getUrl().equals(url))
-            return true;
-        if ( ods.getNickname().equals(nickname))
-            return true;
-        return false;
-    }
-
-    public int hashCode() {
-        int h = 7;
-
-        h = 31 * h + ( null == nickname ? 0 : nickname.hashCode());
-        h = 31 * h + ( null == url ? 0 : url.hashCode());
-
-        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();
-
-    }
-    */
-    public void setLocal(boolean flag){ local = flag;}
-    public boolean isLocal(){return local;}
-
-    public void setId(String i) { 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.
-     */
-    public String getId() { return id;}
-
-    public void setNickname(String name) {
-        nickname = name ;
-    }
-    public String getNickname(){
-        return nickname;
-    }
-    public void setUrl(String u) {
-        char lastChar = u.charAt(u.length()-1);
-        if ( lastChar  != '/')
-            u += "/";
-
-        url = u ;
-    }
-
-    public void setAdminemail (String u) {
-        adminemail = u ;
-    }
-
-    public void setDescription (String u) {
-        description = u;
-    }
-
-    public void setCoordinateSystem (DasCoordinateSystem[] u){
-        coordinateSystem=u ;
-    }
-
-    public void setCapabilities (String[] u){
-        capabilities = u ;
-    }
-
-    public String getUrl(){return url;}
-    public String getAdminemail(){return adminemail;}
-    public String getDescription(){return description;}
-    public String[] getCapabilities(){return capabilities;}
-    public DasCoordinateSystem[] getCoordinateSystem(){return coordinateSystem;}
-
-    public void setRegisterDate(Date d) {
-        registerDate = d;
-    }
-    public Date getRegisterDate() {
-        return registerDate ;
-    }
-    public void setLeaseDate(Date d) {
-        leaseDate =d ;
-    }
-    public Date getLeaseDate() {
-        return leaseDate ;
+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;
+
+  boolean alertAdmin;
+
+  public static String EMPTY_ID = "UNK:-1";
+
+  public Das1Source()
+  {
+    id = EMPTY_ID;
+    url = "";
+    adminemail = "";
+    description = "";
+    //String empty     = "" ;
+    nickname = "";
+    coordinateSystem = new DasCoordinateSystem[0];
+    //coordinateSystem[0] = new DasCoordinateSystem();
+    capabilities = new String[0];
+    labels = new String[0];
+    //capabilities[0]  = empty ;
+    registerDate = new Date();
+    leaseDate = new Date();
+    helperurl = "";
+    local = true;
+  }
+
+  public boolean equals(DasSource other)
+  {
+    System.out.println("Das1Source equals, comparing with other DasSource");
+    if (! (other instanceof Das1Source))
+    {
+      return false;
     }
 
-    public void setLabels(String[] ls) {
-        labels = ls ;
-    }
+    Das1Source ods = (Das1Source) other;
 
-    public String[] getLabels() {
-        return labels;
+    if (ods.getUrl().equals(url))
+    {
+      return true;
     }
-
-    public void setHelperurl(String url) {
-        helperurl = url;
+    if (ods.getNickname().equals(nickname))
+    {
+      return true;
     }
-
-    public String getHelperurl() {
-        return helperurl;
+    return false;
+  }
+
+  public int hashCode()
+  {
+    int h = 7;
+
+    h = 31 * h + (null == nickname ? 0 : nickname.hashCode());
+    h = 31 * h + (null == url ? 0 : url.hashCode());
+
+    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();
+
+       }
+   */
+  public void setLocal(boolean flag)
+  {
+    local = flag;
+  }
+
+  public boolean isLocal()
+  {
+    return local;
+  }
+
+  public void setId(String i)
+  {
+    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.
+   */
+  public String getId()
+  {
+    return id;
+  }
+
+  public void setNickname(String name)
+  {
+    nickname = name;
+  }
+
+  public String getNickname()
+  {
+    return nickname;
+  }
+
+  public void setUrl(String u)
+  {
+    char lastChar = u.charAt(u.length() - 1);
+    if (lastChar != '/')
+    {
+      u += "/";
     }
 
-    public void setAlertAdmin(boolean flag) {
-        alertAdmin = flag;
-    }
-
-    public boolean getAlertAdmin() {
-        return alertAdmin;
-    }
+    url = u;
+  }
+
+  public void setAdminemail(String u)
+  {
+    adminemail = u;
+  }
+
+  public void setDescription(String u)
+  {
+    description = u;
+  }
+
+  public void setCoordinateSystem(DasCoordinateSystem[] u)
+  {
+    coordinateSystem = u;
+  }
+
+  public void setCapabilities(String[] u)
+  {
+    capabilities = u;
+  }
+
+  public String getUrl()
+  {
+    return url;
+  }
+
+  public String getAdminemail()
+  {
+    return adminemail;
+  }
+
+  public String getDescription()
+  {
+    return description;
+  }
+
+  public String[] getCapabilities()
+  {
+    return capabilities;
+  }
+
+  public DasCoordinateSystem[] getCoordinateSystem()
+  {
+    return coordinateSystem;
+  }
+
+  public void setRegisterDate(Date d)
+  {
+    registerDate = d;
+  }
+
+  public Date getRegisterDate()
+  {
+    return registerDate;
+  }
+
+  public void setLeaseDate(Date d)
+  {
+    leaseDate = d;
+  }
+
+  public Date getLeaseDate()
+  {
+    return leaseDate;
+  }
+
+  public void setLabels(String[] ls)
+  {
+    labels = ls;
+  }
+
+  public String[] getLabels()
+  {
+    return labels;
+  }
+
+  public void setHelperurl(String url)
+  {
+    helperurl = url;
+  }
+
+  public String getHelperurl()
+  {
+    return helperurl;
+  }
+
+  public void setAlertAdmin(boolean flag)
+  {
+    alertAdmin = flag;
+  }
+
+  public boolean getAlertAdmin()
+  {
+    return alertAdmin;
+  }
 
 }
diff --git a/src/org/biojava/dasobert/dasregistry/Das2Validator.java b/src/org/biojava/dasobert/dasregistry/Das2Validator.java
index a7fd293..fea8a0f 100755
--- a/src/org/biojava/dasobert/dasregistry/Das2Validator.java
+++ b/src/org/biojava/dasobert/dasregistry/Das2Validator.java
@@ -16,28 +16,29 @@
  * at:
  *
  *      http://www.biojava.org/
- * 
+ *
  * Created on Mar 20, 2006
  *
  */
 package org.biojava.dasobert.dasregistry;
 
-import org.biojava.dasobert.das2.Das2Source;
+import org.biojava.dasobert.das2.*;
+
+public class Das2Validator
+{
+
+  public Das2Validator()
+  {
+    super();
+
+  }
 
-public class Das2Validator {
+  public boolean validate(Das2Source ds)
+  {
 
-    public Das2Validator() {
-        super();
+    // TODO this bit still needs to be implemented!
 
-    }
-    
-    public boolean validate(Das2Source ds){
-        
-        // TODO this bit still needs to be implemented!
-        
-        return true;
-    }
+    return true;
+  }
 
-    
-    
 }
diff --git a/src/org/biojava/dasobert/dasregistry/DasCoordSysComparator.java b/src/org/biojava/dasobert/dasregistry/DasCoordSysComparator.java
index 8715446..3de3702 100755
--- a/src/org/biojava/dasobert/dasregistry/DasCoordSysComparator.java
+++ b/src/org/biojava/dasobert/dasregistry/DasCoordSysComparator.java
@@ -23,94 +23,102 @@
  */
 
 
-package org.biojava.dasobert.dasregistry ;
+package org.biojava.dasobert.dasregistry;
 
-import java.util.Comparator ;
-import java.util.Map ;
-import java.util.HashMap ;
+import java.util.*;
 
-import org.biojava.dasobert.dasregistry.DasCoordinateSystem;
-
-/** a comparator to sort DasSources 
- * @author Andreas Prlic 
+/** a comparator to sort DasSources
+ * @author Andreas Prlic
  */
 
 
 public abstract class DasCoordSysComparator
     implements Comparator
-{ 
-
-    private final String name ;
-    private static final Map COMPS_BY_NAME;
-
+{
+
+  private final String name;
+  private static final Map COMPS_BY_NAME;
+
+  public DasCoordSysComparator(String str)
+  {
+    //System.out.println("new dasSourceComparator " + str);
+    name = str;
+  }
+
+  public static final Comparator BY_NAME = new DasCoordSysComparator("name")
+  {
+    protected Comparable getField(DasCoordinateSystem ds)
+    {
+      return ds.getName();
+    }
+  };
 
-    public DasCoordSysComparator(String str) {
-	//System.out.println("new dasSourceComparator " + str);
-	name = str ;
+  public static final Comparator BY_ID = new DasCoordSysComparator("id")
+  {
+    protected Comparable getField(DasCoordinateSystem ds)
+    {
+      return ds.getUniqueId();
     }
-   
-    public static final Comparator BY_NAME = new DasCoordSysComparator("name") {
-        protected Comparable getField(DasCoordinateSystem ds) {
-            return ds.getName();
-        }
-    };    
-
-    public static final Comparator BY_ID = new DasCoordSysComparator("id") {
-        protected Comparable getField(DasCoordinateSystem ds) {
-            return ds.getUniqueId();
-        }
-    };    
-    public static final Comparator BY_CATEGORY = new DasCoordSysComparator("category") {
-        protected Comparable getField(DasCoordinateSystem ds) {
-            return ds.getCategory();
-        }
-    };
-    public static final Comparator BY_ORGANISM = new DasCoordSysComparator("organism") {
-        protected Comparable getField(DasCoordinateSystem ds) {
-            return ds.getOrganismName();
-        }
-    };
-    public static final Comparator BY_TAXID = new DasCoordSysComparator("taxid") {
-        protected Comparable getField(DasCoordinateSystem ds) {
-            return ds.getNCBITaxId()+"";
-        }
-    };
-   
-    
-
-    static {
-        COMPS_BY_NAME = new HashMap();
-        COMPS_BY_NAME.put(BY_ID.toString(),           BY_ID);
-	COMPS_BY_NAME.put(BY_NAME.toString(),         BY_NAME);
-        COMPS_BY_NAME.put(BY_CATEGORY.toString(),     BY_CATEGORY);
-        COMPS_BY_NAME.put(BY_ORGANISM.toString(),     BY_ORGANISM);
-        COMPS_BY_NAME.put(BY_TAXID.toString(),        BY_TAXID);
+  };
+  public static final Comparator BY_CATEGORY = new DasCoordSysComparator(
+      "category")
+  {
+    protected Comparable getField(DasCoordinateSystem ds)
+    {
+      return ds.getCategory();
     }
-
-   
-
-    public static Comparator fromString(String name) {
-        if (COMPS_BY_NAME.containsKey(name)) {
-            return (Comparator) COMPS_BY_NAME.get(name);
-        } else {
-            throw new IllegalArgumentException("Can't compare by key " + name);
-        }
+  };
+  public static final Comparator BY_ORGANISM = new DasCoordSysComparator(
+      "organism")
+  {
+    protected Comparable getField(DasCoordinateSystem ds)
+    {
+      return ds.getOrganismName();
     }
-
-    protected abstract Comparable getField(DasCoordinateSystem ds);
-
-    /** compare two DasCoordSys objects */
-    public int compare( Object a, Object b) {
-        DasCoordinateSystem x = (DasCoordinateSystem) a ;
-        DasCoordinateSystem y = (DasCoordinateSystem) b ;
-        return getField(x).compareTo(getField(y));
+  };
+  public static final Comparator BY_TAXID = new DasCoordSysComparator("taxid")
+  {
+    protected Comparable getField(DasCoordinateSystem ds)
+    {
+      return ds.getNCBITaxId() + "";
     }
-
-    public String toString() {
-        return name;
+  };
+
+  static
+  {
+    COMPS_BY_NAME = new HashMap();
+    COMPS_BY_NAME.put(BY_ID.toString(), BY_ID);
+    COMPS_BY_NAME.put(BY_NAME.toString(), BY_NAME);
+    COMPS_BY_NAME.put(BY_CATEGORY.toString(), BY_CATEGORY);
+    COMPS_BY_NAME.put(BY_ORGANISM.toString(), BY_ORGANISM);
+    COMPS_BY_NAME.put(BY_TAXID.toString(), BY_TAXID);
+  }
+
+  public static Comparator fromString(String name)
+  {
+    if (COMPS_BY_NAME.containsKey(name))
+    {
+      return (Comparator) COMPS_BY_NAME.get(name);
     }
+    else
+    {
+      throw new IllegalArgumentException("Can't compare by key " + name);
+    }
+  }
 
+  protected abstract Comparable getField(DasCoordinateSystem ds);
 
-}
+  /** compare two DasCoordSys objects */
+  public int compare(Object a, Object b)
+  {
+    DasCoordinateSystem x = (DasCoordinateSystem) a;
+    DasCoordinateSystem y = (DasCoordinateSystem) b;
+    return getField(x).compareTo(getField(y));
+  }
 
+  public String toString()
+  {
+    return name;
+  }
 
+}
diff --git a/src/org/biojava/dasobert/dasregistry/DasCoordinateSystem.java b/src/org/biojava/dasobert/dasregistry/DasCoordinateSystem.java
index 31caaf5..4cb6212 100755
--- a/src/org/biojava/dasobert/dasregistry/DasCoordinateSystem.java
+++ b/src/org/biojava/dasobert/dasregistry/DasCoordinateSystem.java
@@ -23,137 +23,192 @@
  */
 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 () {
-        uniqueId = "";
-        name = "";
-        category ="";
-        organism_name = "";
-        ncbi_tax_id = 0;
-        version = "";
-        testCode = "";
+public class DasCoordinateSystem
+{
+
+  String name;
+  String category;
+  String organism_name;
+  int ncbi_tax_id;
+  String uniqueId;
+  String version;
+  String testCode;
+
+  public DasCoordinateSystem()
+  {
+    uniqueId = "";
+    name = "";
+    category = "";
+    organism_name = "";
+    ncbi_tax_id = 0;
+    version = "";
+    testCode = "";
+  }
+
+  public boolean equals(DasCoordinateSystem other)
+  {
+    boolean match = true;
+    System.out.println("comparing " + this.toString() + " to " + other.toString());
+    // URI has piority
+    if ( (!uniqueId.equals("")) && (uniqueId.equals(other.getUniqueId())))
+    {
+      return true;
     }
 
-    public boolean equals(DasCoordinateSystem other){
-        boolean match = true;
-        System.out.println("comparing " + this.toString() + " to " + other.toString());
-        // URI has piority 
-        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());
-            match = false;
-        }
-        if ( ! version.equals(other.getVersion() )){
-            System.out.println("mismatch in version");
-            match = false;
-        }
-        if ( ! category.equals(other.getCategory())  ) {
-            System.out.println("mismatch in category");
-            match = false;
-        }
-        if ( ! name.equals(other.getName())) {
-            System.out.println("mismatch in name");   
-            match = false;
-        }
-        System.out.println(" match: " + match);
-        
-        return match;
+    if (ncbi_tax_id != other.getNCBITaxId())
+    {
+      System.out.println("mismatch in ncbi tax id " + ncbi_tax_id + " != " +
+                         other.getNCBITaxId());
+      match = false;
     }
-    
-    public Object clone() {
-        DasCoordinateSystem d = new DasCoordinateSystem();
-        d.setTestCode(testCode);
-        d.setCategory(category);
-        d.setName(name);
-        d.setNCBITaxId(ncbi_tax_id);
-        d.setUniqueId(getUniqueId());
-        d.setOrganismName(getOrganismName());
-        d.setVersion(getVersion());
-        return d;
+    if (!version.equals(other.getVersion()))
+    {
+      System.out.println("mismatch in version");
+      match = false;
     }
-    
-    public String getTestCode() {
-        return testCode;
+    if (!category.equals(other.getCategory()))
+    {
+      System.out.println("mismatch in category");
+      match = false;
     }
-
-
-
-    public void setTestCode(String testCode) {
-        if ( testCode == null)
-            testCode = "";
-        this.testCode = testCode;
+    if (!name.equals(other.getName()))
+    {
+      System.out.println("mismatch in name");
+      match = false;
     }
-
-
-
-    public void setUniqueId(String id) { uniqueId = id ;   }
-    public String getUniqueId() { return uniqueId;         }
-
-    public void setName(String n) { name = n; }
-    public String getName() { return name; }
-    
-    public void setCategory(String c) { category = c;}
-    public String getCategory() { return category;}
-
-    public void setOrganismName(String t) { organism_name  =t;} 
-    public String getOrganismName() { return organism_name;}
-
-    public void setNCBITaxId(int id) { ncbi_tax_id = id;}
-    public int getNCBITaxId(){ return ncbi_tax_id ;}
-    
-    
-    
-
-    public String getVersion() {
-        return version;
+    System.out.println(" match: " + match);
+
+    return match;
+  }
+
+  public Object clone()
+  {
+    DasCoordinateSystem d = new DasCoordinateSystem();
+    d.setTestCode(testCode);
+    d.setCategory(category);
+    d.setName(name);
+    d.setNCBITaxId(ncbi_tax_id);
+    d.setUniqueId(getUniqueId());
+    d.setOrganismName(getOrganismName());
+    d.setVersion(getVersion());
+    return d;
+  }
+
+  public String getTestCode()
+  {
+    return testCode;
+  }
+
+  public void setTestCode(String testCode)
+  {
+    if (testCode == null)
+    {
+      testCode = "";
     }
-
-    public void setVersion(String version) {
-        if ( version == null)
-            version = "";
-        this.version = version;
+    this.testCode = testCode;
+  }
+
+  public void setUniqueId(String id)
+  {
+    uniqueId = id;
+  }
+
+  public String getUniqueId()
+  {
+    return uniqueId;
+  }
+
+  public void setName(String n)
+  {
+    name = n;
+  }
+
+  public String getName()
+  {
+    return name;
+  }
+
+  public void setCategory(String c)
+  {
+    category = c;
+  }
+
+  public String getCategory()
+  {
+    return category;
+  }
+
+  public void setOrganismName(String t)
+  {
+    organism_name = t;
+  }
+
+  public String getOrganismName()
+  {
+    return organism_name;
+  }
+
+  public void setNCBITaxId(int id)
+  {
+    ncbi_tax_id = id;
+  }
+
+  public int getNCBITaxId()
+  {
+    return ncbi_tax_id;
+  }
+
+  public String getVersion()
+  {
+    return version;
+  }
+
+  public void setVersion(String version)
+  {
+    if (version == null)
+    {
+      version = "";
     }
-
-    public String toString() {
-        String nam = name;
-        if ( ! version.equals(""))
-            nam += "_" + version;
-        
-	if ( organism_name.equals("") ) 
-	    return nam+","+category ;
-	else 
-	    return nam+","+category+"," + organism_name ;
+    this.version = version;
+  }
+
+  public String toString()
+  {
+    String nam = name;
+    if (!version.equals(""))
+    {
+      nam += "_" + version;
     }
 
-    public static DasCoordinateSystem fromString(String rawString) {
-	String[] spl = rawString.split(",");
-	DasCoordinateSystem dcs = new DasCoordinateSystem();
-	if ( spl.length == 2 ) {
-	    dcs.setName(spl[0]);	   
-	    dcs.setCategory(spl[1]);
-	} 
-	if ( spl.length == 3 ) {
-	    dcs.setName(spl[0]);
-	    dcs.setCategory(spl[1]);
-	    dcs.setOrganismName(spl[2]);
-	}
-	return dcs;
+    if (organism_name.equals(""))
+    {
+      return nam + "," + category;
     }
-
+    else
+    {
+      return nam + "," + category + "," + organism_name;
+    }
+  }
+
+  public static DasCoordinateSystem fromString(String rawString)
+  {
+    String[] spl = rawString.split(",");
+    DasCoordinateSystem dcs = new DasCoordinateSystem();
+    if (spl.length == 2)
+    {
+      dcs.setName(spl[0]);
+      dcs.setCategory(spl[1]);
+    }
+    if (spl.length == 3)
+    {
+      dcs.setName(spl[0]);
+      dcs.setCategory(spl[1]);
+      dcs.setOrganismName(spl[2]);
+    }
+    return dcs;
+  }
 
 }
diff --git a/src/org/biojava/dasobert/dasregistry/DasSource.java b/src/org/biojava/dasobert/dasregistry/DasSource.java
index a2112b6..a5f3619 100755
--- a/src/org/biojava/dasobert/dasregistry/DasSource.java
+++ b/src/org/biojava/dasobert/dasregistry/DasSource.java
@@ -16,90 +16,90 @@
  * at:
  *
  *      http://www.biojava.org/
- * 
+ *
  * Created on Feb 8, 2006
  *
  */
 package org.biojava.dasobert.dasregistry;
 
-import java.util.Date;
+import java.util.*;
+
+public interface DasSource
+{
+
+  public void setLocal(boolean flag);
 
-public interface DasSource {
+  public boolean isLocal();
 
-    public  void setLocal(boolean flag);
+  /** compare if two das sources are equal
+   *
+   * @param ds
+   * @return returns true if two DAS sources are equivalent
+   */
+  public boolean equals(DasSource ds);
 
-    public  boolean isLocal();
+  /** classes that implement equals, should also implement hashKey
+   *
+   * @return the hash code of a das source
+   */
+  public int hashCode();
 
-    /** 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
-     * 
-     * @return the hash code of a das source
-     */
-    public int hashCode();
-    
-    
-    public  void setId(String i);
+  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.
-     * @return String the ID of a Das Source
-     */
-    public  String getId();
+  /** 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();
 
-    public  void setNickname(String name);
+  public void setNickname(String name);
 
-    public  String getNickname();
+  public String getNickname();
 
-    public  void setUrl(String u);
+  public void setUrl(String u);
 
-    public  void setAdminemail(String u);
+  public void setAdminemail(String u);
 
-    public  void setDescription(String u);
+  public void setDescription(String u);
 
-    public  void setCoordinateSystem(DasCoordinateSystem[] u);
+  public void setCoordinateSystem(DasCoordinateSystem[] u);
 
-    public  void setCapabilities(String[] u);
+  public void setCapabilities(String[] u);
 
-    public  String getUrl();
+  public String getUrl();
 
-    public  String getAdminemail();
+  public String getAdminemail();
 
-    public  String getDescription();
+  public String getDescription();
 
-    public  String[] getCapabilities();
+  public String[] getCapabilities();
 
-    public  DasCoordinateSystem[] getCoordinateSystem();
+  public DasCoordinateSystem[] getCoordinateSystem();
 
-    public  void setRegisterDate(Date d);
+  public void setRegisterDate(Date d);
 
-    public  Date getRegisterDate();
+  public Date getRegisterDate();
 
-    public  void setLeaseDate(Date d);
+  public void setLeaseDate(Date d);
 
-    public  Date getLeaseDate();
+  public Date getLeaseDate();
 
-    public  void setLabels(String[] ls);
+  public void setLabels(String[] ls);
 
-    public  String[] getLabels();
+  public String[] getLabels();
 
-    public  void setHelperurl(String url);
+  public void setHelperurl(String url);
 
-    public  String getHelperurl();
+  public String getHelperurl();
 
-    // TestCode is now part of the coordinate system!
-    //public  void setTestCode(String code);
-    //public  String getTestCode();
+  // TestCode is now part of the coordinate system!
+  //public  void setTestCode(String code);
+  //public  String getTestCode();
 
-    public  void setAlertAdmin(boolean flag);
+  public void setAlertAdmin(boolean flag);
 
-    public  boolean getAlertAdmin();
+  public boolean getAlertAdmin();
 
 }
\ 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 c07b32d..2f9db76 100755
--- a/src/org/biojava/dasobert/dasregistry/DasSourceComparator.java
+++ b/src/org/biojava/dasobert/dasregistry/DasSourceComparator.java
@@ -23,118 +23,142 @@
  */
 
 
-package org.biojava.dasobert.dasregistry ;
+package org.biojava.dasobert.dasregistry;
 
-import java.util.Comparator ;
-import java.util.Map ;
-import java.util.HashMap ;
+import java.util.*;
 
-
-/** a comparator to sort DasSources 
+/** a comparator to sort DasSources
  * @author Andreas Prlic, Thomas Down
  */
 
 
 public abstract class DasSourceComparator
     implements Comparator
-{ 
-
-    private final String name ;
-    private static final Map COMPS_BY_NAME;
-
-
-    public DasSourceComparator(String str) {
-	//System.out.println("new dasSourceComparator " + str);
-	name = str ;
+{
+
+  private final String name;
+  private static final Map COMPS_BY_NAME;
+
+  public DasSourceComparator(String str)
+  {
+    //System.out.println("new dasSourceComparator " + str);
+    name = str;
+  }
+
+  public static final Comparator BY_ID = new DasSourceComparator("id")
+  {
+    protected Comparable getField(DasSource ds)
+    {
+      return ds.getId();
     }
-   
-    public static final Comparator BY_ID = new DasSourceComparator("id") {
-        protected Comparable getField(DasSource ds) {
-            return ds.getId();
-        }
-    };    
-
-    public static final Comparator BY_NICKNAME = new DasSourceComparator("nickname") {
-        protected Comparable getField(DasSource ds) {
-            return ds.getNickname();
-        }
-    };    
-    public static final Comparator BY_REGISTER_DATE = new DasSourceComparator("registerdate") {
-        protected Comparable getField(DasSource ds) {
-            return ds.getRegisterDate();
-        }
-    };
-    public static final Comparator BY_LEASE_DATE = new DasSourceComparator("leasedate") {
-        protected Comparable getField(DasSource ds) {
-            return ds.getLeaseDate();
-        }
-    };
-    public static final Comparator BY_URL = new DasSourceComparator("url") {
-        protected Comparable getField(DasSource ds) {
-            return ds.getUrl();
-        }
-    };
-    public static final Comparator BY_ADMIN_EMAIL = new DasSourceComparator("adminemail") {
-        protected Comparable getField(DasSource ds) {
-            return ds.getAdminemail();
-        }
-    };
-    public static final Comparator BY_DESCRIPTION = new DasSourceComparator("description") {
-        protected Comparable getField(DasSource ds) {
-            return ds.getDescription();
-        }
-    };
-    public static final Comparator BY_CAPABILITIES = new DasSourceComparator("capabilities") {
-        protected Comparable getField(DasSource ds) {
-            String[] caps = ds.getCapabilities();
-            return caps.length == 0 ? "" : caps[0];
-        }
-    };
-    public static final Comparator BY_COORDINATE_SYSTEM = new DasSourceComparator("coordinateSystem") {
-        protected Comparable getField(DasSource ds) {
-            DasCoordinateSystem[] dcss = ds.getCoordinateSystem();
-            return dcss.length == 0 ? "" : dcss[0].toString();
-        }
-    };
-
-    static {
-        COMPS_BY_NAME = new HashMap();
-        COMPS_BY_NAME.put(BY_ID.toString(),                BY_ID);
-        COMPS_BY_NAME.put(BY_NICKNAME.toString(),          BY_NICKNAME);
-        COMPS_BY_NAME.put(BY_REGISTER_DATE.toString(),     BY_REGISTER_DATE);
-        COMPS_BY_NAME.put(BY_LEASE_DATE.toString(),        BY_LEASE_DATE);
-        COMPS_BY_NAME.put(BY_URL.toString(),               BY_URL);
-        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);
+  };
+
+  public static final Comparator BY_NICKNAME = new DasSourceComparator(
+      "nickname")
+  {
+    protected Comparable getField(DasSource ds)
+    {
+      return ds.getNickname();
     }
-
-   
-
-    public static Comparator fromString(String name) {
-        if (COMPS_BY_NAME.containsKey(name)) {
-            return (Comparator) COMPS_BY_NAME.get(name);
-        } else {
-            throw new IllegalArgumentException("Can't compare by key " + name);
-        }
+  };
+  public static final Comparator BY_REGISTER_DATE = new DasSourceComparator(
+      "registerdate")
+  {
+    protected Comparable getField(DasSource ds)
+    {
+      return ds.getRegisterDate();
     }
-
-    protected abstract Comparable getField(DasSource ds);
-
-    /** compare two DasSource objects */
-    public int compare( Object a, Object b) {
-        
-        DasSource x = (DasSource) a ;
-        DasSource y = (DasSource) b ;
-        return getField(x).compareTo(getField(y));
+  };
+  public static final Comparator BY_LEASE_DATE = new DasSourceComparator(
+      "leasedate")
+  {
+    protected Comparable getField(DasSource ds)
+    {
+      return ds.getLeaseDate();
     }
-
-    public String toString() {
-        return name;
+  };
+  public static final Comparator BY_URL = new DasSourceComparator("url")
+  {
+    protected Comparable getField(DasSource ds)
+    {
+      return ds.getUrl();
     }
+  };
+  public static final Comparator BY_ADMIN_EMAIL = new DasSourceComparator(
+      "adminemail")
+  {
+    protected Comparable getField(DasSource ds)
+    {
+      return ds.getAdminemail();
+    }
+  };
+  public static final Comparator BY_DESCRIPTION = new DasSourceComparator(
+      "description")
+  {
+    protected Comparable getField(DasSource ds)
+    {
+      return ds.getDescription();
+    }
+  };
+  public static final Comparator BY_CAPABILITIES = new DasSourceComparator(
+      "capabilities")
+  {
+    protected Comparable getField(DasSource ds)
+    {
+      String[] caps = ds.getCapabilities();
+      return caps.length == 0 ? "" : caps[0];
+    }
+  };
+  public static final Comparator BY_COORDINATE_SYSTEM = new DasSourceComparator(
+      "coordinateSystem")
+  {
+    protected Comparable getField(DasSource ds)
+    {
+      DasCoordinateSystem[] dcss = ds.getCoordinateSystem();
+      return dcss.length == 0 ? "" : dcss[0].toString();
+    }
+  };
+
+  static
+  {
+    COMPS_BY_NAME = new HashMap();
+    COMPS_BY_NAME.put(BY_ID.toString(), BY_ID);
+    COMPS_BY_NAME.put(BY_NICKNAME.toString(), BY_NICKNAME);
+    COMPS_BY_NAME.put(BY_REGISTER_DATE.toString(), BY_REGISTER_DATE);
+    COMPS_BY_NAME.put(BY_LEASE_DATE.toString(), BY_LEASE_DATE);
+    COMPS_BY_NAME.put(BY_URL.toString(), BY_URL);
+    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);
+  }
+
+  public static Comparator fromString(String name)
+  {
+    if (COMPS_BY_NAME.containsKey(name))
+    {
+      return (Comparator) COMPS_BY_NAME.get(name);
+    }
+    else
+    {
+      throw new IllegalArgumentException("Can't compare by key " + name);
+    }
+  }
 
+  protected abstract Comparable getField(DasSource ds);
 
-}
+  /** compare two DasSource objects */
+  public int compare(Object a, Object b)
+  {
 
+    DasSource x = (DasSource) a;
+    DasSource y = (DasSource) b;
+    return getField(x).compareTo(getField(y));
+  }
 
+  public String toString()
+  {
+    return name;
+  }
+
+}
diff --git a/src/org/biojava/dasobert/eventmodel/FeatureEvent.java b/src/org/biojava/dasobert/eventmodel/FeatureEvent.java
index 4c9ac37..44de5cc 100755
--- a/src/org/biojava/dasobert/eventmodel/FeatureEvent.java
+++ b/src/org/biojava/dasobert/eventmodel/FeatureEvent.java
@@ -16,57 +16,62 @@
  * at:
  *
  *      http://www.biojava.org/
- * 
+ *
  * Created on Oct 28, 2005
  *
  */
 package org.biojava.dasobert.eventmodel;
 
-import java.util.Map;
+import java.util.*;
 
-import org.biojava.dasobert.dasregistry.Das1Source;
-public class FeatureEvent {
-    
-    Map[] features;
-    Das1Source dasSource;
-    int comeBackLater;
-    
-    public FeatureEvent(Map[] features,Das1Source dasSource) {
-        super();
-        this.features =features;
-        this.dasSource = dasSource;
-        comeBackLater = -1;
-    }
-    
-    public int getComeBackLater(){
-        return comeBackLater;
-    }
-    
-    public void setComeBackLater(int comeBackLater){
-        this.comeBackLater = comeBackLater;
-    }
-    
-    
-    /** 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);
-     * }      
-     * </pre>
-     * @return a Map containng the features
-     */
-    public Map[] getFeatures(){
-        return features;
-    }
-    
-    public Das1Source getDasSource(){
-        return dasSource;
-    }
-    
-}
+import org.biojava.dasobert.dasregistry.*;
+
+public class FeatureEvent
+{
+
+  Map[] features;
+  Das1Source dasSource;
+  int comeBackLater;
+
+  public FeatureEvent(Map[] features, Das1Source dasSource)
+  {
+    super();
+    this.features = features;
+    this.dasSource = dasSource;
+    comeBackLater = -1;
+  }
 
+  public int getComeBackLater()
+  {
+    return comeBackLater;
+  }
+
+  public void setComeBackLater(int comeBackLater)
+  {
+    this.comeBackLater = comeBackLater;
+  }
+
+  /** 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);
+   * }
+   * </pre>
+   * @return a Map containng the features
+   */
+  public Map[] getFeatures()
+  {
+    return features;
+  }
+
+  public Das1Source getDasSource()
+  {
+    return dasSource;
+  }
+
+}
diff --git a/src/org/biojava/dasobert/eventmodel/FeatureListener.java b/src/org/biojava/dasobert/eventmodel/FeatureListener.java
index 0091ef1..1ae5827 100755
--- a/src/org/biojava/dasobert/eventmodel/FeatureListener.java
+++ b/src/org/biojava/dasobert/eventmodel/FeatureListener.java
@@ -16,7 +16,7 @@
  * at:
  *
  *      http://www.biojava.org/
- * 
+ *
  * Created on Oct 28, 2005
  *
  */
@@ -25,25 +25,21 @@ package org.biojava.dasobert.eventmodel;
 //import org.biojava.spice.multipanel.eventmodel.FeatureEvent;
 
 /**  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 
-     * 
-     * @param e
-     */
-    public void newFeatures(FeatureEvent e);
-    
-    /** the server says that he is busy and we should try again in x seconds
-     * 
-     * @param e
-     */
-    public void comeBackLater(FeatureEvent e);
-    
-}
+ *
+ */
+public interface FeatureListener
+{
+
+  /** 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
+   *
+   * @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 7b136a4..b5acf89 100755
--- a/src/org/biojava/dasobert/eventmodel/ObjectListener.java
+++ b/src/org/biojava/dasobert/eventmodel/ObjectListener.java
@@ -16,32 +16,32 @@
  * at:
  *
  *      http://www.biojava.org/
- * 
+ *
  * Created on Nov 1, 2005
  *
  */
 package org.biojava.dasobert.eventmodel;
 
 /** 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 
-     * 
-     * @param accessionCode
-     */
-    public void newObjectRequested(String accessionCode);
-    
-    /** no object with that accessionCode has been found
-     * 
-     * @param accessionCode
-     */
-    public void noObjectFound(String accessionCode);
-    
-    
-   // public void exceptionOccured(Exception e);
-   
+public interface ObjectListener
+{
+
+  /** a new object has been requested
+   *
+   * @param accessionCode
+   */
+  public void newObjectRequested(String accessionCode);
+
+  /** no object with that accessionCode has been found
+   *
+   * @param accessionCode
+   */
+  public void noObjectFound(String accessionCode);
+
+  // public void exceptionOccured(Exception e);
+
 }
diff --git a/src/org/biojava/dasobert/eventmodel/SequenceEvent.java b/src/org/biojava/dasobert/eventmodel/SequenceEvent.java
index c3123ff..2cbc79e 100755
--- a/src/org/biojava/dasobert/eventmodel/SequenceEvent.java
+++ b/src/org/biojava/dasobert/eventmodel/SequenceEvent.java
@@ -16,29 +16,32 @@
  * at:
  *
  *      http://www.biojava.org/
- * 
+ *
  * Created on Nov 20, 2005
  *
  */
 package org.biojava.dasobert.eventmodel;
 
+public class SequenceEvent
+{
+
+  String sequence;
+  String accessionCode;
+  public SequenceEvent(String accessionCode, String seq)
+  {
+    super();
+    sequence = seq;
+    this.accessionCode = accessionCode;
+  }
 
-public class SequenceEvent {
+  public String getAccessionCode()
+  {
+    return accessionCode;
+  }
 
-    String sequence;
-    String accessionCode;
-    public SequenceEvent(String accessionCode, String seq) {
-        super();
-        sequence = seq;
-        this.accessionCode = accessionCode;
-    }
-    
-    public String getAccessionCode(){
-        return accessionCode;
-    }
-    
-    public String getSequence(){
-        return sequence;
-    }
+  public String getSequence()
+  {
+    return sequence;
+  }
 
 }
diff --git a/src/org/biojava/dasobert/eventmodel/SequenceListener.java b/src/org/biojava/dasobert/eventmodel/SequenceListener.java
index 58cbdb3..c71a6d9 100755
--- a/src/org/biojava/dasobert/eventmodel/SequenceListener.java
+++ b/src/org/biojava/dasobert/eventmodel/SequenceListener.java
@@ -16,7 +16,7 @@
  * at:
  *
  *      http://www.biojava.org/
- * 
+ *
  * Created on Jun 10, 2005
  *
  */
@@ -28,28 +28,29 @@ package org.biojava.dasobert.eventmodel;
  * @author Andreas Prlic
  *
  */
-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
-     * */
-    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
-     * */
-    public void selectionLocked(boolean flag);
-    
-    public void newSequence(SequenceEvent e);
-    
-    /** clear what has been selected
-     * 
-     *
-     */
-    public void clearSelection();
+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
+   * */
+  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
+   * */
+  public void selectionLocked(boolean flag);
+
+  public void newSequence(SequenceEvent e);
+
+  /** clear what has been selected
+   *
+   *
+   */
+  public void clearSelection();
 }
diff --git a/src/org/jibble/epsgraphics/EpsDocument.java b/src/org/jibble/epsgraphics/EpsDocument.java
index 486fc31..a53df85 100755
--- a/src/org/jibble/epsgraphics/EpsDocument.java
+++ b/src/org/jibble/epsgraphics/EpsDocument.java
@@ -1,24 +1,23 @@
 /*
-Copyright Paul James Mutton, 2001-2004, http://www.jibble.org/
+ Copyright Paul James Mutton, 2001-2004, http://www.jibble.org/
 
-This file is part of EpsGraphics2D.
+ 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/
+ 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/
 
-$Author$
-$Id$
+ $Author$
+ $Id$
 
-*/
+ */
 
 package org.jibble.epsgraphics;
 
-import java.util.*;
 import java.io.*;
-
+import java.util.*;
 
 /**
  * This represents an EPS document. Several EpsGraphics2D objects may point
@@ -28,208 +27,240 @@ import java.io.*;
  *           <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);
+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;
     }
-
-    /**
-     * 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);
+    if (x < minX)
+    {
+      minX = (float) x;
     }
-
-
-    /**
-     * Returns the title of the EPS document.
-     */
-    public synchronized String getTitle() {
-        return _title;
+    if (y > maxY)
+    {
+      maxY = (float) y;
     }
-
-
-    /**
-     * 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;
-        }
+    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);
-        }
+  }
+
+  /**
+   * 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;
     }
-
-
-    /**
-     * 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();
+    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;
 
-
-    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();
+    try
+    {
+      _bufferedWriter.write(line + "\n");
     }
-
-
-    public synchronized void flush() throws IOException {
-        _bufferedWriter.flush();
+    catch (IOException e)
+    {
+      throw new EpsException("Could not write to the output file: " + e);
     }
-
-    public synchronized void close() throws IOException {
-        if (_stringWriter == null) {
-            writeFooter(_bufferedWriter);
-            _bufferedWriter.flush();
-            _bufferedWriter.close();
-        }
+  }
+
+  /**
+   * 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();
+  }
 
-    public boolean isClipSet() {
-        return _isClipSet;
+  private void writeFooter(Writer writer)
+      throws IOException
+  {
+    writer.write("grestore\n");
+    if (isClipSet())
+    {
+      writer.write("grestore\n");
     }
-
-    public void setClipSet(boolean isClipSet) {
-        _isClipSet = isClipSet;
+    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 float minX;
+  private float minY;
+  private float maxX;
+  private float maxY;
 
-    private boolean _isClipSet = false;
+  private boolean _isClipSet = false;
 
-    private String _title;
-    private StringWriter _stringWriter;
-    private BufferedWriter _bufferedWriter = null;
+  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;
+  // 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 3f0611f..c9ae519 100755
--- a/src/org/jibble/epsgraphics/EpsException.java
+++ b/src/org/jibble/epsgraphics/EpsException.java
@@ -1,25 +1,28 @@
-/* 
-Copyright Paul James Mutton, 2001-2004, http://www.jibble.org/
+/*
+ Copyright Paul James Mutton, 2001-2004, http://www.jibble.org/
 
-This file is part of EpsGraphics2D.
+ 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/
+ 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/
 
-$Author$
-$Id$
+ $Author$
+ $Id$
 
-*/
+ */
 
 package org.jibble.epsgraphics;
 
-public class EpsException extends RuntimeException {
-    
-    public EpsException(String message) {
-        super(message);
-    }
-    
+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 7955440..45eeb5b 100755
--- a/src/org/jibble/epsgraphics/EpsGraphics2D.java
+++ b/src/org/jibble/epsgraphics/EpsGraphics2D.java
@@ -1,30 +1,30 @@
 /*
-Copyright Paul James Mutton, 2001-2004, http://www.jibble.org/
+ Copyright Paul James Mutton, 2001-2004, http://www.jibble.org/
 
-This file is part of EpsGraphics2D.
+ 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/
+ 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/
 
-$Author$
-$Id$
+ $Author$
+ $Id$
 
-*/
+ */
 
 package org.jibble.epsgraphics;
 
-import java.awt.*;
-import java.awt.image.*;
-import java.awt.image.renderable.*;
-import java.awt.geom.*;
 import java.io.*;
 import java.text.*;
-import java.awt.font.*;
 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
@@ -70,1275 +70,1376 @@ import java.util.*;
  *           <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");
+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);
         }
-    }
-
-
-    /**
-     * 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;
+        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++;
         }
-        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 if (type == PathIterator.SEG_CUBICTO)
+        {
+          append(x1 + " " + y1 + " " + x2 + " " + y2 + " " + x3 + " " + y3 +
+                 " curveto");
+          count++;
+          x0 = x3;
+          y0 = y3;
         }
-        else {
-            setColor(originalColor.darker());
+        else if (type == PathIterator.SEG_LINETO)
+        {
+          append(x1 + " " + y1 + " lineto");
+          count++;
+          x0 = x1;
+          y0 = y1;
         }
-
-        drawLine(x, y, x + width, y);
-        drawLine(x, y, x, y + height);
-
-        if (raised) {
-            setColor(originalColor.darker());
+        else if (type == PathIterator.SEG_MOVETO)
+        {
+          append(x1 + " " + y1 + " moveto");
+          count++;
+          x0 = x1;
+          y0 = y1;
         }
-        else {
-            setColor(originalColor.brighter());
+        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;
         }
-
-        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 if (type == PathIterator.WIND_EVEN_ODD)
+        {
+          // Ignore.
         }
-        else {
-            setColor(originalColor.darker());
+        else if (type == PathIterator.WIND_NON_ZERO)
+        {
+          // Ignore.
         }
-        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]));
+        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('\\');
         }
-
-        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);
+        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]) + " ");
         }
-    }
-
-
-    /**
-     * 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");
-        }
-
+      }
+      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");
-
-        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());
-        }
-
+      }
+      else
+      {
+        _document.setClipSet(true);
+        append("gsave");
+      }
+      draw(clip, "clip");
+      _clip = clip;
+      _clipTransform = (AffineTransform) _transform.clone();
+    }
+    else
+    {
+      if (_document.isClipSet())
+      {
         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;
+        _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();
         }
-        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);
+      }
+    }
+    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/www/Data.java b/src/uk/ac/ebi/www/Data.java
index bc8ec84..9bb671e 100755
--- a/src/uk/ac/ebi/www/Data.java
+++ b/src/uk/ac/ebi/www/Data.java
@@ -7,114 +7,143 @@
 
 package uk.ac.ebi.www;
 
-public class Data  implements java.io.Serializable {
-    private java.lang.String type;
-    private java.lang.String content;
+public class Data
+    implements java.io.Serializable
+{
+  private java.lang.String type;
+  private java.lang.String content;
 
-    public Data() {
-    }
+  public Data()
+  {
+  }
 
-    public java.lang.String getType() {
-        return type;
-    }
+  public java.lang.String getType()
+  {
+    return type;
+  }
 
-    public void setType(java.lang.String type) {
-        this.type = type;
-    }
+  public void setType(java.lang.String type)
+  {
+    this.type = type;
+  }
 
-    public java.lang.String getContent() {
-        return content;
-    }
+  public java.lang.String getContent()
+  {
+    return content;
+  }
 
-    public void setContent(java.lang.String content) {
-        this.content = content;
-    }
+  public void setContent(java.lang.String content)
+  {
+    this.content = content;
+  }
 
-    private java.lang.Object __equalsCalc = null;
-    public synchronized boolean equals(java.lang.Object obj) {
-        if (!(obj instanceof Data)) return false;
-        Data other = (Data) obj;
-        if (obj == null) return false;
-        if (this == obj) return true;
-        if (__equalsCalc != null) {
-            return (__equalsCalc == obj);
-        }
-        __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())));
-        __equalsCalc = null;
-        return _equals;
+  private java.lang.Object __equalsCalc = null;
+  public synchronized boolean equals(java.lang.Object obj)
+  {
+    if (! (obj instanceof Data))
+    {
+      return false;
+    }
+    Data other = (Data) obj;
+    if (obj == null)
+    {
+      return false;
+    }
+    if (this == obj)
+    {
+      return true;
     }
+    if (__equalsCalc != null)
+    {
+      return (__equalsCalc == obj);
+    }
+    __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())));
+    __equalsCalc = null;
+    return _equals;
+  }
 
-    private boolean __hashCodeCalc = false;
-    public synchronized int hashCode() {
-        if (__hashCodeCalc) {
-            return 0;
-        }
-        __hashCodeCalc = true;
-        int _hashCode = 1;
-        if (getType() != null) {
-            _hashCode += getType().hashCode();
-        }
-        if (getContent() != null) {
-            _hashCode += getContent().hashCode();
-        }
-        __hashCodeCalc = false;
-        return _hashCode;
+  private boolean __hashCodeCalc = false;
+  public synchronized int hashCode()
+  {
+    if (__hashCodeCalc)
+    {
+      return 0;
+    }
+    __hashCodeCalc = true;
+    int _hashCode = 1;
+    if (getType() != null)
+    {
+      _hashCode += getType().hashCode();
+    }
+    if (getContent() != null)
+    {
+      _hashCode += getContent().hashCode();
     }
+    __hashCodeCalc = false;
+    return _hashCode;
+  }
 
-    // Type metadata
-    private static org.apache.axis.description.TypeDesc typeDesc =
-        new org.apache.axis.description.TypeDesc(Data.class);
+  // Type metadata
+  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();
-        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"));
-        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"));
-        typeDesc.addFieldDesc(field);
-    };
+  static
+  {
+    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"));
+    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"));
+    typeDesc.addFieldDesc(field);
+  };
 
-    /**
-     * 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(
+  /**
+   * 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(
+  /**
+   * 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/InputParams.java b/src/uk/ac/ebi/www/InputParams.java
index 15de139..83d68a9 100755
--- a/src/uk/ac/ebi/www/InputParams.java
+++ b/src/uk/ac/ebi/www/InputParams.java
@@ -7,370 +7,449 @@
 
 package uk.ac.ebi.www;
 
-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() {
-    }
-
-    public java.lang.String getProgram() {
-        return program;
-    }
-
-    public void setProgram(java.lang.String program) {
-        this.program = program;
-    }
-
-    public java.lang.String getDatabase() {
-        return database;
-    }
-
-    public void setDatabase(java.lang.String database) {
-        this.database = database;
-    }
-
-    public java.lang.String getMatrix() {
-        return matrix;
-    }
-
-    public void setMatrix(java.lang.String matrix) {
-        this.matrix = matrix;
-    }
-
-    public float getExp() {
-        return exp;
-    }
-
-    public void setExp(float exp) {
-        this.exp = exp;
-    }
-
-    public boolean isEchofilter() {
-        return echofilter;
-    }
-
-    public void setEchofilter(boolean echofilter) {
-        this.echofilter = echofilter;
-    }
-
-    public java.lang.String getFilter() {
-        return filter;
-    }
-
-    public void setFilter(java.lang.String filter) {
-        this.filter = filter;
-    }
-
-    public int getNumal() {
-        return numal;
-    }
-
-    public void setNumal(int numal) {
-        this.numal = numal;
-    }
-
-    public int getScores() {
-        return scores;
-    }
-
-    public void setScores(int scores) {
-        this.scores = scores;
-    }
-
-    public java.lang.String getSensitivity() {
-        return sensitivity;
-    }
-
-    public void setSensitivity(java.lang.String sensitivity) {
-        this.sensitivity = sensitivity;
-    }
-
-    public java.lang.String getSort() {
-        return sort;
-    }
-
-    public void setSort(java.lang.String sort) {
-        this.sort = sort;
-    }
-
-    public java.lang.String getStats() {
-        return stats;
-    }
-
-    public void setStats(java.lang.String stats) {
-        this.stats = stats;
-    }
-
-    public java.lang.String getStrand() {
-        return strand;
-    }
-
-    public void setStrand(java.lang.String strand) {
-        this.strand = strand;
-    }
-
-    public java.lang.String getOutformat() {
-        return outformat;
-    }
-
-    public void setOutformat(java.lang.String outformat) {
-        this.outformat = outformat;
-    }
-
-    public int getTopcombon() {
-        return topcombon;
-    }
-
-    public void setTopcombon(int topcombon) {
-        this.topcombon = topcombon;
-    }
-
-    public boolean isAsync() {
-        return async;
-    }
-
-    public void setAsync(boolean async) {
-        this.async = async;
-    }
-
-    public java.lang.String getEmail() {
-        return email;
-    }
-
-    public void setEmail(java.lang.String email) {
-        this.email = email;
-    }
-
-    private java.lang.Object __equalsCalc = null;
-    public synchronized boolean equals(java.lang.Object obj) {
-        if (!(obj instanceof InputParams)) return false;
-        InputParams other = (InputParams) obj;
-        if (obj == null) return false;
-        if (this == obj) return true;
-        if (__equalsCalc != null) {
-            return (__equalsCalc == obj);
-        }
-        __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())));
-        __equalsCalc = null;
-        return _equals;
-    }
-
-    private boolean __hashCodeCalc = false;
-    public synchronized int hashCode() {
-        if (__hashCodeCalc) {
-            return 0;
-        }
-        __hashCodeCalc = true;
-        int _hashCode = 1;
-        if (getProgram() != null) {
-            _hashCode += getProgram().hashCode();
-        }
-        if (getDatabase() != null) {
-            _hashCode += getDatabase().hashCode();
-        }
-        if (getMatrix() != null) {
-            _hashCode += getMatrix().hashCode();
-        }
-        _hashCode += new Float(getExp()).hashCode();
-        _hashCode += new Boolean(isEchofilter()).hashCode();
-        if (getFilter() != null) {
-            _hashCode += getFilter().hashCode();
-        }
-        _hashCode += getNumal();
-        _hashCode += getScores();
-        if (getSensitivity() != null) {
-            _hashCode += getSensitivity().hashCode();
-        }
-        if (getSort() != null) {
-            _hashCode += getSort().hashCode();
-        }
-        if (getStats() != null) {
-            _hashCode += getStats().hashCode();
-        }
-        if (getStrand() != null) {
-            _hashCode += getStrand().hashCode();
-        }
-        if (getOutformat() != null) {
-            _hashCode += getOutformat().hashCode();
-        }
-        _hashCode += getTopcombon();
-        _hashCode += new Boolean(isAsync()).hashCode();
-        if (getEmail() != null) {
-            _hashCode += getEmail().hashCode();
-        }
-        __hashCodeCalc = false;
-        return _hashCode;
-    }
-
-    // Type metadata
-    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();
-        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"));
-        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"));
-        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"));
-        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"));
-        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"));
-        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"));
-        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"));
-        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"));
-        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"));
-        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"));
-        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"));
-        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"));
-        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"));
-        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"));
-        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"));
-        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"));
-        typeDesc.addFieldDesc(field);
-    };
-
-    /**
-     * 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(
+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()
+  {
+  }
+
+  public java.lang.String getProgram()
+  {
+    return program;
+  }
+
+  public void setProgram(java.lang.String program)
+  {
+    this.program = program;
+  }
+
+  public java.lang.String getDatabase()
+  {
+    return database;
+  }
+
+  public void setDatabase(java.lang.String database)
+  {
+    this.database = database;
+  }
+
+  public java.lang.String getMatrix()
+  {
+    return matrix;
+  }
+
+  public void setMatrix(java.lang.String matrix)
+  {
+    this.matrix = matrix;
+  }
+
+  public float getExp()
+  {
+    return exp;
+  }
+
+  public void setExp(float exp)
+  {
+    this.exp = exp;
+  }
+
+  public boolean isEchofilter()
+  {
+    return echofilter;
+  }
+
+  public void setEchofilter(boolean echofilter)
+  {
+    this.echofilter = echofilter;
+  }
+
+  public java.lang.String getFilter()
+  {
+    return filter;
+  }
+
+  public void setFilter(java.lang.String filter)
+  {
+    this.filter = filter;
+  }
+
+  public int getNumal()
+  {
+    return numal;
+  }
+
+  public void setNumal(int numal)
+  {
+    this.numal = numal;
+  }
+
+  public int getScores()
+  {
+    return scores;
+  }
+
+  public void setScores(int scores)
+  {
+    this.scores = scores;
+  }
+
+  public java.lang.String getSensitivity()
+  {
+    return sensitivity;
+  }
+
+  public void setSensitivity(java.lang.String sensitivity)
+  {
+    this.sensitivity = sensitivity;
+  }
+
+  public java.lang.String getSort()
+  {
+    return sort;
+  }
+
+  public void setSort(java.lang.String sort)
+  {
+    this.sort = sort;
+  }
+
+  public java.lang.String getStats()
+  {
+    return stats;
+  }
+
+  public void setStats(java.lang.String stats)
+  {
+    this.stats = stats;
+  }
+
+  public java.lang.String getStrand()
+  {
+    return strand;
+  }
+
+  public void setStrand(java.lang.String strand)
+  {
+    this.strand = strand;
+  }
+
+  public java.lang.String getOutformat()
+  {
+    return outformat;
+  }
+
+  public void setOutformat(java.lang.String outformat)
+  {
+    this.outformat = outformat;
+  }
+
+  public int getTopcombon()
+  {
+    return topcombon;
+  }
+
+  public void setTopcombon(int topcombon)
+  {
+    this.topcombon = topcombon;
+  }
+
+  public boolean isAsync()
+  {
+    return async;
+  }
+
+  public void setAsync(boolean async)
+  {
+    this.async = async;
+  }
+
+  public java.lang.String getEmail()
+  {
+    return email;
+  }
+
+  public void setEmail(java.lang.String email)
+  {
+    this.email = email;
+  }
+
+  private java.lang.Object __equalsCalc = null;
+  public synchronized boolean equals(java.lang.Object obj)
+  {
+    if (! (obj instanceof InputParams))
+    {
+      return false;
+    }
+    InputParams other = (InputParams) obj;
+    if (obj == null)
+    {
+      return false;
+    }
+    if (this == obj)
+    {
+      return true;
+    }
+    if (__equalsCalc != null)
+    {
+      return (__equalsCalc == obj);
+    }
+    __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())));
+    __equalsCalc = null;
+    return _equals;
+  }
+
+  private boolean __hashCodeCalc = false;
+  public synchronized int hashCode()
+  {
+    if (__hashCodeCalc)
+    {
+      return 0;
+    }
+    __hashCodeCalc = true;
+    int _hashCode = 1;
+    if (getProgram() != null)
+    {
+      _hashCode += getProgram().hashCode();
+    }
+    if (getDatabase() != null)
+    {
+      _hashCode += getDatabase().hashCode();
+    }
+    if (getMatrix() != null)
+    {
+      _hashCode += getMatrix().hashCode();
+    }
+    _hashCode += new Float(getExp()).hashCode();
+    _hashCode += new Boolean(isEchofilter()).hashCode();
+    if (getFilter() != null)
+    {
+      _hashCode += getFilter().hashCode();
+    }
+    _hashCode += getNumal();
+    _hashCode += getScores();
+    if (getSensitivity() != null)
+    {
+      _hashCode += getSensitivity().hashCode();
+    }
+    if (getSort() != null)
+    {
+      _hashCode += getSort().hashCode();
+    }
+    if (getStats() != null)
+    {
+      _hashCode += getStats().hashCode();
+    }
+    if (getStrand() != null)
+    {
+      _hashCode += getStrand().hashCode();
+    }
+    if (getOutformat() != null)
+    {
+      _hashCode += getOutformat().hashCode();
+    }
+    _hashCode += getTopcombon();
+    _hashCode += new Boolean(isAsync()).hashCode();
+    if (getEmail() != null)
+    {
+      _hashCode += getEmail().hashCode();
+    }
+    __hashCodeCalc = false;
+    return _hashCode;
+  }
+
+  // Type metadata
+  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();
+    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"));
+    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"));
+    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"));
+    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"));
+    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"));
+    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"));
+    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"));
+    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"));
+    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"));
+    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"));
+    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"));
+    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"));
+    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"));
+    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"));
+    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"));
+    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"));
+    typeDesc.addFieldDesc(field);
+  };
+
+  /**
+   * 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(
+  }
+
+  /**
+   * 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/WSFile.java b/src/uk/ac/ebi/www/WSFile.java
index 4344b7e..66bb1dc 100755
--- a/src/uk/ac/ebi/www/WSFile.java
+++ b/src/uk/ac/ebi/www/WSFile.java
@@ -7,114 +7,143 @@
 
 package uk.ac.ebi.www;
 
-public class WSFile  implements java.io.Serializable {
-    private java.lang.String type;
-    private java.lang.String ext;
+public class WSFile
+    implements java.io.Serializable
+{
+  private java.lang.String type;
+  private java.lang.String ext;
 
-    public WSFile() {
-    }
+  public WSFile()
+  {
+  }
 
-    public java.lang.String getType() {
-        return type;
-    }
+  public java.lang.String getType()
+  {
+    return type;
+  }
 
-    public void setType(java.lang.String type) {
-        this.type = type;
-    }
+  public void setType(java.lang.String type)
+  {
+    this.type = type;
+  }
 
-    public java.lang.String getExt() {
-        return ext;
-    }
+  public java.lang.String getExt()
+  {
+    return ext;
+  }
 
-    public void setExt(java.lang.String ext) {
-        this.ext = ext;
-    }
+  public void setExt(java.lang.String ext)
+  {
+    this.ext = ext;
+  }
 
-    private java.lang.Object __equalsCalc = null;
-    public synchronized boolean equals(java.lang.Object obj) {
-        if (!(obj instanceof WSFile)) return false;
-        WSFile other = (WSFile) obj;
-        if (obj == null) return false;
-        if (this == obj) return true;
-        if (__equalsCalc != null) {
-            return (__equalsCalc == obj);
-        }
-        __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())));
-        __equalsCalc = null;
-        return _equals;
+  private java.lang.Object __equalsCalc = null;
+  public synchronized boolean equals(java.lang.Object obj)
+  {
+    if (! (obj instanceof WSFile))
+    {
+      return false;
+    }
+    WSFile other = (WSFile) obj;
+    if (obj == null)
+    {
+      return false;
+    }
+    if (this == obj)
+    {
+      return true;
     }
+    if (__equalsCalc != null)
+    {
+      return (__equalsCalc == obj);
+    }
+    __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())));
+    __equalsCalc = null;
+    return _equals;
+  }
 
-    private boolean __hashCodeCalc = false;
-    public synchronized int hashCode() {
-        if (__hashCodeCalc) {
-            return 0;
-        }
-        __hashCodeCalc = true;
-        int _hashCode = 1;
-        if (getType() != null) {
-            _hashCode += getType().hashCode();
-        }
-        if (getExt() != null) {
-            _hashCode += getExt().hashCode();
-        }
-        __hashCodeCalc = false;
-        return _hashCode;
+  private boolean __hashCodeCalc = false;
+  public synchronized int hashCode()
+  {
+    if (__hashCodeCalc)
+    {
+      return 0;
+    }
+    __hashCodeCalc = true;
+    int _hashCode = 1;
+    if (getType() != null)
+    {
+      _hashCode += getType().hashCode();
+    }
+    if (getExt() != null)
+    {
+      _hashCode += getExt().hashCode();
     }
+    __hashCodeCalc = false;
+    return _hashCode;
+  }
 
-    // Type metadata
-    private static org.apache.axis.description.TypeDesc typeDesc =
-        new org.apache.axis.description.TypeDesc(WSFile.class);
+  // Type metadata
+  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();
-        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"));
-        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"));
-        typeDesc.addFieldDesc(field);
-    };
+  static
+  {
+    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"));
+    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"));
+    typeDesc.addFieldDesc(field);
+  };
 
-    /**
-     * 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(
+  /**
+   * 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(
+  /**
+   * 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/WSWUBlast.java b/src/uk/ac/ebi/www/WSWUBlast.java
index becd6ea..e7f6f87 100755
--- a/src/uk/ac/ebi/www/WSWUBlast.java
+++ b/src/uk/ac/ebi/www/WSWUBlast.java
@@ -7,12 +7,28 @@
 
 package uk.ac.ebi.www;
 
-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;
-    public java.lang.String checkStatus(java.lang.String jobid) throws java.rmi.RemoteException;
-    public byte[] poll(java.lang.String jobid, java.lang.String type) throws java.rmi.RemoteException;
-    public uk.ac.ebi.www.WSFile[] getResults(java.lang.String jobid) throws java.rmi.RemoteException;
-    public byte[] test(java.lang.String jobid, java.lang.String type) throws java.rmi.RemoteException;
-    public byte[] polljob(java.lang.String jobid, java.lang.String outformat) throws java.rmi.RemoteException;
-    public byte[] doWUBlast(uk.ac.ebi.www.InputParams params, byte[] content) throws java.rmi.RemoteException;
+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;
+
+  public java.lang.String checkStatus(java.lang.String jobid)
+      throws java.rmi.RemoteException;
+
+  public byte[] poll(java.lang.String jobid, java.lang.String type)
+      throws java.rmi.RemoteException;
+
+  public uk.ac.ebi.www.WSFile[] getResults(java.lang.String jobid)
+      throws java.rmi.RemoteException;
+
+  public byte[] test(java.lang.String jobid, java.lang.String type)
+      throws java.rmi.RemoteException;
+
+  public byte[] polljob(java.lang.String jobid, java.lang.String outformat)
+      throws java.rmi.RemoteException;
+
+  public byte[] doWUBlast(uk.ac.ebi.www.InputParams params, byte[] content)
+      throws java.rmi.RemoteException;
 }
diff --git a/src/uk/ac/ebi/www/WSWUBlastService.java b/src/uk/ac/ebi/www/WSWUBlastService.java
index fcc8b16..bc65727 100755
--- a/src/uk/ac/ebi/www/WSWUBlastService.java
+++ b/src/uk/ac/ebi/www/WSWUBlastService.java
@@ -7,10 +7,14 @@
 
 package uk.ac.ebi.www;
 
-public interface WSWUBlastService extends javax.xml.rpc.Service {
-    public java.lang.String getWSWUBlastAddress();
+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;
+  public uk.ac.ebi.www.WSWUBlast getWSWUBlast()
+      throws javax.xml.rpc.ServiceException;
 
-    public uk.ac.ebi.www.WSWUBlast getWSWUBlast(java.net.URL portAddress) throws javax.xml.rpc.ServiceException;
+  public uk.ac.ebi.www.WSWUBlast getWSWUBlast(java.net.URL portAddress)
+      throws javax.xml.rpc.ServiceException;
 }
diff --git a/src/uk/ac/ebi/www/WSWUBlastServiceLocator.java b/src/uk/ac/ebi/www/WSWUBlastServiceLocator.java
index 2e8067c..08f0509 100755
--- a/src/uk/ac/ebi/www/WSWUBlastServiceLocator.java
+++ b/src/uk/ac/ebi/www/WSWUBlastServiceLocator.java
@@ -7,90 +7,123 @@
 
 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";
+  // 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";
 
-    public java.lang.String getWSWUBlastAddress() {
-        return WSWUBlast_address;
-    }
+  public java.lang.String getWSWUBlastAddress()
+  {
+    return WSWUBlast_address;
+  }
 
-    // The WSDD service name defaults to the port name.
-    private java.lang.String WSWUBlastWSDDServiceName = "WSWUBlast";
+  // The WSDD service name defaults to the port name.
+  private java.lang.String WSWUBlastWSDDServiceName = "WSWUBlast";
 
-    public java.lang.String getWSWUBlastWSDDServiceName() {
-        return WSWUBlastWSDDServiceName;
-    }
+  public java.lang.String getWSWUBlastWSDDServiceName()
+  {
+    return WSWUBlastWSDDServiceName;
+  }
 
-    public void setWSWUBlastWSDDServiceName(java.lang.String name) {
-        WSWUBlastWSDDServiceName = name;
-    }
+  public void setWSWUBlastWSDDServiceName(java.lang.String name)
+  {
+    WSWUBlastWSDDServiceName = name;
+  }
 
-    public uk.ac.ebi.www.WSWUBlast getWSWUBlast() throws javax.xml.rpc.ServiceException {
-       java.net.URL endpoint;
-        try {
-            endpoint = new java.net.URL(WSWUBlast_address);
-        }
-        catch (java.net.MalformedURLException e) {
-            return null; // unlikely as URL was validated in WSDL2Java
-        }
-        return getWSWUBlast(endpoint);
+  public uk.ac.ebi.www.WSWUBlast getWSWUBlast()
+      throws javax.xml.rpc.ServiceException
+  {
+    java.net.URL endpoint;
+    try
+    {
+      endpoint = new java.net.URL(WSWUBlast_address);
     }
-
-    public uk.ac.ebi.www.WSWUBlast getWSWUBlast(java.net.URL portAddress) throws javax.xml.rpc.ServiceException {
-        try {
-            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) {
-            return null;
-        }
+    catch (java.net.MalformedURLException e)
+    {
+      return null; // unlikely as URL was validated in WSDL2Java
     }
+    return getWSWUBlast(endpoint);
+  }
 
-    /**
-     * 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.WSWUBlast.class.isAssignableFrom(serviceEndpointInterface)) {
-                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) {
-            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()));
+  public uk.ac.ebi.www.WSWUBlast getWSWUBlast(java.net.URL portAddress)
+      throws javax.xml.rpc.ServiceException
+  {
+    try
+    {
+      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)
+    {
+      return null;
+    }
+  }
 
-    /**
-     * 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 {
-        java.rmi.Remote _stub = getPort(serviceEndpointInterface);
-        ((org.apache.axis.client.Stub) _stub).setPortName(portName);
+  /**
+   * 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.WSWUBlast.class.isAssignableFrom(
+          serviceEndpointInterface))
+      {
+        uk.ac.ebi.www.WSWUBlastSoapBindingStub _stub = new uk.ac.ebi.www.
+            WSWUBlastSoapBindingStub(new java.net.URL(WSWUBlast_address), this);
+        _stub.setPortName(getWSWUBlastWSDDServiceName());
         return _stub;
+      }
     }
-
-    public javax.xml.namespace.QName getServiceName() {
-        return new javax.xml.namespace.QName("http://www.ebi.ac.uk/WSWUBlast", "WSWUBlastService");
+    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
+  {
+    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/WSWUBlast",
+                                         "WSWUBlastService");
+  }
 
-    private java.util.HashSet ports = null;
+  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("WSWUBlast"));
-        }
-        return ports.iterator();
+  public java.util.Iterator getPorts()
+  {
+    if (ports == null)
+    {
+      ports = new java.util.HashSet();
+      ports.add(new javax.xml.namespace.QName("WSWUBlast"));
     }
+    return ports.iterator();
+  }
 
 }
diff --git a/src/uk/ac/ebi/www/WSWUBlastSoapBindingStub.java b/src/uk/ac/ebi/www/WSWUBlastSoapBindingStub.java
index ea3ee73..842bf8b 100755
--- a/src/uk/ac/ebi/www/WSWUBlastSoapBindingStub.java
+++ b/src/uk/ac/ebi/www/WSWUBlastSoapBindingStub.java
@@ -7,317 +7,490 @@
 
 package uk.ac.ebi.www;
 
-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 {
-         this(null);
+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
+  {
+    this(null);
+  }
+
+  public WSWUBlastSoapBindingStub(java.net.URL endpointURL,
+                                  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
+  {
+    if (service == null)
+    {
+      super.service = new org.apache.axis.client.Service();
     }
-
-    public WSWUBlastSoapBindingStub(java.net.URL endpointURL, javax.xml.rpc.Service service) throws org.apache.axis.AxisFault {
-         this(service);
-         super.cachedEndpoint = endpointURL;
+    else
+    {
+      super.service = service;
     }
-
-    public WSWUBlastSoapBindingStub(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;
+    qName = new javax.xml.namespace.QName("http://www.ebi.ac.uk/WSWUBlast",
+                                          "inputParams");
+    cachedSerQNames.add(qName);
+    cls = uk.ac.ebi.www.InputParams.class;
+    cachedSerClasses.add(cls);
+    cachedSerFactories.add(beansf);
+    cachedDeserFactories.add(beandf);
+
+    qName = new javax.xml.namespace.QName("http://www.ebi.ac.uk/WSWUBlast",
+                                          "WSArrayofFile");
+    cachedSerQNames.add(qName);
+    cls = uk.ac.ebi.www.WSFile[].class;
+    cachedSerClasses.add(cls);
+    cachedSerFactories.add(arraysf);
+    cachedDeserFactories.add(arraydf);
+
+    qName = new javax.xml.namespace.QName("http://www.ebi.ac.uk/WSWUBlast",
+                                          "WSArrayofData");
+    cachedSerQNames.add(qName);
+    cls = uk.ac.ebi.www.Data[].class;
+    cachedSerClasses.add(cls);
+    cachedSerFactories.add(arraysf);
+    cachedDeserFactories.add(arraydf);
+
+    qName = new javax.xml.namespace.QName("http://www.ebi.ac.uk/WSWUBlast",
+                                          "data");
+    cachedSerQNames.add(qName);
+    cls = uk.ac.ebi.www.Data.class;
+    cachedSerClasses.add(cls);
+    cachedSerFactories.add(beansf);
+    cachedDeserFactories.add(beandf);
+
+    qName = new javax.xml.namespace.QName("http://www.ebi.ac.uk/WSWUBlast",
+                                          "WSFile");
+    cachedSerQNames.add(qName);
+    cls = uk.ac.ebi.www.WSFile.class;
+    cachedSerClasses.add(cls);
+    cachedSerFactories.add(beansf);
+    cachedDeserFactories.add(beandf);
+
+  }
+
+  private 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();
+        if (_call.isPropertySupported(key))
+        {
+          _call.setProperty(key, super.cachedProperties.get(key));
         }
-            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;
-            qName = new javax.xml.namespace.QName("http://www.ebi.ac.uk/WSWUBlast", "inputParams");
-            cachedSerQNames.add(qName);
-            cls = uk.ac.ebi.www.InputParams.class;
-            cachedSerClasses.add(cls);
-            cachedSerFactories.add(beansf);
-            cachedDeserFactories.add(beandf);
-
-            qName = new javax.xml.namespace.QName("http://www.ebi.ac.uk/WSWUBlast", "WSArrayofFile");
-            cachedSerQNames.add(qName);
-            cls = uk.ac.ebi.www.WSFile[].class;
-            cachedSerClasses.add(cls);
-            cachedSerFactories.add(arraysf);
-            cachedDeserFactories.add(arraydf);
-
-            qName = new javax.xml.namespace.QName("http://www.ebi.ac.uk/WSWUBlast", "WSArrayofData");
-            cachedSerQNames.add(qName);
-            cls = uk.ac.ebi.www.Data[].class;
-            cachedSerClasses.add(cls);
-            cachedSerFactories.add(arraysf);
-            cachedDeserFactories.add(arraydf);
-
-            qName = new javax.xml.namespace.QName("http://www.ebi.ac.uk/WSWUBlast", "data");
-            cachedSerQNames.add(qName);
-            cls = uk.ac.ebi.www.Data.class;
-            cachedSerClasses.add(cls);
-            cachedSerFactories.add(beansf);
-            cachedDeserFactories.add(beandf);
-
-            qName = new javax.xml.namespace.QName("http://www.ebi.ac.uk/WSWUBlast", "WSFile");
-            cachedSerQNames.add(qName);
-            cls = uk.ac.ebi.www.WSFile.class;
-            cachedSerClasses.add(cls);
-            cachedSerFactories.add(beansf);
-            cachedDeserFactories.add(beandf);
-
-    }
-
-    private 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();
-                if(_call.isPropertySupported(key))
-                    _call.setProperty(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.
-            // 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(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);
+        //  else
+        //   _call.setScopedProperty(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(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;
     }
-
-    public byte[] poll(java.lang.String jobid, java.lang.String type) throws java.rmi.RemoteException {
-        if (super.cachedEndpoint == null) {
-            throw new org.apache.axis.NoEndPointException();
-        }
-        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);
-        _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);
-        _call.setReturnType(new javax.xml.namespace.QName("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"));
-
-        java.lang.Object _resp = _call.invoke(new java.lang.Object[] {jobid, type});
-
-        if (_resp instanceof java.rmi.RemoteException) {
-            throw (java.rmi.RemoteException)_resp;
-        }
-        else {
-            try {
-                return (byte[]) _resp;
-            } catch (java.lang.Exception _exception) {
-                return (byte[]) org.apache.axis.utils.JavaUtils.convert(_resp, byte[].class);
-            }
-        }
+    catch (java.lang.Throwable t)
+    {
+      throw new org.apache.axis.AxisFault(
+          "Failure trying to get the Call object", t);
     }
-
-    public java.lang.String runWUBlast(uk.ac.ebi.www.InputParams params, uk.ac.ebi.www.Data[] content) throws java.rmi.RemoteException {
-        if (super.cachedEndpoint == null) {
-            throw new org.apache.axis.NoEndPointException();
-        }
-        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);
-        _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);
-        _call.setReturnType(new javax.xml.namespace.QName("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"));
-
-        java.lang.Object _resp = _call.invoke(new java.lang.Object[] {params, content});
-
-        if (_resp instanceof java.rmi.RemoteException) {
-            throw (java.rmi.RemoteException)_resp;
-        }
-        else {
-            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 byte[] poll(java.lang.String jobid, java.lang.String type)
+      throws java.rmi.RemoteException
+  {
+    if (super.cachedEndpoint == null)
+    {
+      throw new org.apache.axis.NoEndPointException();
     }
-
-    public byte[] test(java.lang.String jobid, java.lang.String type) throws java.rmi.RemoteException {
-        if (super.cachedEndpoint == null) {
-            throw new org.apache.axis.NoEndPointException();
-        }
-        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);
-        _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);
-        _call.setReturnType(new javax.xml.namespace.QName("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"));
-
-        java.lang.Object _resp = _call.invoke(new java.lang.Object[] {jobid, type});
-
-        if (_resp instanceof java.rmi.RemoteException) {
-            throw (java.rmi.RemoteException)_resp;
-        }
-        else {
-            try {
-                return (byte[]) _resp;
-            } catch (java.lang.Exception _exception) {
-                return (byte[]) org.apache.axis.utils.JavaUtils.convert(_resp, byte[].class);
-            }
-        }
+    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);
+    _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);
+    _call.setReturnType(new javax.xml.namespace.QName(
+        "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"));
+
+    java.lang.Object _resp = _call.invoke(new java.lang.Object[]
+                                          {jobid, type});
+
+    if (_resp instanceof java.rmi.RemoteException)
+    {
+      throw (java.rmi.RemoteException) _resp;
     }
-
-    public java.lang.String checkStatus(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.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);
-        _call.setReturnType(new javax.xml.namespace.QName("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"));
-
-        java.lang.Object _resp = _call.invoke(new java.lang.Object[] {jobid});
-
-        if (_resp instanceof java.rmi.RemoteException) {
-            throw (java.rmi.RemoteException)_resp;
-        }
-        else {
-            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);
-            }
-        }
+    else
+    {
+      try
+      {
+        return (byte[]) _resp;
+      }
+      catch (java.lang.Exception _exception)
+      {
+        return (byte[]) org.apache.axis.utils.JavaUtils.convert(_resp, byte[].class);
+      }
     }
-
-    public uk.ac.ebi.www.WSFile[] getResults(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.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);
-        _call.setReturnType(new javax.xml.namespace.QName("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"));
-
-        java.lang.Object _resp = _call.invoke(new java.lang.Object[] {jobid});
-
-        if (_resp instanceof java.rmi.RemoteException) {
-            throw (java.rmi.RemoteException)_resp;
-        }
-        else {
-            try {
-                return (uk.ac.ebi.www.WSFile[]) _resp;
-            } catch (java.lang.Exception _exception) {
-                return (uk.ac.ebi.www.WSFile[]) org.apache.axis.utils.JavaUtils.convert(_resp, uk.ac.ebi.www.WSFile[].class);
-            }
-        }
+  }
+
+  public java.lang.String runWUBlast(uk.ac.ebi.www.InputParams params,
+                                     uk.ac.ebi.www.Data[] content)
+      throws java.rmi.RemoteException
+  {
+    if (super.cachedEndpoint == null)
+    {
+      throw new org.apache.axis.NoEndPointException();
     }
-
-    public byte[] polljob(java.lang.String jobid, java.lang.String outformat) throws java.rmi.RemoteException {
-        if (super.cachedEndpoint == null) {
-            throw new org.apache.axis.NoEndPointException();
-        }
-        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);
-        _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);
-        _call.setReturnType(new javax.xml.namespace.QName("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"));
-
-        java.lang.Object _resp = _call.invoke(new java.lang.Object[] {jobid, outformat});
-
-        if (_resp instanceof java.rmi.RemoteException) {
-            throw (java.rmi.RemoteException)_resp;
-        }
-        else {
-            try {
-                return (byte[]) _resp;
-            } catch (java.lang.Exception _exception) {
-                return (byte[]) org.apache.axis.utils.JavaUtils.convert(_resp, byte[].class);
-            }
-        }
+    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);
+    _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);
+    _call.setReturnType(new javax.xml.namespace.QName(
+        "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"));
+
+    java.lang.Object _resp = _call.invoke(new java.lang.Object[]
+                                          {params, content});
+
+    if (_resp instanceof java.rmi.RemoteException)
+    {
+      throw (java.rmi.RemoteException) _resp;
     }
-
-    public byte[] doWUBlast(uk.ac.ebi.www.InputParams params, byte[] content) throws java.rmi.RemoteException {
-        if (super.cachedEndpoint == null) {
-            throw new org.apache.axis.NoEndPointException();
-        }
-        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);
-        _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);
-        _call.setReturnType(new javax.xml.namespace.QName("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"));
-
-        java.lang.Object _resp = _call.invoke(new java.lang.Object[] {params, content});
-
-        if (_resp instanceof java.rmi.RemoteException) {
-            throw (java.rmi.RemoteException)_resp;
-        }
-        else {
-            try {
-                return (byte[]) _resp;
-            } catch (java.lang.Exception _exception) {
-                return (byte[]) org.apache.axis.utils.JavaUtils.convert(_resp, byte[].class);
-            }
-        }
+    else
+    {
+      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 byte[] test(java.lang.String jobid, java.lang.String type)
+      throws java.rmi.RemoteException
+  {
+    if (super.cachedEndpoint == null)
+    {
+      throw new org.apache.axis.NoEndPointException();
+    }
+    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);
+    _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);
+    _call.setReturnType(new javax.xml.namespace.QName(
+        "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"));
+
+    java.lang.Object _resp = _call.invoke(new java.lang.Object[]
+                                          {jobid, type});
+
+    if (_resp instanceof java.rmi.RemoteException)
+    {
+      throw (java.rmi.RemoteException) _resp;
+    }
+    else
+    {
+      try
+      {
+        return (byte[]) _resp;
+      }
+      catch (java.lang.Exception _exception)
+      {
+        return (byte[]) org.apache.axis.utils.JavaUtils.convert(_resp, byte[].class);
+      }
+    }
+  }
+
+  public java.lang.String checkStatus(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.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);
+    _call.setReturnType(new javax.xml.namespace.QName(
+        "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"));
+
+    java.lang.Object _resp = _call.invoke(new java.lang.Object[]
+                                          {jobid});
+
+    if (_resp instanceof java.rmi.RemoteException)
+    {
+      throw (java.rmi.RemoteException) _resp;
+    }
+    else
+    {
+      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 uk.ac.ebi.www.WSFile[] getResults(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.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);
+    _call.setReturnType(new javax.xml.namespace.QName(
+        "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"));
+
+    java.lang.Object _resp = _call.invoke(new java.lang.Object[]
+                                          {jobid});
+
+    if (_resp instanceof java.rmi.RemoteException)
+    {
+      throw (java.rmi.RemoteException) _resp;
+    }
+    else
+    {
+      try
+      {
+        return (uk.ac.ebi.www.WSFile[]) _resp;
+      }
+      catch (java.lang.Exception _exception)
+      {
+        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
+  {
+    if (super.cachedEndpoint == null)
+    {
+      throw new org.apache.axis.NoEndPointException();
+    }
+    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);
+    _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);
+    _call.setReturnType(new javax.xml.namespace.QName(
+        "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"));
+
+    java.lang.Object _resp = _call.invoke(new java.lang.Object[]
+                                          {jobid, outformat});
+
+    if (_resp instanceof java.rmi.RemoteException)
+    {
+      throw (java.rmi.RemoteException) _resp;
+    }
+    else
+    {
+      try
+      {
+        return (byte[]) _resp;
+      }
+      catch (java.lang.Exception _exception)
+      {
+        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
+  {
+    if (super.cachedEndpoint == null)
+    {
+      throw new org.apache.axis.NoEndPointException();
+    }
+    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);
+    _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);
+    _call.setReturnType(new javax.xml.namespace.QName(
+        "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"));
+
+    java.lang.Object _resp = _call.invoke(new java.lang.Object[]
+                                          {params, content});
+
+    if (_resp instanceof java.rmi.RemoteException)
+    {
+      throw (java.rmi.RemoteException) _resp;
+    }
+    else
+    {
+      try
+      {
+        return (byte[]) _resp;
+      }
+      catch (java.lang.Exception _exception)
+      {
+        return (byte[]) org.apache.axis.utils.JavaUtils.convert(_resp, byte[].class);
+      }
     }
+  }
 
 }
diff --git a/src/vamsas/IMsaWS.java b/src/vamsas/IMsaWS.java
index bd0fdbb..7d02a94 100755
--- a/src/vamsas/IMsaWS.java
+++ b/src/vamsas/IMsaWS.java
@@ -1,34 +1,37 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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;
 
-import vamsas.objects.simple.SequenceSet;
-import vamsas.objects.simple.Alignment;
-import vamsas.objects.simple.MsaResult;
-import vamsas.objects.simple.WsJobId;
+import vamsas.objects.simple.*;
 
+public interface IMsaWS
+{
+  public WsJobId align(SequenceSet s)
+      throws Exception;
 
-public interface IMsaWS {
-    public WsJobId align(SequenceSet s) throws Exception;
-    public Alignment getalign(String job_id) throws Exception;
-    public MsaResult getResult(String job_id) throws Exception;
-    public WsJobId cancel(String jobId) throws Exception;
-}
+  public Alignment getalign(String job_id)
+      throws Exception;
+
+  public MsaResult getResult(String job_id)
+      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 0055baf..bd9adfa 100755
--- a/src/vamsas/objects/simple/Alignment.java
+++ b/src/vamsas/objects/simple/Alignment.java
@@ -6,163 +6,184 @@
  */
 
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* 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;
-    private java.lang.Object __equalsCalc = null;
-    private boolean __hashCodeCalc = false;
-
-    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.
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
- * @return gapchar
- */
-    public java.lang.String getGapchar() {
-        return gapchar;
-    }
-
-    /**
- * Sets the gapchar value for this Alignment.
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
  *
- * @param gapchar
- */
-    public void setGapchar(java.lang.String gapchar) {
-        this.gapchar = gapchar;
-    }
-
-    /**
- * Gets the method value for this Alignment.
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
  *
- * @return method
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-    public java.lang.String[] getMethod() {
-        return method;
-    }
+package vamsas.objects.simple;
 
-    /**
- * Sets the method value for this Alignment.
- *
- * @param method
- */
-    public void setMethod(java.lang.String[] method) {
-        this.method = 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;
+  private java.lang.Object __equalsCalc = null;
+  private boolean __hashCodeCalc = false;
+
+  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;
+  }
+
+  public synchronized boolean equals(java.lang.Object obj)
+  {
+    if (! (obj instanceof Alignment))
+    {
+      return false;
     }
 
-    /**
- * Gets the seqs value for this Alignment.
- *
- * @return seqs
- */
-    public vamsas.objects.simple.SequenceSet getSeqs() {
-        return seqs;
-    }
+    Alignment other = (Alignment) obj;
 
-    /**
- * Sets the seqs value for this Alignment.
- *
- * @param seqs
- */
-    public void setSeqs(vamsas.objects.simple.SequenceSet seqs) {
-        this.seqs = seqs;
+    if (obj == null)
+    {
+      return false;
     }
 
-    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);
-        }
-
-        __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;
+    if (this == obj)
+    {
+      return true;
     }
 
-    public synchronized int hashCode() {
-        if (__hashCodeCalc) {
-            return 0;
-        }
+    if (__equalsCalc != null)
+    {
+      return (__equalsCalc == obj);
+    }
 
-        __hashCodeCalc = true;
+    __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;
+  }
+
+  public synchronized int hashCode()
+  {
+    if (__hashCodeCalc)
+    {
+      return 0;
+    }
 
-        int _hashCode = super.hashCode();
+    __hashCodeCalc = true;
 
-        if (getGapchar() != null) {
-            _hashCode += getGapchar().hashCode();
-        }
+    int _hashCode = super.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 (getGapchar() != null)
+    {
+      _hashCode += getGapchar().hashCode();
+    }
 
-                if ((obj != null) && !obj.getClass().isArray()) {
-                    _hashCode += obj.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();
-        }
+    if (getSeqs() != null)
+    {
+      _hashCode += getSeqs().hashCode();
+    }
 
-        __hashCodeCalc = false;
+    __hashCodeCalc = false;
 
-        return _hashCode;
-    }
+    return _hashCode;
+  }
 }
diff --git a/src/vamsas/objects/simple/Alignment_Helper.java b/src/vamsas/objects/simple/Alignment_Helper.java
index 8fafb88..c1f7bad 100755
--- a/src/vamsas/objects/simple/Alignment_Helper.java
+++ b/src/vamsas/objects/simple/Alignment_Helper.java
@@ -6,78 +6,85 @@
  */
 
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 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"));
+  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);
-    }
+    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 6dc1d11..26eb6b7 100755
--- a/src/vamsas/objects/simple/JpredResult.java
+++ b/src/vamsas/objects/simple/JpredResult.java
@@ -7,97 +7,116 @@
 
 package vamsas.objects.simple;
 
-public class JpredResult  extends vamsas.objects.simple.Result  implements java.io.Serializable {
-    private java.lang.String aligfile;
-    private java.lang.String predfile;
+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) {
-           this.aligfile = aligfile;
-           this.predfile = predfile;
-    }
+  public JpredResult()
+  {
+  }
 
+  public JpredResult(
+      java.lang.String aligfile,
+      java.lang.String predfile)
+  {
+    this.aligfile = aligfile;
+    this.predfile = predfile;
+  }
 
-    /**
-     * Gets the aligfile value for this JpredResult.
-     * 
-     * @return aligfile
-     */
-    public java.lang.String getAligfile() {
-        return aligfile;
-    }
+  /**
+   * Gets the aligfile value for this JpredResult.
+   *
+   * @return aligfile
+   */
+  public java.lang.String getAligfile()
+  {
+    return aligfile;
+  }
 
+  /**
+   * Sets the aligfile value for this JpredResult.
+   *
+   * @param aligfile
+   */
+  public void setAligfile(java.lang.String aligfile)
+  {
+    this.aligfile = aligfile;
+  }
 
-    /**
-     * Sets the aligfile value for this JpredResult.
-     * 
-     * @param aligfile
-     */
-    public void setAligfile(java.lang.String aligfile) {
-        this.aligfile = aligfile;
-    }
+  /**
+   * Gets the predfile value for this JpredResult.
+   *
+   * @return predfile
+   */
+  public java.lang.String getPredfile()
+  {
+    return predfile;
+  }
 
+  /**
+   * Sets the predfile value for this JpredResult.
+   *
+   * @param predfile
+   */
+  public void setPredfile(java.lang.String predfile)
+  {
+    this.predfile = predfile;
+  }
 
-    /**
-     * Gets the predfile value for this JpredResult.
-     * 
-     * @return predfile
-     */
-    public java.lang.String getPredfile() {
-        return predfile;
+  private java.lang.Object __equalsCalc = null;
+  public synchronized boolean equals(java.lang.Object obj)
+  {
+    if (! (obj instanceof JpredResult))
+    {
+      return false;
     }
-
-
-    /**
-     * Sets the predfile value for this JpredResult.
-     * 
-     * @param predfile
-     */
-    public void setPredfile(java.lang.String predfile) {
-        this.predfile = predfile;
+    JpredResult other = (JpredResult) obj;
+    if (obj == null)
+    {
+      return false;
     }
-
-    private java.lang.Object __equalsCalc = null;
-    public synchronized boolean equals(java.lang.Object obj) {
-        if (!(obj instanceof JpredResult)) return false;
-        JpredResult other = (JpredResult) 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.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;
+    if (this == obj)
+    {
+      return true;
+    }
+    if (__equalsCalc != null)
+    {
+      return (__equalsCalc == obj);
     }
+    __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())));
+    __equalsCalc = null;
+    return _equals;
+  }
 
-    private boolean __hashCodeCalc = false;
-    public synchronized int hashCode() {
-        if (__hashCodeCalc) {
-            return 0;
-        }
-        __hashCodeCalc = true;
-        int _hashCode = super.hashCode();
-        if (getAligfile() != null) {
-            _hashCode += getAligfile().hashCode();
-        }
-        if (getPredfile() != null) {
-            _hashCode += getPredfile().hashCode();
-        }
-        __hashCodeCalc = false;
-        return _hashCode;
+  private boolean __hashCodeCalc = false;
+  public synchronized int hashCode()
+  {
+    if (__hashCodeCalc)
+    {
+      return 0;
+    }
+    __hashCodeCalc = true;
+    int _hashCode = super.hashCode();
+    if (getAligfile() != null)
+    {
+      _hashCode += getAligfile().hashCode();
+    }
+    if (getPredfile() != null)
+    {
+      _hashCode += getPredfile().hashCode();
     }
+    __hashCodeCalc = false;
+    return _hashCode;
+  }
 
 }
diff --git a/src/vamsas/objects/simple/JpredResult_Helper.java b/src/vamsas/objects/simple/JpredResult_Helper.java
index 34acfa8..12dff09 100755
--- a/src/vamsas/objects/simple/JpredResult_Helper.java
+++ b/src/vamsas/objects/simple/JpredResult_Helper.java
@@ -7,54 +7,63 @@
 
 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);
+public class JpredResult_Helper
+{
+  // Type metadata
+  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();
-        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"));
-        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"));
-        typeDesc.addFieldDesc(elemField);
-    }
+  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();
+    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"));
+    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"));
+    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(
+  /**
+   * 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(
+  /**
+   * 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/MsaResult.java b/src/vamsas/objects/simple/MsaResult.java
index af39fe2..c8327dd 100755
--- a/src/vamsas/objects/simple/MsaResult.java
+++ b/src/vamsas/objects/simple/MsaResult.java
@@ -6,101 +6,114 @@
  */
 
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 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;
     }
 
-    public MsaResult(vamsas.objects.simple.Alignment msa) {
-        this.msa = msa;
-    }
+    MsaResult other = (MsaResult) obj;
 
-    /**
- * Gets the msa value for this MsaResult.
- *
- * @return msa
- */
-    public vamsas.objects.simple.Alignment getMsa() {
-        return msa;
+    if (obj == null)
+    {
+      return false;
     }
 
-    /**
- * Sets the msa value for this MsaResult.
- *
- * @param msa
- */
-    public void setMsa(vamsas.objects.simple.Alignment msa) {
-        this.msa = msa;
+    if (this == obj)
+    {
+      return true;
     }
 
-    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);
+    }
 
-        if (__equalsCalc != null) {
-            return (__equalsCalc == obj);
-        }
+    __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;
 
-        boolean _equals;
-        _equals = super.equals(obj) &&
-            (((this.msa == null) && (other.getMsa() == null)) ||
-            ((this.msa != null) && this.msa.equals(other.getMsa())));
-        __equalsCalc = null;
+    return _equals;
+  }
 
-        return _equals;
+  public synchronized int hashCode()
+  {
+    if (__hashCodeCalc)
+    {
+      return 0;
     }
 
-    public synchronized int hashCode() {
-        if (__hashCodeCalc) {
-            return 0;
-        }
-
-        __hashCodeCalc = true;
+    __hashCodeCalc = true;
 
-        int _hashCode = super.hashCode();
+    int _hashCode = super.hashCode();
 
-        if (getMsa() != null) {
-            _hashCode += getMsa().hashCode();
-        }
+    if (getMsa() != null)
+    {
+      _hashCode += getMsa().hashCode();
+    }
 
-        __hashCodeCalc = false;
+    __hashCodeCalc = false;
 
-        return _hashCode;
-    }
+    return _hashCode;
+  }
 }
diff --git a/src/vamsas/objects/simple/MsaResult_Helper.java b/src/vamsas/objects/simple/MsaResult_Helper.java
index 841b069..b43e05b 100755
--- a/src/vamsas/objects/simple/MsaResult_Helper.java
+++ b/src/vamsas/objects/simple/MsaResult_Helper.java
@@ -6,66 +6,73 @@
  */
 
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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);
+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"));
+  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);
-    }
+    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;
-    }
+  /**
+   * 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/Msfalignment.java b/src/vamsas/objects/simple/Msfalignment.java
index f891957..242b14f 100755
--- a/src/vamsas/objects/simple/Msfalignment.java
+++ b/src/vamsas/objects/simple/Msfalignment.java
@@ -7,97 +7,116 @@
 
 package vamsas.objects.simple;
 
-public class Msfalignment  implements java.io.Serializable {
-    private java.lang.String msf;
-    private java.lang.String notes;
+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) {
-           this.msf = msf;
-           this.notes = notes;
-    }
+  public Msfalignment()
+  {
+  }
 
+  public Msfalignment(
+      java.lang.String msf,
+      java.lang.String notes)
+  {
+    this.msf = msf;
+    this.notes = notes;
+  }
 
-    /**
-     * Gets the msf value for this Msfalignment.
-     * 
-     * @return msf
-     */
-    public java.lang.String getMsf() {
-        return msf;
-    }
+  /**
+   * Gets the msf value for this Msfalignment.
+   *
+   * @return msf
+   */
+  public java.lang.String getMsf()
+  {
+    return msf;
+  }
 
+  /**
+   * Sets the msf value for this Msfalignment.
+   *
+   * @param msf
+   */
+  public void setMsf(java.lang.String msf)
+  {
+    this.msf = msf;
+  }
 
-    /**
-     * Sets the msf value for this Msfalignment.
-     * 
-     * @param msf
-     */
-    public void setMsf(java.lang.String msf) {
-        this.msf = msf;
-    }
+  /**
+   * Gets the notes value for this Msfalignment.
+   *
+   * @return notes
+   */
+  public java.lang.String getNotes()
+  {
+    return notes;
+  }
 
+  /**
+   * Sets the notes value for this Msfalignment.
+   *
+   * @param notes
+   */
+  public void setNotes(java.lang.String notes)
+  {
+    this.notes = notes;
+  }
 
-    /**
-     * Gets the notes value for this Msfalignment.
-     * 
-     * @return notes
-     */
-    public java.lang.String getNotes() {
-        return notes;
+  private java.lang.Object __equalsCalc = null;
+  public synchronized boolean equals(java.lang.Object obj)
+  {
+    if (! (obj instanceof Msfalignment))
+    {
+      return false;
     }
-
-
-    /**
-     * Sets the notes value for this Msfalignment.
-     * 
-     * @param notes
-     */
-    public void setNotes(java.lang.String notes) {
-        this.notes = notes;
+    Msfalignment other = (Msfalignment) obj;
+    if (obj == null)
+    {
+      return false;
     }
-
-    private java.lang.Object __equalsCalc = null;
-    public synchronized boolean equals(java.lang.Object obj) {
-        if (!(obj instanceof Msfalignment)) return false;
-        Msfalignment other = (Msfalignment) obj;
-        if (obj == null) return false;
-        if (this == obj) return true;
-        if (__equalsCalc != null) {
-            return (__equalsCalc == obj);
-        }
-        __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())));
-        __equalsCalc = null;
-        return _equals;
+    if (this == obj)
+    {
+      return true;
+    }
+    if (__equalsCalc != null)
+    {
+      return (__equalsCalc == obj);
     }
+    __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())));
+    __equalsCalc = null;
+    return _equals;
+  }
 
-    private boolean __hashCodeCalc = false;
-    public synchronized int hashCode() {
-        if (__hashCodeCalc) {
-            return 0;
-        }
-        __hashCodeCalc = true;
-        int _hashCode = 1;
-        if (getMsf() != null) {
-            _hashCode += getMsf().hashCode();
-        }
-        if (getNotes() != null) {
-            _hashCode += getNotes().hashCode();
-        }
-        __hashCodeCalc = false;
-        return _hashCode;
+  private boolean __hashCodeCalc = false;
+  public synchronized int hashCode()
+  {
+    if (__hashCodeCalc)
+    {
+      return 0;
+    }
+    __hashCodeCalc = true;
+    int _hashCode = 1;
+    if (getMsf() != null)
+    {
+      _hashCode += getMsf().hashCode();
+    }
+    if (getNotes() != null)
+    {
+      _hashCode += getNotes().hashCode();
     }
+    __hashCodeCalc = false;
+    return _hashCode;
+  }
 
 }
diff --git a/src/vamsas/objects/simple/Msfalignment_Helper.java b/src/vamsas/objects/simple/Msfalignment_Helper.java
index 9452a8b..9b9288d 100755
--- a/src/vamsas/objects/simple/Msfalignment_Helper.java
+++ b/src/vamsas/objects/simple/Msfalignment_Helper.java
@@ -7,54 +7,63 @@
 
 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);
+public class Msfalignment_Helper
+{
+  // Type metadata
+  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();
-        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"));
-        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"));
-        typeDesc.addFieldDesc(elemField);
-    }
+  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();
+    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"));
+    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"));
+    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(
+  /**
+   * 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(
+  /**
+   * 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/Object.java b/src/vamsas/objects/simple/Object.java
index 69ca312..4a37bc9 100755
--- a/src/vamsas/objects/simple/Object.java
+++ b/src/vamsas/objects/simple/Object.java
@@ -6,70 +6,80 @@
  */
 
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 abstract class Object implements java.io.Serializable {
-    private java.lang.Object __equalsCalc = null;
-    private boolean __hashCodeCalc = false;
+public abstract class Object
+    implements java.io.Serializable
+{
+  private java.lang.Object __equalsCalc = null;
+  private boolean __hashCodeCalc = false;
+
+  public Object()
+  {
+  }
 
-    public Object() {
+  public synchronized boolean equals(java.lang.Object obj)
+  {
+    if (! (obj instanceof Object))
+    {
+      return false;
     }
 
-    public synchronized boolean equals(java.lang.Object obj) {
-        if (!(obj instanceof Object)) {
-            return false;
-        }
+    //Object other = (Object) obj;
 
-        //Object other = (Object) obj;
+    if (obj == null)
+    {
+      return false;
+    }
 
-        if (obj == null) {
-            return false;
-        }
+    if (this == obj)
+    {
+      return true;
+    }
 
-        if (this == obj) {
-            return true;
-        }
+    if (__equalsCalc != null)
+    {
+      return (__equalsCalc == obj);
+    }
 
-        if (__equalsCalc != null) {
-            return (__equalsCalc == obj);
-        }
+    __equalsCalc = obj;
 
-        __equalsCalc = obj;
+    boolean _equals;
+    _equals = true;
+    __equalsCalc = null;
 
-        boolean _equals;
-        _equals = true;
-        __equalsCalc = null;
+    return _equals;
+  }
 
-        return _equals;
+  public synchronized int hashCode()
+  {
+    if (__hashCodeCalc)
+    {
+      return 0;
     }
 
-    public synchronized int hashCode() {
-        if (__hashCodeCalc) {
-            return 0;
-        }
+    __hashCodeCalc = true;
 
-        __hashCodeCalc = true;
+    int _hashCode = 1;
+    __hashCodeCalc = false;
 
-        int _hashCode = 1;
-        __hashCodeCalc = false;
-
-        return _hashCode;
-    }
+    return _hashCode;
+  }
 }
diff --git a/src/vamsas/objects/simple/Object_Helper.java b/src/vamsas/objects/simple/Object_Helper.java
index 3f34437..513790d 100755
--- a/src/vamsas/objects/simple/Object_Helper.java
+++ b/src/vamsas/objects/simple/Object_Helper.java
@@ -6,59 +6,65 @@
  */
 
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 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..fbcfddf 100755
--- a/src/vamsas/objects/simple/Result.java
+++ b/src/vamsas/objects/simple/Result.java
@@ -7,318 +7,336 @@
 
 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;
-    }
-
-
-    /**
-     * 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;
+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;
     }
-
-
-    /**
-     * Gets the state value for this Result.
-     * 
-     * @return state
-     */
-    public int getState() {
-        return state;
+    Result other = (Result) obj;
+    if (obj == null)
+    {
+      return false;
     }
-
-
-    /**
-     * Sets the state value for this Result.
-     * 
-     * @param state
-     */
-    public void setState(int state) {
-        this.state = state;
+    if (this == obj)
+    {
+      return true;
     }
-
-
-    /**
-     * Gets the status value for this Result.
-     * 
-     * @return status
-     */
-    public java.lang.String getStatus() {
-        return status;
+    if (__equalsCalc != null)
+    {
+      return (__equalsCalc == obj);
     }
-
-
-    /**
-     * Sets the status value for this Result.
-     * 
-     * @param status
-     */
-    public void setStatus(java.lang.String status) {
-        this.status = status;
+    __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 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..e4f4b8b 100755
--- a/src/vamsas/objects/simple/Result_Helper.java
+++ b/src/vamsas/objects/simple/Result_Helper.java
@@ -7,99 +7,117 @@
 
 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(
+  /**
+   * 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(
+  /**
+   * 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 42c36d2..8b334f4 100755
--- a/src/vamsas/objects/simple/Secstructpred.java
+++ b/src/vamsas/objects/simple/Secstructpred.java
@@ -7,68 +7,86 @@
 
 package vamsas.objects.simple;
 
-public class Secstructpred  implements java.io.Serializable {
-    private java.lang.String output;
+public class Secstructpred
+    implements java.io.Serializable
+{
+  private java.lang.String output;
 
-    public Secstructpred() {
-    }
-
-    public Secstructpred(
-           java.lang.String output) {
-           this.output = output;
-    }
+  public Secstructpred()
+  {
+  }
 
+  public Secstructpred(
+      java.lang.String output)
+  {
+    this.output = output;
+  }
 
-    /**
-     * Gets the output value for this Secstructpred.
-     * 
-     * @return output
-     */
-    public java.lang.String getOutput() {
-        return output;
-    }
+  /**
+   * Gets the output value for this Secstructpred.
+   *
+   * @return output
+   */
+  public java.lang.String getOutput()
+  {
+    return output;
+  }
 
+  /**
+   * Sets the output value for this Secstructpred.
+   *
+   * @param output
+   */
+  public void setOutput(java.lang.String output)
+  {
+    this.output = output;
+  }
 
-    /**
-     * Sets the output value for this Secstructpred.
-     * 
-     * @param output
-     */
-    public void setOutput(java.lang.String output) {
-        this.output = output;
+  private java.lang.Object __equalsCalc = null;
+  public synchronized boolean equals(java.lang.Object obj)
+  {
+    if (! (obj instanceof Secstructpred))
+    {
+      return false;
     }
-
-    private java.lang.Object __equalsCalc = null;
-    public synchronized boolean equals(java.lang.Object obj) {
-        if (!(obj instanceof Secstructpred)) return false;
-        Secstructpred other = (Secstructpred) obj;
-        if (obj == null) return false;
-        if (this == obj) return true;
-        if (__equalsCalc != null) {
-            return (__equalsCalc == obj);
-        }
-        __equalsCalc = obj;
-        boolean _equals;
-        _equals = true && 
-            ((this.output==null && other.getOutput()==null) || 
-             (this.output!=null &&
-              this.output.equals(other.getOutput())));
-        __equalsCalc = null;
-        return _equals;
+    Secstructpred other = (Secstructpred) obj;
+    if (obj == null)
+    {
+      return false;
+    }
+    if (this == obj)
+    {
+      return true;
     }
+    if (__equalsCalc != null)
+    {
+      return (__equalsCalc == obj);
+    }
+    __equalsCalc = obj;
+    boolean _equals;
+    _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) {
-            return 0;
-        }
-        __hashCodeCalc = true;
-        int _hashCode = 1;
-        if (getOutput() != null) {
-            _hashCode += getOutput().hashCode();
-        }
-        __hashCodeCalc = false;
-        return _hashCode;
+  private boolean __hashCodeCalc = false;
+  public synchronized int hashCode()
+  {
+    if (__hashCodeCalc)
+    {
+      return 0;
+    }
+    __hashCodeCalc = true;
+    int _hashCode = 1;
+    if (getOutput() != null)
+    {
+      _hashCode += getOutput().hashCode();
     }
+    __hashCodeCalc = false;
+    return _hashCode;
+  }
 
 }
diff --git a/src/vamsas/objects/simple/Secstructpred_Helper.java b/src/vamsas/objects/simple/Secstructpred_Helper.java
index 80991ce..7e2ef3d 100755
--- a/src/vamsas/objects/simple/Secstructpred_Helper.java
+++ b/src/vamsas/objects/simple/Secstructpred_Helper.java
@@ -7,49 +7,57 @@
 
 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);
+public class Secstructpred_Helper
+{
+  // Type metadata
+  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();
-        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"));
-        typeDesc.addFieldDesc(elemField);
-    }
+  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();
+    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"));
+    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(
+  /**
+   * 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(
+  /**
+   * 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..308d34e 100755
--- a/src/vamsas/objects/simple/Sequence.java
+++ b/src/vamsas/objects/simple/Sequence.java
@@ -7,97 +7,116 @@
 
 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;
+  private java.lang.String seq;
 
-    public Sequence() {
-    }
-
-    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;
+  }
 
-    /**
-     * Gets the seq value for this Sequence.
-     * 
-     * @return seq
-     */
-    public java.lang.String getSeq() {
-        return seq;
+  private java.lang.Object __equalsCalc = null;
+  public synchronized boolean equals(java.lang.Object obj)
+  {
+    if (! (obj instanceof Sequence))
+    {
+      return false;
     }
-
-
-    /**
-     * Sets the seq value for this Sequence.
-     * 
-     * @param seq
-     */
-    public void setSeq(java.lang.String seq) {
-        this.seq = seq;
+    Sequence other = (Sequence) obj;
+    if (obj == null)
+    {
+      return false;
     }
-
-    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;
+    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;
-    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;
+  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;
+  }
 
 }
diff --git a/src/vamsas/objects/simple/SequenceSet.java b/src/vamsas/objects/simple/SequenceSet.java
index 488440d..1bb765f 100755
--- a/src/vamsas/objects/simple/SequenceSet.java
+++ b/src/vamsas/objects/simple/SequenceSet.java
@@ -6,108 +6,124 @@
  */
 
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 SequenceSet implements java.io.Serializable {
-    private vamsas.objects.simple.Sequence[] seqs;
-    private java.lang.Object __equalsCalc = null;
-    private boolean __hashCodeCalc = false;
-
-    public SequenceSet() {
+public class SequenceSet
+    implements java.io.Serializable
+{
+  private vamsas.objects.simple.Sequence[] seqs;
+  private java.lang.Object __equalsCalc = null;
+  private boolean __hashCodeCalc = false;
+
+  public SequenceSet()
+  {
+  }
+
+  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;
+  }
+
+  /**
+   * 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;
     }
 
-    public SequenceSet(vamsas.objects.simple.Sequence[] seqs) {
-        this.seqs = seqs;
-    }
+    SequenceSet other = (SequenceSet) obj;
 
-    /**
- * Gets the seqs value for this SequenceSet.
- *
- * @return seqs
- */
-    public vamsas.objects.simple.Sequence[] getSeqs() {
-        return seqs;
+    if (obj == null)
+    {
+      return false;
     }
 
-    /**
- * Sets the seqs value for this SequenceSet.
- *
- * @param seqs
- */
-    public void setSeqs(vamsas.objects.simple.Sequence[] seqs) {
-        this.seqs = seqs;
+    if (this == obj)
+    {
+      return true;
     }
 
-    public synchronized boolean equals(java.lang.Object obj) {
-        if (!(obj instanceof SequenceSet)) {
-            return false;
-        }
-
-        SequenceSet other = (SequenceSet) obj;
-
-        if (obj == null) {
-            return false;
-        }
+    if (__equalsCalc != null)
+    {
+      return (__equalsCalc == obj);
+    }
 
-        if (this == obj) {
-            return true;
-        }
+    __equalsCalc = obj;
 
-        if (__equalsCalc != null) {
-            return (__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;
 
-        __equalsCalc = obj;
+    return _equals;
+  }
 
-        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;
+  public synchronized int hashCode()
+  {
+    if (__hashCodeCalc)
+    {
+      return 0;
     }
 
-    public synchronized int hashCode() {
-        if (__hashCodeCalc) {
-            return 0;
-        }
-
-        __hashCodeCalc = true;
+    __hashCodeCalc = true;
 
-        int _hashCode = 1;
+    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 (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();
-                }
-            }
+        if ( (obj != null) && !obj.getClass().isArray())
+        {
+          _hashCode += obj.hashCode();
         }
+      }
+    }
 
-        __hashCodeCalc = false;
+    __hashCodeCalc = false;
 
-        return _hashCode;
-    }
+    return _hashCode;
+  }
 }
diff --git a/src/vamsas/objects/simple/SequenceSet_Helper.java b/src/vamsas/objects/simple/SequenceSet_Helper.java
index ac5944f..9f6bedc 100755
--- a/src/vamsas/objects/simple/SequenceSet_Helper.java
+++ b/src/vamsas/objects/simple/SequenceSet_Helper.java
@@ -6,66 +6,73 @@
  */
 
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 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"));
+  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);
-    }
+    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..04fc493 100755
--- a/src/vamsas/objects/simple/Sequence_Helper.java
+++ b/src/vamsas/objects/simple/Sequence_Helper.java
@@ -7,54 +7,63 @@
 
 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(
+  /**
+   * 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(
+  /**
+   * 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 e3e35a5..cd5fe54 100755
--- a/src/vamsas/objects/simple/WsJobId.java
+++ b/src/vamsas/objects/simple/WsJobId.java
@@ -6,122 +6,138 @@
  */
 
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* 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;
-    private java.lang.Object __equalsCalc = null;
-    private boolean __hashCodeCalc = false;
-
-    public WsJobId() {
-    }
-
-    public WsJobId(java.lang.String jobId, int status) {
-        this.jobId = jobId;
-        this.status = status;
-    }
-
-    /**
- * Gets the jobId value for this WsJobId.
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
- * @return jobId
- */
-    public java.lang.String getJobId() {
-        return jobId;
-    }
-
-    /**
- * Sets the jobId value for this WsJobId.
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
  *
- * @param jobId
- */
-    public void setJobId(java.lang.String jobId) {
-        this.jobId = jobId;
-    }
-
-    /**
- * Gets the status value for this WsJobId.
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
  *
- * @return status
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-    public int getStatus() {
-        return status;
-    }
+package vamsas.objects.simple;
 
-    /**
- * Sets the status value for this WsJobId.
- *
- * @param status
- */
-    public void setStatus(int status) {
-        this.status = status;
+public class WsJobId
+    implements java.io.Serializable
+{
+  private java.lang.String jobId;
+  private int status;
+  private java.lang.Object __equalsCalc = null;
+  private boolean __hashCodeCalc = false;
+
+  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;
+  }
+
+  /**
+   * 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;
+  }
+
+  public synchronized boolean equals(java.lang.Object obj)
+  {
+    if (! (obj instanceof WsJobId))
+    {
+      return false;
     }
 
-    public synchronized boolean equals(java.lang.Object obj) {
-        if (!(obj instanceof WsJobId)) {
-            return false;
-        }
+    WsJobId other = (WsJobId) obj;
 
-        WsJobId other = (WsJobId) obj;
+    if (obj == null)
+    {
+      return false;
+    }
 
-        if (obj == null) {
-            return false;
-        }
+    if (this == obj)
+    {
+      return true;
+    }
 
-        if (this == obj) {
-            return true;
-        }
+    if (__equalsCalc != null)
+    {
+      return (__equalsCalc == obj);
+    }
 
-        if (__equalsCalc != null) {
-            return (__equalsCalc == obj);
-        }
+    __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;
 
-        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;
+  }
 
-        return _equals;
+  public synchronized int hashCode()
+  {
+    if (__hashCodeCalc)
+    {
+      return 0;
     }
 
-    public synchronized int hashCode() {
-        if (__hashCodeCalc) {
-            return 0;
-        }
-
-        __hashCodeCalc = true;
+    __hashCodeCalc = true;
 
-        int _hashCode = 1;
+    int _hashCode = 1;
 
-        if (getJobId() != null) {
-            _hashCode += getJobId().hashCode();
-        }
+    if (getJobId() != null)
+    {
+      _hashCode += getJobId().hashCode();
+    }
 
-        _hashCode += getStatus();
-        __hashCodeCalc = false;
+    _hashCode += getStatus();
+    __hashCodeCalc = false;
 
-        return _hashCode;
-    }
+    return _hashCode;
+  }
 }
diff --git a/src/vamsas/objects/simple/WsJobId_Helper.java b/src/vamsas/objects/simple/WsJobId_Helper.java
index 46d2805..43eed40 100755
--- a/src/vamsas/objects/simple/WsJobId_Helper.java
+++ b/src/vamsas/objects/simple/WsJobId_Helper.java
@@ -6,72 +6,79 @@
  */
 
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public 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 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"));
+  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);
-    }
+    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);
+  }
 }
-- 
1.7.10.2